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Changeset 0:c11972e98d44 (2017-05-18)

Next changeset 1:4007fdb3af5e (2017-05-19)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862

diff -r 000000000000 -r c11972e98d44 README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,7 @@
+QIIME 1.9.1 Galaxy Wrapper
+--------------------------
+
+Note: Many of these tools output html files that will not display properly
+unless sanitization is turned off in Galaxy. This can be done globally via the
+`santize_all_html` option in `galaxy.ini` or on a per tool basis using the
+`santize_whitelist_file` in `galaxy.ini`.

diff -r 000000000000 -r c11972e98d44 beta_diversity_through_plots_html_generation.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/beta_diversity_through_plots_html_generation.py Thu May 18 09:38:55 2017 -0400

[

@@ -0,0 +1,63 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import argparse
+import os
+import re
+
+
+def generate_index_html(dir_list, args):
+    with open(args.html_file, 'w') as index_html_file:
+        s = ""
+        s += '<html>\n'
+        s += '\t<head><title>PCoA beta diversity results</title></head>\n'
+        s += '\t<body>\n'
+        s += '\t\t<a href="http://www.qiime.org" target="_blank">'
+        s += '<img src="http://qiime.org/_static/wordpressheader.png" '
+        s += 'alt="www.qiime.org""/></a>\n'
+        s += '\t\t<p>\n'
+        s += '\t\t\tBeta diversity metrics\n'
+        s += '\t\t\t<ul>\n'
+
+        for directory in dir_list:
+            regexp_result = re.search(
+                '([a-zA-Z\_]*)_emperor_pcoa_plot',
+                directory)
+            metric = regexp_result.group(1)
+            s += '\t\t\t\t<li>' + metric + ': '
+            s += '<a href="' + directory
+            s += '/index.html">PCoA results</a></td>\n'
+            s += '\t\t\t\t</li>\n'
+
+        s += '\t\t\t</ul>\n'
+        s += '\t\t</p>\n'
+        s += '\t</body>\n'
+        s += '</html>\n'
+
+        index_html_file.write(s)
+
+
+def build_html(args):
+    os.mkdir(args.html_dir)
+
+    dir_list = [name for name in os.listdir(args.data_directory)
+                if os.path.isdir(os.path.join(
+                    args.data_directory,
+                    name))]
+
+    generate_index_html(dir_list, args)
+
+    for directory in dir_list:
+        input_path = os.path.join(args.data_directory, directory)
+        cmd = 'cp -r ' + input_path + ' ' + args.html_dir
+        os.system(cmd)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--data_directory', required=True)
+    parser.add_argument('--html_file', required=True)
+    parser.add_argument('--html_dir', required=True)
+    args = parser.parse_args()
+
+    build_html(args)

diff -r 000000000000 -r c11972e98d44 generate_test_data.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_test_data.sh Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,1126 @@\n+#!/usr/bin/env bash\n+\n+# Data are from test data in https://github.com/biocore/qiime\n+\n+# align_seqs\n+align_seqs.py \\\n+ --input_fasta_fp \'test-data/align_seqs/unaligned.fna\' \\\n+ -o \'align_seqs_pynast_uclust\' \\\n+ --alignment_method \'pynast\' \\\n+ --pairwise_alignment_method \'uclust\' \\\n+ --template_fp \'test-data/align_seqs/core_set_aligned.fasta.imputed\' \\\n+ --min_percent_id \'0.75\'\n+\n+align_seqs.py \\\n+ --input_fasta_fp \'test-data/align_seqs/unaligned.fna\' \\\n+ -o \'align_seqs_pynast_muscle\' \\\n+ --alignment_method \'pynast\' \\\n+ --pairwise_alignment_method \'muscle\' \\\n+ --min_length \'50\' \\\n+ --min_percent_id \'0.75\'\n+\n+align_seqs.py \\\n+ --input_fasta_fp \'test-data/align_seqs/unaligned.fna\' \\\n+ -o \'align_seqs_pynast_pair_hmm\' \\\n+ --alignment_method \'pynast\' \\\n+ --pairwise_alignment_method \'pair_hmm\' \\\n+ --min_percent_id \'0.75\'\n+\n+#align_seqs.py \\\n+# --input_fasta_fp \'test-data/align_seqs/unaligned.fna\' \\\n+# -o \'align_seqs_pynast_clustal\' \\\n+# --alignment_method \'pynast\' \\\n+# --pairwise_alignment_method \'clustal\' \\\n+# --min_percent_id \'0.75\'\n+\n+align_seqs.py \\\n+ --input_fasta_fp \'test-data/align_seqs/unaligned.fna\' \\\n+ -o \'align_seqs_pynast_blast\' \\\n+ --alignment_method \'pynast\' \\\n+ --pairwise_alignment_method \'blast\' \\\n+ --min_percent_id \'0.75\'\n+\n+align_seqs.py \\\n+ --input_fasta_fp \'test-data/align_seqs/unaligned.fna\' \\\n+ -o \'align_seqs_pynast_mafft\' \\\n+ --alignment_method \'pynast\' \\\n+ --pairwise_alignment_method \'mafft\' \\\n+ --min_percent_id \'0.75\'\n+\n+#align_seqs.py \\\n+# --input_fasta_fp \'test-data/align_seqs/unaligned.fna\' \\\n+# -o \'align_seqs_infernal\' \\\n+# --alignment_method \'infernal\' \\\n+# --template_fp \'test-data/align_seqs/seed.16s.reference_model.sto\' \\\n+# --min_percent_id \'0.75\'\n+\n+#align_seqs.py \\\n+# --input_fasta_fp \'test-data/align_seqs/unaligned.fna\' \\\n+# -o \'align_seqs_clustalw\' \\\n+# --alignment_method \'clustalw\' \\\n+# --min_percent_id \'0.75\'\n+\n+align_seqs.py \\\n+ --input_fasta_fp \'test-data/align_seqs/unaligned.fna\' \\\n+ -o \'align_seqs_muscle\' \\\n+ --alignment_method \'muscle\' \\\n+ --min_percent_id \'0.75\'\n+\n+align_seqs.py \\\n+ --input_fasta_fp \'test-data/align_seqs/unaligned.fna\' \\\n+ -o \'align_seqs_mafft\' \\\n+ --alignment_method \'mafft\' \\\n+ --min_percent_id \'0.75\'\n+\n+#alpha_rarefaction\n+alpha_rarefaction.py \\\n+ --otu_table_fp "test-data/alpha_rarefaction/otu_table.biom" \\\n+ --mapping_fp "test-data/alpha_rarefaction/mapping_file.txt" \\\n+ -o alpha_rarefaction \\\n+ --num_steps \'2\' \\\n+ --tree_fp "test-data/alpha_rarefaction/rep_set.tre" \\\n+ --min_rare_depth \'10\' \\\n+ --max_rare_depth \'50\' \\\n+ --retain_intermediate_files\n+rm -rf alpha_rarefaction\n+\n+# assign_taxonomy\n+assign_taxonomy.py \\\n+ --input_fasta_fp \'test-data/assign_taxonomy/uclust_input_seqs.fasta\' \\\n+ --assignment_method \'uclust\' \\\n+ --min_consensus_fraction \'0.51\' \\\n+ --similarity \'0.9\' \\\n+ --uclust_max_accepts \'3\' \\\n+ -o assign_taxonomy_uclust\n+cp assign_taxonomy_uclust/uclust_input_seqs_tax_assignments.txt \'test-data/assign_taxonomy/uclust_taxonomic_assignation.txt\'\n+rm -rf assign_taxonomy_uclust\n+\n+#assign_taxonomy.py \\\n+# --input_fasta_fp \'test-data/assign_taxonomy/rdp_input_seqs.fasta\' \\\n+# --id_to_taxonomy_fp \'test-data/assign_taxonomy/rdp_id_to_taxonomy.txt\' \\\n+# --assignment_method \'rdp\' \\\n+# --confidence \'3\' \\\n+# -o assign_taxonomy_rdp\n+\n+#assign_taxonomy.py \\\n+# --input_fasta_fp \'test-data/assign_taxonomy/rtax_ref_seq_set.fna\' \\\n+# --id_to_taxonomy_fp \'test-data/assign_taxonomy/rtax_id_to_taxonomy.txt\' \\\n+# --assignment_method \'rtax\' \\\n+# --read_1_seqs_fp \'test-data/assign_taxonomy/read_1.seqs.fna\' \\\n+# --read_2_seqs_fp \'test-data/assign_taxonomy/read_2.seqs.fna\' \\\n+# --single_ok \\\n+# --no_single_ok_generic \\\n+# --read_id_regex "\\S+\\s+(\\S+)" \\\n+# --amplicon_id_regex "(\\S+)\\s+(\\S+?)\\/" \\\n+# --header_id_regex "\\S+\\s+(\\S'..b"ble_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \\\n+ --output_dir summarize_taxa_through_plots_mapping_sort \\\n+ --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt' \\\n+ --sort\n+biom convert \\\n+ -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L2.biom' \\\n+ -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L2_json.biom' \\\n+ --to-json\n+biom convert \\\n+ -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L3.biom' \\\n+ -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L3_json.biom' \\\n+ --to-json\n+biom convert \\\n+ -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L4.biom' \\\n+ -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L4_json.biom' \\\n+ --to-json\n+biom convert \\\n+ -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L5.biom' \\\n+ -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L5_json.biom' \\\n+ --to-json\n+biom convert \\\n+ -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L6.biom' \\\n+ -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L6_json.biom' \\\n+ --to-json\n+cp summarize_taxa_through_plots_mapping_sort/*.txt test-data/summarize_taxa_through_plots/mapping_sort/\n+cp summarize_taxa_through_plots_mapping_sort/*_json.biom test-data/summarize_taxa_through_plots/mapping_sort/\n+cp summarize_taxa_through_plots_mapping_sort/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping_sort/area_charts.html'\n+cp summarize_taxa_through_plots_mapping_sort/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping_sort/bar_charts.html'\n+\n+summarize_taxa_through_plots.py \\\n+ --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \\\n+ --output_dir summarize_taxa_through_plots_without_mapping\n+biom convert \\\n+ -i 'summarize_taxa_through_plots_without_mapping/otu_table_L2.biom' \\\n+ -o 'summarize_taxa_through_plots_without_mapping/otu_table_L2_json.biom' \\\n+ --to-json\n+biom convert \\\n+ -i 'summarize_taxa_through_plots_without_mapping/otu_table_L3.biom' \\\n+ -o 'summarize_taxa_through_plots_without_mapping/otu_table_L3_json.biom' \\\n+ --to-json\n+biom convert \\\n+ -i 'summarize_taxa_through_plots_without_mapping/otu_table_L4.biom' \\\n+ -o 'summarize_taxa_through_plots_without_mapping/otu_table_L4_json.biom' \\\n+ --to-json\n+biom convert \\\n+ -i 'summarize_taxa_through_plots_without_mapping/otu_table_L5.biom' \\\n+ -o 'summarize_taxa_through_plots_without_mapping/otu_table_L5_json.biom' \\\n+ --to-json\n+biom convert \\\n+ -i 'summarize_taxa_through_plots_without_mapping/otu_table_L6.biom' \\\n+ -o 'summarize_taxa_through_plots_without_mapping/otu_table_L6_json.biom' \\\n+ --to-json\n+cp summarize_taxa_through_plots_without_mapping/*.txt test-data/summarize_taxa_through_plots/without_mapping/\n+cp summarize_taxa_through_plots_without_mapping/*_json.biom test-data/summarize_taxa_through_plots/without_mapping/\n+cp summarize_taxa_through_plots_without_mapping/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/without_mapping/area_charts.html'\n+cp summarize_taxa_through_plots_without_mapping/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/without_mapping/bar_charts.html'\n+\n+# upgma_cluster\n+upgma_cluster.py \\\n+ --input_path 'test-data/upgma_cluster/' \\\n+ --output_path 'test-data/upgma_cluster/'\n+\n+# validate_mapping_file\n+validate_mapping_file.py \\\n+ -m 'test-data/validate_mapping_file/map.tsv' \\\n+ -o validate_mapping_file_output \\\n+ -c '_'\n+cp validate_mapping_file_output/*.html 'test-data/validate_mapping_file/map.tsv.html'\n+cp validate_mapping_file_output/*.log 'test-data/validate_mapping_file/map.tsv.log'\n+cp validate_mapping_file_output/*corrected.txt 'test-data/validate_mapping_file/map.tsv_corrected.txt'\n+rm -rf validate_mapping_file_output\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n"

diff -r 000000000000 -r c11972e98d44 jackknifed_beta_diversity_output_management.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/jackknifed_beta_diversity_output_management.py Thu May 18 09:38:55 2017 -0400

[

@@ -0,0 +1,99 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import argparse
+import os
+
+
+def generate_index_html(dir_list, args):
+    with open(args.html_file, 'w') as index_html_file:
+        s = '<html>\n'
+        s += '\t<head>\n'
+        s += '\t\t<title>Jackknifed beta diversity results</title>\n'
+        s += '\t</head>\n'
+        s += '\t<body>\n'
+        s += '\t\t<a href="http://www.qiime.org" target="_blank">'
+        s += '<img src="http://qiime.org/_static/wordpressheader.png"'
+        s += 'alt="www.qiime.org""/></a>\n'
+        s += '\t\t<p>\n'
+        s += '\t\t\tEmperor PCoA plot after jacknifed beta diversity\n'
+        s += '\t\t\t<ul>\n'
+
+        for directory in dir_list:
+            if directory == 'rarefaction' or directory == 'unrarefied_bdiv':
+                continue
+
+            s += '\t\t\t\t<li><a href="' + directory
+            s += '/index.html">PCoA plots</a></td></li>\n'
+
+        s += '\t\t\t</ul>\n'
+        s += '\t\t</p>\n'
+        s += '\t</body>\n'
+        s += '</html>\n'
+        index_html_file.write(s)
+
+
+def build_html(args):
+    os.mkdir(args.html_dir)
+
+    dir_list = [name for name in os.listdir(args.data_directory)
+                if os.path.isdir(os.path.join(
+                    args.data_directory,
+                    name))]
+
+    generate_index_html(dir_list, args)
+
+    os.mkdir(args.data_directory + '/pcoa')
+    os.mkdir(args.data_directory + '/rare_dm')
+    os.mkdir(args.data_directory + '/rare_upgma')
+    os.mkdir(args.data_directory + '/upgma_cmp')
+    os.mkdir(args.data_directory + '/rare_upgma_consensus')
+
+    for directory in dir_list:
+        if directory == 'rarefaction' or directory == 'unrarefied_bdiv':
+            continue
+
+        input_dir = os.path.join(args.data_directory, directory)
+
+        input_path = os.path.join(input_dir, "emperor_pcoa_plots")
+        output_path = os.path.join(args.html_dir, directory)
+        cmd = 'cp -r ' + input_path + ' ' + output_path
+        os.system(cmd)
+
+        input_path = os.path.join(input_dir, "pcoa/*")
+        output_path = os.path.join(args.data_directory, "pcoa")
+        cmd = 'cp -r ' + input_path + ' ' + output_path
+        os.system(cmd)
+
+        input_path = os.path.join(input_dir, "rare_dm/*")
+        output_path = os.path.join(args.data_directory, "rare_dm")
+        cmd = 'cp -r ' + input_path + ' ' + output_path
+        os.system(cmd)
+
+        input_path = os.path.join(input_dir, "rare_upgma/*")
+        output_path = os.path.join(args.data_directory, "rare_upgma")
+        cmd = 'cp -r ' + input_path + ' ' + output_path
+        os.system(cmd)
+
+        input_path = os.path.join(input_dir, "upgma_cmp/*")
+        output_path = os.path.join(args.data_directory, "upgma_cmp")
+        cmd = 'cp -r ' + input_path + ' ' + output_path
+        os.system(cmd)
+
+        input_path = os.path.join(input_dir, "rare_upgma_consensus.tre")
+        output_path = os.path.join(
+            args.data_directory,
+            "rare_upgma_consensus",
+            directory + '.tre')
+        cmd = 'cp ' + input_path + ' ' + output_path
+        os.system(cmd)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--data_directory', required=True)
+    parser.add_argument('--html_file', required=True)
+    parser.add_argument('--html_dir', required=True)
+    args = parser.parse_args()
+
+    build_html(args)

diff -r 000000000000 -r c11972e98d44 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,57 @@
+<?xml version="1.0" ?>
+<macros>
+    <token name="@WRAPPER_VERSION@">1.9.1</token>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@WRAPPER_VERSION@">qiime</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <xml name="citations">
+        <citation type="doi">10.1038/nmeth.f.303</citation>
+    </xml>
+
+    <xml name="pick_otus_reference_source">
+        <conditional name="references">
+            <param name="source_selector" type="select" label="Use reference sequences from">
+                <option value="cached">Local cache</option>
+                <option value="history">History</option>
+            </param>
+            <when value="cached">
+                <param argument="--refseqs_fp" label="Reference sequences" type="select">
+                    <options from_data_table="qiime_rep_set"/>
+                </param>
+            </when>
+            <when value="history">
+                <param argument="--refseqs_fp" type="data" format="fasta" label="Reference sequences to search against"/>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="pick_otus_similarity">
+        <param argument="--similarity" type="float" value="0.97" label="Sequence similarity threshold"/>
+    </xml>
+    <xml name="pick_otus_denovo_otu_id_prefix">
+        <param argument="--denovo_otu_id_prefix" type="text" value="denovo" label="OTU identifier prefix for the de novo OTU pickers"/>
+    </xml>
+    <xml name="pick_otus_enable_rev_strand_match">
+        <param argument="--enable_rev_strand_match" type="boolean" truevalue="--enable_rev_strand_match" falsevalue="" checked="false" label="Enable reverse strand matching?" help="Will double the amount of memory used"/>
+    </xml>
+    <xml name="pick_otus_suppress_presort_by_abundance_uclust">
+        <param argument="--suppress_presort_by_abundance_uclust" type="boolean" truevalue="--suppress_presort_by_abundance_uclust" falsevalue="" checked="false" label="Suppress presorting of sequences by abundance?"/>
+    </xml>
+    <xml name="pick_otus_max">
+        <param argument="--max_accepts" type="integer" value="1" label="Max_accepts value"/>
+        <param argument="--max_rejects" type="integer" value="8" label="Max_rejects value"/>
+    </xml>
+    <xml name="pick_otus_stepwords">
+        <param argument="--stepwords" type="integer" value="8" label="Stepwords value"/>
+    </xml>
+    <xml name="pick_otus_word_length">
+        <param argument="--word_length" type="integer" value="8" label="Word length value"/>
+    </xml>
+    <xml name="pick_otus_suppress_prefilter_exact_match">
+        <param argument="--suppress_prefilter_exact_match" type="boolean" truevalue="--suppress_prefilter_exact_match" falsevalue="" checked="false" label="Don't collapse exact matches before calling?"/>
+    </xml>
+</macros>

diff -r 000000000000 -r c11972e98d44 split_libraries.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/split_libraries.xml Thu May 18 09:38:55 2017 -0400

[

b'@@ -0,0 +1,176 @@\n+<tool id="qiime_split_libraries" name="Split libraries" version="@WRAPPER_VERSION@.0">\n+ <description>according to barcodes specified in mapping file</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <version_command>split_libraries.py --version</version_command>\n+ <command detect_errors="aggressive"><![CDATA[\n+ split_libraries.py\n+ --map \'$map\'\n+ -o split_libraries\n+ --fasta \'$fasta\'\n+\n+ #if str($add_qual.add_qual_test) == \'true\'\n+ --qual \'$add_qual.qual\'\n+ --min_qual_score \'$add_qual.min_qual_score\'\n+ --qual_score_window \'$add_qual.qual_score_window\'\n+ $add_qual.discard_bad_windows\n+ $add_qual.record_qual_scores\n+ #end if\n+\n+ --min_seq_length \'$min_seq_length\'\n+ --max_seq_length \'$max_seq_length\'\n+ $trim_seq_length\n+ $keep_primer\n+ $keep_barcode\n+ --max_ambig \'$max_ambig\'\n+ --max_homopolymer \'$max_homopolymer\'\n+ --max_primer_mismatch \'$max_primer_mismatch\'\n+ #if str( $barcode_selector.barcode_type ) != "custom_length"\n+ --barcode_type \'$barcode_selector.barcode_type\'\n+ #else\n+ --barcode_type \'$barcode_selector.barcode_length\'\n+ #end if\n+ --max_barcode_errors \'$max_barcode_errors\'\n+ --start_numbering_at \'$start_numbering_at\'\n+ $retain_unassigned_reads\n+ $disable_bc_correction\n+ $disable_primers\n+ $reverse_primers_test.reverse_primers\n+ #if str($reverse_primers_test.reverse_primers) == \'--reverse_primers\':\n+ --reverse_primer_mismatches \'$reverse_primers_test.reverse_primer_mismatches\'\n+ #end if\n+ #if str($median_length_filtering):\n+ --median_length_filtering \'$median_length_filtering\'\n+ #end if\n+ #if str($added_demultiplex_field):\n+ --added_demultiplex_field \'$added_demultiplex_field\'\n+ #end if\n+ ]]></command>\n+ <inputs>\n+ <param argument="--map" label="Metadata mapping filepath" type="data" format="tabular,txt,tsv,csv" help="The file must contain header line indicating SampleID in the first column and BarcodeSequence in the second, LinkerPrimerSequence in the third. It is recommended to check the mapping file using the dedicated file"/>\n+ <param argument="--fasta" type="data" format="fasta" label="Input fasta files" multiple="True"/>\n+ <conditional name="add_qual">\n+ <param name="add_qual_test" type="select" label="Add quality files">\n+ <option value="true">Yes</option>\n+ <option value="false" selected="true">No</option>\n+ </param>\n+ <when value="true">\n+ <param argument="--qual" type="data" format="qual,qual454,qualillumina,qualsolexa,qualsolid" label="Input quality files (optional)" multiple="True"/>\n+ <param argument="--min_qual_score" type="integer" value="25" label="Minimum average quality score allowed in read"/>\n+ <param argument="--qual_score_window" type="integer" value="0" label="Size of the sliding window" help="If the average score of a continuous set of w nucleotides falls below the threshold, the sequence is discarded. A good value would be 50. 0 (zero) means no filtering. Must pass a .qual file (see -q parameter) if this functionality is enabled. Default behavior for this function is to truncate the sequence at the beginning of the poor quality window, and test for minimal length (-l parameter) of the resulting sequence"/>\n+ <param argument="--discard_bad_windows" type="boolean" label="Discard any sequences where a bad window is found?" truevalue="--discard_bad_windows" falsevalue="" checked="False" help="It will'..b'="add_qual_test" value="true"/>\n+ <param name="qual" value="split_libraries/reads_1.qual,split_libraries/reads_2.qual"/>\n+ <param name="min_qual_score" value="25"/>\n+ <param name="qual_score_window" value="0"/>\n+ <param name="discard_bad_windows" value=""/>\n+ <param name="record_qual_scores" value="--record_qual_scores"/>\n+ <param name="min_seq_length" value="200" />\n+ <param name="max_seq_length" value="1000" />\n+ <param name="trim_seq_length" value=""/>\n+ <param name="keep_primer" value=""/>\n+ <param name="keep_barcode" value=""/>\n+ <param name="max_ambig" value="6" />\n+ <param name="max_homopolymer" value="6"/>\n+ <param name="max_primer_mismatch" value="0"/>\n+ <param name="barcode_type" value="golay_12"/>\n+ <param name="barcode_length" value=""/>\n+ <param name="max_barcode_errors" value="1.5"/>\n+ <param name="start_numbering_at" value="1"/>\n+ <param name="retain_unassigned_reads" value=""/>\n+ <param name="disable_bc_correction" value=""/>\n+ <param name="disable_primers" value=""/>\n+ <param name="reverse_primers" value=""/>\n+ <param name="reverse_primer_mismatches" value=""/>\n+ <param name="truncate_ambi_bases" value=""/>\n+ <output name="sequences">\n+ <assert_contents>\n+ <has_text text="PC.634_1" />\n+ <has_text text="bc_diffs" />\n+ </assert_contents>\n+ </output>\n+ <output name="log" file="split_libraries/split_library_log"/>\n+ <output name="histograms" file="split_libraries/histograms.txt"/>\n+ <output name="quality">\n+ <assert_contents>\n+ <has_text text="PC.634_1" />\n+ <has_text text="bc_diffs" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**What it does**\n+\n+This tool splits libraries according to barcodes specified in mapping file.\n+\n+Since newer sequencing technologies provide many reads per run (e.g. the 454 GS FLX Titanium series can produce 400-600 million base pairs with 400-500 base pair read lengths) researchers are now finding it useful to combine multiple samples into a single 454 run. This multiplexing is achieved through the application of a pyrosequencing-tailored nucleotide barcode design (described in (Parameswaran et al., 2007)). By assigning individual, unique sample specific barcodes, multiple sequencing runs may be performed in parallel and the resulting reads can later be binned according to sample. The script %prog performs this task, in addition to several quality filtering steps including user defined cut-offs for: sequence lengths; end-trimming; minimum quality score. To summarize, by using the fasta, mapping, and quality files, the program %prog will parse sequences that meet user defined quality thresholds and then rename each read with the appropriate Sample ID, thus formatting the sequence data for downstream analysis. If a combination of different sequencing technologies are used in any particular study, %prog can be used to perform the quality-filtering for each library individually and the output may then be combined.\n+\n+Sequences from samples that are not found in the mapping file (no corresponding barcode) and sequences without the correct primer sequence will be excluded. Additional scripts can be used to exclude sequences that match a given reference sequence (e.g. the human genome; exclude_seqs_by_blast.py) and/or sequences that are flagged as chimeras (identify_chimeric_seqs.py).\n+\n+More information about this tool is available on\n+`QIIME documentation <http://qiime.org/scripts/split_libraries.html>`_.\n+ ]]></help>\n+ <citations>\n+ <expand macro="citations"/>\n+ </citations>\n+</tool>\n'

diff -r 000000000000 -r c11972e98d44 test-data/align_seqs/core_set_aligned.fasta.imputed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/align_seqs/core_set_aligned.fasta.imputed Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,100 @@\n+>114239\n+............................................................................................................aGAGTTT-GA--T-CC-T-G-GCTC-AG-AT-TGAA-C-GC--TGG-C--G-GT-A-TG--C----T-T--AACACA-T-GC-A-AGT-CGA-A-CG----------G-TAA-CA-G-----------------------------CAG-A-AG----------------------------------------------------CTT-G----------------------------------------------------------------------------------CTT-CT------------------GGCT--G--AC--G--AG-T-GG-C-GG-A--C-------------GGG-TGAGT-A--AC-GC-G-T-A-GG---A-A--T-CT-G--C-CTTA---CA-G------------------------------------------------------------------T-GG----GGG-AT-AG-CCC-------------------------G-G-T-----------------------GAA-A---ACC-GGA-TTAA-TA---CC-G--C-AT-A----------C--------------------G-------------------------------------CC-C-----------------------------------------------------------------------------------------------------------------------T-AC-G--------------------------------------------------------------------------------------------------------------------------------------G-G-G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAA--G-CTG--G-----G--GA-T--C--------------------------------------------------------------------------------------------------------------------TTC-G----------------------------------------------------------------------------------------------------------------------G-A--CC-TG--G---C-A--------------C----T-G---T-TA-G---AT---G-A-----G-CCT-GCG--T-GAG--A------TT--A--G-CT-T----G---TTGG-T-G-GG-G-T----AAT-GG---C-CTACCA--A-GG-C-A--A-CG-A------------TCT-C-T------AG-CT-G-G-TCT-G-AG----A--GG-AC--G-AT-C-AG-CCAC-A-CTGGG--A-C-TG-A-GA-C-AC-G-GCCCAG-A-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TG---GG-G-A-ATA-TTGCA-C-AA-T-GG--GC-GA-G----A-G-CC-T-GA-TG-CA-GCAA-TACC-G-CG-T---G-T-G--T--GA-A-G--A--A-G-G--C----CTG-AG---------G-G-T-T-G-T--A---AA-G-CAC--------TT-TC-A-A--T--TG---TGA-A--G---AAAAGCT---T-TT-GG----T--T--AA-T---A----------AC-C-TTGAGTC-TT-GA-CA-TTAA-C-A--A-TA-C---------AA-----------GAAGC-ACC-GG-C-TAA---C--T-CCGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---GG-AG-GGT-GCA-A-G-CG-TTAA-T-CGG-AA-TT-A--C-T--GGGC-GTA----AA-GAGT-AC--G-TA-G-G-T-G------------G--T-TC-G-T-T-AA----GTC---A---G-ATG-TG-A-AA-GC--CC-CGG-G--------------------------------------------------------------------CT-C-AA-------------------------------------------------------------------------CC-T-G-GG-AA-C----T-G-C-A-T-T--------T---GAA-A-C-T-G-GCA--A-A-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-T-G-A-G-T-A-----T-GG--TA-G-A------------G-GC-G-GG-T----AG--AA-T-TCA-TAGT--GT-A-GCG-GTGAAA-TG-CGT-AGAT-ATTA-T-G-A--GG-A-AT-A-CC-AG--T--G--GC-GAA-G--G-C---G----G--C-C-CGCTG------G-AC-CA--------------------------------------------------------------AT-'..b'-------------------------------------T-T-G-A-G-G-C-----A-CG--CT-C-A------------G-GC-A-GG-C----GG--AATT-CCC-G-GT--GT-A-GCG-GTGAAA-TG-CGT-AGAT-A-TC-G-GGA--GG-A-AC-A-CC-GA--A--G--GC-GAA-G--G-C---A----G--C-C-TGCTG------G-GG-CT--------------------------------------------------------------GT-C-C-T--GA--CG-----GT-CA-GG--G-A-CGA--AA-G-C--------------T-GGGG-GAG-C-G-AACC--GG-ATTA-G-ATA-C-----CC-G-G-GTA-G-T----C-CC--A-G-CCG-T-AAA--C-CATG-GG--CG-CT---------T-GG--C--G-T-CG-T-CC-------------------------------------------------------------------------------------------GTA-A-------------------------------------------------------------------------------------------------------------------------------------------------------G-GG--C-G-G-T-GC-C------GC--A----GC-TAA--CG-C-G-G--T--AA-GC--G----C-CCC-GCC-T-G-GG-GAG-TA---CGG-----G-C--G-C-A-A-GCC-T--GAA-ACTC-AAA---------GGAA-TTG-GCGGG-G-G-CCCG----C-A--C-A-A-CCG-GT-G--G--AG-CG-T--CT-GGT-TC-AATT-C-G-ATG-CTAA-C-CG-A-AA-A-A-CC-TT-A-CC-CGGGC-TT-G-AC-A-T-G------------G-TGG-G-A-------------A-AC-C-C-C--TG--C-GA-A-A-G--C-G-G--G-G-G-G--T-GCCG-TCC-------------------------------------T--CT--------------------------------------------GGACGGA----A---TC-CCA---C--CA---------------------------------------------------C-A-G-G-T-GGTG-CA-TGG-CC--GTC-GTC-A-GC-TC---G-TG-TC-G--TGA-GA-TGT-T-GG-G-TT-AA-GT-CCCGC-AA--------C-GAG-CGC-A-ACC-C-C-TG--CC--C-TTAG--T-T-G-C-T---AC-C-C--C----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTAAG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G----G-G------------A----G---C-A--CT---------------C-T-A-A-G-GG-G--AC-C-G-CCC--G-C------------------------------------G-A---TAA----------------------------------G-C-C-G--G-A-GG-A--AGG-T--GGGG-A-TGAC-GTC--AGGT-C---AGT-A-T-G-C-C-C-TTT----AT-G--CC-C-G-GG-GC-TA-CAC-AGGCG-C--TA--CAGTG---G-CCGG-G-A--C-AAT-GG-GA--------------------------------------------------------------------------------------------------T-G-C-G-A--C-CCAG-T--A---------------------------------------A-TG-G-G-----------G--A-G-CT---A----------A--TCC-C------C-C-AAACC-CG-G-T-C-A-TGG-TGC--------AGA-T-TGAGG-GC--T-GAAA-CT-C-------------------------------------------------------------------------------------------------G-CCCTC-A-T-G-AA-G-CC-GGAAT-CG-G-TA--G-TA-AT-G-G-C----GGA-TC-A-G-CT------AA--GCC-GC-C-GT-G-AAT-ACGT-T-CTCGGGCCT-TGCA----CACACCG-CCC-GTC-----A---CG--CCA-CG-GA-A--G---TCA-G-TC-TT-CCC--G-GAA------G--C-CCC-CG-G-G-C-T-AA-C-C-GG-T-C------------------------------------------------------T-TC-G---------------------------------------------------------------------------------------------G--A-CC--GG-A--GG-C--A---GG-GGA--CG--ATG-G----G-AAG-GC-TGG------------------------CA--ACT-GGGG-CG-AAG-tcgtaacaa-ggtaa-ccgt-aggggaa-cctg-cggc-tggatcacctcctt.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n'

diff -r 000000000000 -r c11972e98d44 test-data/align_seqs/unaligned.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/align_seqs/unaligned.fna Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,122 @@\n+>r0 PC.634_176\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGTTGACTTGGTGGGCCGTTACCCCGCCAACTATCTAATGGAACGCATCCCCATCGATAACCGAAATTCTTTAATAGTGAAACCATGCGGAAATACTATACTATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTTATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCATC\n+>r102 PC.634_91\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACCTATCATTGCCTTGGTGGGCCGTTACCCCCCAACTAGCTAATAGGACGCATGCCCATCTGATACCTCGAATGATTTAATTATTAAAAGATGCCTTCAAATAATATTATGGGGTGTTAATCCACGTTTCCATGGGCTATCCCCCTGTATCAGCCAGGTTGCATACGCGTTACTCACCCGTGCGCCGG\n+>r111 PC.634_173\n+TTGGTCCGTGTCTCAGTACCAATGTGGGGGGTTAACCTCTCAGTCCCCCTATGTATCGTTGCCTTGGTGAGCCGTTACCTCACCAACTAGCTAATACAACGCATGCCCATCTTTAACCACCGGAGTTTTTAACCCAAGAAGATGCCTTCTCGAATGTTATGGGGAATTAGTACCAATTTCTCAGTGTTATGCCCCTGTTAAAGGTAGGTTGCATACGCGTTACGCACCCGTGCGCCGGTCGCCACCAAAG\n+>r129 PC.354_202\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCTGTTACCCCGCCAACCAGCTAATCAGACGCGGATCCATCGTATACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCTGTATACGGCAGGTTATCCACGCGTT\n+>r143 PC.356_295\n+CTGGACCGTGTCTCAGTTCCAGTGTGGGGGGCCTTCCTCTCAGAACCCCTACGCATCGTCGCCACGGTGGGCCGTTACCCCGCCGTCAAGCTAATGCGCCGCATGCCCAGCCGCCACCGGATTCCTCCTTTCGCCCGGTCCGGATGCCCGGTCCGGGCGGCATGGGGTATTAGGCCGGGTTTCCCCGGGTTATCCCCCTCGTGGCGGGCAGGTTCCATACGTGTTACTCACCCGTGCGCCGGTCGCCGGCAGGTG\n+>r146 PC.607_50\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCGACCTCTCAGTCCGGCTACCGATCGTCGGCTTGGTGAGCCGTTACCTCACCAACTACCTAATCGGACGCGAGCCCATCTTCGAGCGATAAAATCTTTGATACCAGCAGGATGTCCTCCCGGTATGTTATGCGGTATTAGCGACCGTTTCCAGCCGTTATTCCCCTCTCGAAGGCAGGTTGCTCACGTGTTACTCACCCGTCCG\n+>r148 PC.355_122\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCCCTCCAACCAGCTAATCAGACGCGGGTCCATCCTGTACCACCGGAGTTTTTCACACTGTACCATGCGGTACTGTGCGCTTATGCGGTTTTAGCACCTATTTCTAAGTGTTATCCCCCTGTACAGGGCAGGTTACCCACGCGTTACTCACCCGTCCGCCACTAAG\n+>r153 PC.634_58\n+TTGGTCCGTGTCTCAGTACCAATGTGGGGGGTTAACCTCTCAGTCCCCCTATGTATCGTCGCCTTGGTGAGCCGTTACCTCACCAACCAGCTAATACAACGCATGCCCATCATCAACCACCGGAGTTTTCAACCCCATGCGATGCCGCATGAGATATTATGGGGTATTAGTACCAATTTCTCAGTGTTATCCCCCTGTTGATGGTAGGTTGCATACGCGTTACGCACCCG\n+>r158 PC.355_372\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCCCTCCAACCAGCTAATCAGACGCGGGTCCATCCTGTACCACCGGAGTTTTTCACACTGTACCATGCGGTACTGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTATACGGCAGGTTCTCCACGCGTTACTCACCCGTCCG\n+>r162 PC.355_13\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTCAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCTTACCAACTAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGACATGCGTCTAGTGTTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCTTGGG\n+>r175 PC.634_133\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTATGGATCGTTGACTTGGTAGGCCGTTACCCCACCAACTATCTAATCCAACGCGAGCCCATCCTTCGGCACCTCAGTTTTGGTATTTCTATCATGCGGTAAAAATACGTTATGCGGTATTACTGTCCGTTTCCAGACACTATCCCCCTCCGAAGGGCAGGTTGCTCACGCGTTACTCACCCGTCCGCC\n+>r178 PC.634_139\n+CTGGACCGTCTCTCAGTTCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCAGACATGAGCCCATCTTTCAGCGGATTGCTCCTTTGATAACAGGATCATGCGATCCCGTTCATTTCATTGCGGTATTAGCACACCTTTCGATGTGTTATCCCCCTCTGAAAGG\n+>r181 PC.593_362\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCCCGCCGACTAGCTAATGCGCCGCATGCCCATCCGTCACCGGATTGCTCCTTTGACCGCTCCGGGATGCCCCGGAATGGTGTTACGCGGAATTAGTCGGAATTTCTTCCGGTTATTCCCCTGTGACGGGCAGGTTGCATACGTGTTACTCACCCGTGCGCCGG\n+>r192 PC.593_342\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACGCATCGTCGCCTTGGTGAGCCGTTACCTCACCAACCAGCTAATGCGCCATAAGTCCATCCTCTACCAGTGCCTTGCAGCACTTTTAATACGGTCACCATGCAGTGTCCCTACCTATGCGGTCTTAGCTGCCGTTTCCAGCAGTTATCCCCCTGTAAAGGCCAGGTT\n+>r28 PC.634_44\n+CTGGGCCGTGTCTCAGTCCCAGTCTGGATGATCATCCTCTCAAACCATCTAACGATCGTCGACTTGGTGAGCCTTTACCTCACCAACTATCTAATCGTACGCAGGCCATTCCTAAAGCGCATAAATGCTTTAATCCGAAGATCATATGCGGTATTAGCCACTCTTTCGAGTAGTTATCCCTCACTTTAGGGTATGTTCCCACGCGTTACTCAGCCGTCCG\n+>r38 PC.355_384\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTAGGCCGTTACCCCACCAACCAGCTAATCAGACGCGGGCTCATCTTATACTACCGGAGTTTTTCACACAGAAACATGCGTCCCCGTGCGCTTATGCGGTATTAGCAGTCATTT'..b'CCGTCCACCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTAGGCCGTTACCCTGCCAACTGGCTAATCAGACGCGGGTCCATCCCATACCACCGGAGTTTTTCACACAGGAGCATGCGCTTCCGTGCGCTTATGCGGTATTAGCACCTGTTTCCAGGTGGTATCCCCCCGGTGTGGGGCAGGTTGCCCACGCGTTACTCACCCGTCCG\n+>New.0.ReferenceOTU51 PC.607_171\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGCTGCCCCGCCAACAAGCTAATCAGACGCGGGCCCCTCCCATACCGCCGGAACTTTCCCCAGAAAGGCATGCGCCTCCCTGGTTTATGCGGTATTAGCAGCCGTTTCCGGCTGTTATCCCCCTGTATGGGGCAGGTTGCCCACGCGTTACTCACCCGTCCGCC\n+>New.0.ReferenceOTU52 PC.636_379\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACTAGCTAATGCGCCGCATGGCCATCCGTAGCCGGTGTTACCCTTTAAACCCCAAGAGATGCCTCTCGGAGTTATTACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTACGGGCAGGTTCCATACGTGTTACTCACCCGTGCGCCGGTCGCCGGCAG\n+>New.0.ReferenceOTU54 PC.593_343\n+CTGGTCCGTGTCTCAGTCCCAATGTGGCCGGCCACCCTCTCAGGTCGGCTACTGATCGTCGCCTTGGTGGGCTTTTATCTCACCAACTAGCTAATCAGACGCAGATCCATCCCATACCACCGGAGTTTTTCACACAGGGCCATGCAGCCTCGTGCGCTTATGCGGTATTAGCAGCCGTTTCCGGCTGTTATCCCCCGGTATGGGGCAGGTTATCCACG\n+>New.0.ReferenceOTU57 PC.634_31\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCCG\n+>New.0.ReferenceOTU6 PC.634_150\n+CTGGACCGTGTTCCAGTTCCAGTGTGACTGATCATCCTCTCAGACCAGTTAACCATCGTCGCCTTGGTAGGCCTTTACCCCACCAACCAGCTAATGGTACGCGGACTCATCAAAAAGCAACAGCATATGCAGAGGCCATCTTTCCCACATAAGATAGATATGCAGCGTATTCGGTATTAGCAGCCGTTTCCAGCTGTTATCCCAAACTT\n+>New.0.ReferenceOTU7 PC.356_363\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGTCTTGGTGGTCCGTTACACCGCCAACTAACTAATGCGACGCATGCCCATCCGCCACCGGAATCAACCTTTGGCACCAACAGGATGTCCCATAGGTGCATTATGCCGTATTAGACGGAATTTCTCCCGATTATCCGGCTGTGGCAGGCAGGTTGCATACGTGTT\n+>New.0.ReferenceOTU9 PC.355_240\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTGCCCCGCCAACCAGCTAATCAGACGCGGGCCCATCCCGCACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTATACGGCAGGTTCTCCACGCGTT\n+>New.0.CleanUp.ReferenceOTU12 PC.607_297\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTATGCATCATCGTCTTGGTGGGCCTTTACCCCGCCAACCAACTAATGCACCGCAGGTCCATCCGCGCCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTCCTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTTACTCACCCG\n+>New.0.CleanUp.ReferenceOTU17 PC.634_123\n+CTGGGCCGTATCTCAGTCCCAATGTGGCCGGCCAACCTCTCAGTCCGGCTACTGATCGTCGCCTTGGTGAGCCGTTACCTCACCAACTAGCTAATCAGACGCGAGGCCATCTTTCAGCGATAAATCTTTGACATAAATGCCATGCGACACCTATGTGTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTCCT\n+>New.0.CleanUp.ReferenceOTU19 PC.607_312\n+TTGGTCCGTGTCTCAGTACCAATGTGGGGGGTTAACCTCTCAGTCCCCCTATGTATCGTGGTCTTGGTGAGCCGTTACCCCACCAACTAACTAATACAACGCATGCCCATCCATTACCACCGGAGTTTTCAACCCAAGAAGATGCCTCCCTGGATGTTATGGGGTATTAGTACCGATTTCTCAGTGTTATCCCCCTGTAATGGGTAGGTTGCATACGCGTTACGCACCCGTGCGCCGGTCGCCGACAAT\n+>New.0.CleanUp.ReferenceOTU29 PC.354_255\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTAGACATCGTCGCCTTGGTGGGCCGTTGCCCCGCCAACTAGCTAATGTCACGCATGCCCATCCGTTGCCGGAATCGCTTCCTTTGGCCGCAGGGCCATGCAGCCCCGCGGCATTACGCGGTATTAGACGGGATTTCTCCCGATTATCCCCCTGCAACGGGCAGGTCGCATACGCGTTACT\n+>New.0.CleanUp.ReferenceOTU33 PC.607_365\n+TTGGTCCGTGTCTCAGTACCAATGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCTTTGGTGGGCCGTTACCCCGCCAACTGGCTAATGCGCCGCATGCCCATCCTTTGCCGGAATTGCTTCCTTTGACTCCCAAACCATGTGGTAAGGGAGTGTTATGCAGTATTAGTCGGAATTTCTCCCGGTTATCCTCCTGCAAAGGGCAGGTTGCATACGTGTTACTCACCCGTGCGCCGG\n+>New.0.CleanUp.ReferenceOTU7 PC.634_157\n+TTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGTCGGTTTGGTGGGCCGTTACCCCGCCAACTGCCTAATGGAACGCATGCCTATCTATCAGCGATGAATCTTTAGCAAATATCCCCATGCGGGGCCCCTGCTTCATGCGGTATTAGTCCGACTTTCGCCGGGTTATCCCCCTCTGATAGGCAAGTTGCATACGCGTTACTC\n+>New.0.CleanUp.ReferenceOTU9 PC.355_327\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCGGGTCCATCTTACACCACCGGAGTTTTTAAGGAAAAGACATGCATCTTTCCCTGTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCTGTACAGGGCAGGTTACCCACGCGTTACTCACCCGTCCGCCACTAAGAT\n'

diff -r 000000000000 -r c11972e98d44 test-data/alpha_diversity/alphadiv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alpha_diversity/alphadiv Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,10 @@
+ chao1 observed_species
+PC.636 173.0 63.0
+PC.635 332.5 91.0
+PC.356 189.9375 83.0
+PC.481 223.583333333 81.0
+PC.354 176.8 64.0
+PC.593 90.0 48.0
+PC.355 127.0 62.0
+PC.607 211.0 78.0
+PC.634 146.0 64.0

diff -r 000000000000 -r c11972e98d44 test-data/alpha_diversity/otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alpha_diversity/otu_table.biom Thu May 18 09:38:55 2017 -0400

[

b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "0", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Staphylococcaceae"]}}, {"id": "1", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "2", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "3", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "4", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "5", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "6", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "7", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "8", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "9", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "10", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "11", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "12", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "13", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "14", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}}, {"id": "15", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Streptococcaceae"]}}, {"id": "16", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "17", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Coriobacteriales", "f__Coriobacteriaceae"]}}, {"id": "18", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Coriobacteriales", "f__Coriobacteriaceae"]}}, {"id": "19", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "20", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Porphyromonadaceae"]}}, {"id": "21", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}}, {"id": "22", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "23", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}}, {"id": "24", "metadata": {"taxonomy": ["Root", "k__Bacteria"]}}, {"id": "25", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "26", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}}, {"id": "27", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "28", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", 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[322, 7, 1.0], [323, 2, 1.0], [324, 0, 1.0], [325, 0, 1.0], [326, 2, 1.0], [326, 4, 1.0], [327, 7, 1.0], [328, 7, 1.0], [329, 4, 1.0], [330, 7, 1.0], [331, 6, 1.0], [332, 2, 1.0], [332, 4, 1.0], [333, 2, 1.0], [334, 7, 1.0], [335, 2, 2.0], [336, 7, 1.0], [337, 1, 1.0], [338, 1, 1.0], [339, 5, 2.0], [340, 1, 1.0], [341, 0, 1.0], [342, 0, 3.0], [342, 3, 1.0], [342, 5, 1.0], [342, 6, 1.0], [343, 0, 2.0], [343, 1, 1.0], [343, 2, 2.0], [344, 1, 1.0], [345, 0, 1.0], [346, 8, 1.0], [347, 0, 3.0], [347, 4, 1.0], [347, 5, 2.0], [347, 8, 2.0], [348, 7, 1.0], [349, 5, 3.0], [350, 1, 2.0], [350, 3, 7.0], [350, 6, 2.0], [351, 3, 1.0], [352, 3, 1.0], [353, 5, 1.0], [354, 8, 1.0], [355, 3, 2.0], [355, 4, 1.0], [355, 5, 4.0], [355, 6, 1.0], [356, 8, 1.0], [357, 7, 1.0], [357, 8, 1.0], [358, 1, 1.0], [359, 5, 2.0], [359, 8, 1.0], [360, 1, 1.0], [361, 1, 1.0], [362, 6, 1.0], [362, 8, 3.0], [363, 1, 1.0], [364, 8, 1.0], [365, 8, 1.0], [366, 6, 1.0], [367, 6, 1.0], [368, 6, 1.0], [369, 7, 1.0], [370, 1, 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[404, 6, 1.0], [405, 3, 1.0], [406, 0, 1.0], [406, 1, 1.0], [406, 2, 1.0], [406, 3, 2.0], [406, 6, 2.0], [406, 8, 1.0], [407, 8, 1.0], [408, 8, 4.0], [409, 0, 1.0], [410, 3, 9.0], [410, 8, 3.0], [411, 0, 1.0], [411, 6, 1.0], [412, 7, 1.0], [413, 0, 1.0], [414, 0, 2.0], [414, 1, 10.0], [414, 8, 8.0], [415, 6, 1.0], [416, 2, 1.0], [416, 3, 3.0], [417, 6, 1.0], [418, 0, 1.0]], "columns": [{"id": "PC.636", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.354", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2728", "matrix_type": "sparse", "shape": [419, 9], "format_url": "http://www.qiime.org/svn_documentation/documentation/biom_format.html", "date": "2012-02-07T06:12:49.215476", "type": "OTU table", "id": null, "matrix_element_type": "float"}\n\\ No newline at end of file\n'

diff -r 000000000000 -r c11972e98d44 test-data/alpha_diversity/rep_set.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alpha_diversity/rep_set.tre Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,1 @@\n+((((117:0.01623,(196:0.02706,306:0.01045)0.430:0.00015)0.914:0.00014,(314:0.02521,104:0.00015)0.465:0.01855)0.885:0.02154,407:0.02223)0.848:0.01046,(259:0.01763,185:0.02203)0.762:0.00511,((353:0.04271,(335:0.01062,(394:0.04443,169:0.00014)0.910:0.01046)0.671:0.00521)0.239:0.00014,((245:0.05025,((229:0.01061,95:0.00523)0.825:0.02163,(45:0.00543,(380:0.02839,(366:0.02249,((100:0.00528,411:0.00534)0.801:0.00586,((80:0.02709,62:0.00014)0.787:0.00524,4:0.01624)0.743:0.00448)0.385:0.00528)0.821:0.01601)0.407:0.00986)0.749:0.0047)1.000:0.00014)0.884:0.01045,(((404:0.02473,(321:0.05743,345:0.04116)0.770:0.01042)0.871:0.0175,(159:0.00512,(((((130:0.00524,223:0.02109)0.768:0.00506,53:0.00505)0.700:0.00015,((417:0.00455,(((309:0.04229,(332:0.00014,(152:0.03495,49:0.01132)0.757:0.00501)0.726:0.00689)0.484:0.01637,93:0.00014)0.782:0.00501,(128:0.01468,(254:0.00886,367:0.00882)0.813:0.00016)0.838:0.01501)0.773:0.00525)0.893:0.01078,(350:0.00518,(203:0.01589,7:0.03797)0.303:0.00015)0.778:0.00522)0.803:0.00528)0.893:0.01013,(388:0.03663,(110:0.02502,144:0.00823)0.883:0.02317)0.392:0.01286)0.340:0.00015,((251:0.03298,129:0.00595)0.743:0.02131,((187:0.01683,(192:0.04094,333:0.02254)0.819:0.01106)0.075:0.00016,(291:0.03997,374:0.02052)0.773:0.01301)0.706:0.00748)0.960:0.03217)0.827:0.00518)0.783:0.00016)0.968:0.01009,((((((331:0.0213,60:0.01357)0.425:0.01773,((109:0.02075,(317:0.07537,264:0.01319)0.577:0.02234)0.840:0.02594,(312:0.13538,173:0.0804)0.863:0.04059)0.906:0.04474)0.732:0.00594,(250:0.02106,253:0.01877)0.861:0.01467)1.000:0.08412,((37:0.02019,(284:0.01874,301:0.05561)0.553:0.01707)0.821:0.01394,(((391:0.01339,94:0.03006)0.863:0.01092,((141:0.02689,(90:0.01568,166:0.01544)0.845:0.01038)0.773:0.00831,(216:0.02563,288:0.04234)0.553:0.02164)0.778:0.00999)0.751:0.00694,((174:0.04134,(19:0.01184,((11:0.01042,(279:0.0051,(97:0.03227,172:0.00015)0.826:0.00518)0.773:0.00507)0.865:0.01734,(202:0.02027,(198:0.0444,(16:0.02344,297:0.01386)0.707:0.01593)0.900:0.01926)0.904:0.01639)0.717:0.00775)0.879:0.01642)0.783:0.01157,((((124:0.06649,((405:0.00158,89:0.0157)0.911:0.02924,(81:0.05513,((32:0.01302,(111:0.01924,418:0.01395)0.079:0.00502)0.876:0.01356,(67:0.01066,140:0.00015)0.894:0.01716)0.882:0.02725)0.951:0.03825)0.231:0.01554)0.841:0.01263,(((((41:0.0103,171:0.0168)0.841:0.01081,(278:0.01609,305:0.01125)0.772:0.00474)0.784:0.00577,((84:0.0344,(186:0.04377,142:0.03554)0.843:0.01608)0.912:0.02736,(372:0.02034,(287:0.03183,409:0.01693)0.856:0.01073)0.745:0.00582)0.571:0.00506)0.753:0.00517,((268:0.03304,(213:0.01051,382:0.01052)0.811:0.00998)0.952:0.02716,(9:0.08093,(52:0.03741,(359:0.02766,58:0.07021)0.869:0.02854)0.679:0.01388)0.836:0.01208)0.521:0.00015)0.899:0.01075,(((364:0.0264,66:0.01994)0.913:0.0207,(222:0.00015,10:0.02739)0.845:0.01067)0.860:0.01237,(61:0.03289,(((330:0.04019,351:0.02244)0.698:0.0276,(323:0.12995,(289:0.00535,(413:0.02178,139:0.01068)0.762:0.00528)0.942:0.00015)0.819:0.0102)0.938:0.00015,303:0.01596)0.858:0.01157)0.209:0.00476)0.954:0.02615)0.496:0.00014)0.832:0.00517,(((214:0.05163,230:0.07569)0.927:0.03951,((280:0.03044,(194:0.01081,(65:0.01809,(316:0.04535,(((387:0.00014,(30:0.02953,145:0.00015)0.831:0.00568)0.806:0.00587,(204:0.01043,346:0.00438)0.793:0.00431)0.960:0.03307,((343:0.01764,393:0.01827)0.727:0.00451,(127:0.02335,83:0.0179)0.759:0.00672)0.588:0.00574)0.643:0.00015)0.950:0.0228)0.748:0.00571)0.961:0.04287)0.925:0.03217,(241:0.01939,43:0.08019)0.857:0.02177)0.849:0.01507)0.829:0.01924,((((132:0.03373,(221:0.02342,352:0.04396)0.946:0.03287)0.888:0.01823,((373:0.10091,177:0.13147)0.751:0.00015,(((293:0.0161,86:0.00014)0.968:0.03626,102:0.04302)0.693:0.00897,(((123:0.01071,(209:0.00014,(376:0.0,156:0.0):0.00014)0.842:0.01038)0.945:0.0265,(210:0.00016,146:0.01595)0.549:0.01437)0.654:0.00218,((12:0.0484,8:0.02104)0.969:0.0424,(272:0.02828,(22:0.01045,29:0.02189)0.760:0.00525)0.749:0.00487)0.701:0.01121)0.821:0.01228)0.883:0.01772)0.724:0.00651)0.902:0.02042,(((((408:0.00014,(38:0.0526,78:0.0007'..b'2675)0.998:0.096)0.929:0.03959,((285:0.00015,(108:0.00014,(149:0.07407,((344:0.01413,151:0.01634)0.736:0.00657,(134:0.02781,(212:0.02652,(378:0.00015,(238:0.04745,247:0.04301)0.703:0.00014)0.966:0.02148)0.015:0.00015)0.466:0.01024)0.756:0.00588)0.883:0.01526)0.969:0.03759)0.988:0.03167,370:0.00014)0.867:0.02372)0.998:0.08133,158:0.00015)0.922:0.03621,((358:0.01281,(20:0.02969,99:0.02372)0.985:0.06249)0.998:0.11815,(190:0.06903,(357:0.06998,356:0.00015)0.829:0.02015)0.858:0.03439)0.919:0.05706)0.807:0.02571,193:0.01711)0.882:0.02352)0.729:0.01709,(248:0.0579,((244:0.03253,(206:0.05079,(((262:0.01325,255:0.03775)0.835:0.01673,88:0.02516)0.336:0.00015,40:0.02313)0.090:0.01515)0.865:0.01872)0.925:0.03028,(263:0.0345,(36:0.0456,183:0.04272)0.933:0.04591)0.868:0.02359)0.930:0.04794)0.957:0.06027)0.972:0.06398)0.617:0.00519)0.724:0.00431,((277:0.01408,(227:0.04382,233:0.00014)1.000:0.09125)0.682:0.0064,((((((((14:0.00015,188:0.00525)0.779:0.00517,(257:0.01105,375:0.04818)0.740:0.00015)0.775:0.01082,(119:0.00016,(313:0.01642,347:0.00015)0.843:0.01076)0.674:0.0108)0.000:0.00016,(298:0.0345,((325:0.05824,(184:0.00016,(178:0.06962,(340:0.06024,(((175:0.08004,(270:0.02469,282:0.06081)0.944:0.04574)0.357:0.01243,(258:0.06066,((365:0.00016,((26:0.00534,70:0.03876)0.939:0.01609,(195:0.03389,(44:0.01056,(180:0.0222,386:0.02757)0.969:0.00014)0.868:0.02803)0.745:0.00533)0.343:0.01063)0.802:0.00638,125:0.0208)0.354:0.01817)0.372:0.00767)0.820:0.0178,(218:0.03567,147:0.00245)0.981:0.05918)0.768:0.0159)0.847:0.01215)0.768:0.00569)0.978:0.02296)0.000:0.00015,(237:0.03489,296:0.01051)0.925:0.01719)0.896:0.01736)0.515:0.0105)0.741:0.01842,((126:0.01118,179:0.02795)0.939:0.02231,(160:0.01105,(329:0.01155,(336:0.00015,34:0.01644)0.840:0.02223)0.949:0.02512)0.759:0.00599)0.000:0.00334)0.952:0.0329,384:0.01969)0.777:0.00942,133:0.04451)0.888:0.02052,(208:0.0403,(23:0.01161,((115:0.00837,46:0.08317)0.999:0.11513,(276:0.02789,162:0.02676)0.797:0.03037)0.884:0.03986)0.910:0.0309)0.796:0.0182)0.951:0.03291)0.958:0.03269)0.545:0.00537)0.583:0.00014)0.727:0.00654,(((((295:0.02551,(368:0.02676,47:0.03946)0.602:0.00136)0.826:0.00588,((((228:0.00015,((290:0.01639,354:0.01649)0.568:0.01074,197:0.0162)0.879:0.00016)0.924:0.00529,256:0.00519)0.880:0.00015,(231:0.01531,403:0.02714)0.818:0.00041)0.733:0.00505,(191:0.0051,(33:0.02234,377:0.03943)0.879:0.01609)0.882:0.01086)0.858:0.01046)0.759:0.00506,(77:0.02734,(114:0.02206,50:0.03351)0.705:0.00412)0.855:0.01095)0.861:0.01075,((48:0.01954,(389:0.00015,13:0.01579)0.776:0.00512)0.800:0.00644,(((107:0.00513,116:0.01096)0.872:0.01062,(150:0.01086,(401:0.00014,189:0.05119)0.390:0.01048)0.911:0.01611)0.887:0.01052,(307:0.00016,((395:0.01672,402:0.01628)0.732:0.00525,(((((243:0.01546,(265:0.03394,412:0.01126)0.542:0.01041)0.781:0.00609,(326:0.01055,167:0.0162)0.760:0.0052)0.814:0.0052,(294:0.05971,(308:0.01435,381:0.0377)0.751:0.00763)0.895:0.0161)0.987:0.00014,(112:0.03413,25:0.01612)0.905:0.00014)0.876:0.00015,(252:0.00015,342:0.01556)0.980:0.02642)0.502:0.00526)0.893:0.01027)0.907:0.01031)0.851:0.00014)0.868:0.01018)0.889:0.01626,(((106:0.00831,(302:0.03114,85:0.01229)0.901:0.02187)0.886:0.01264,((((275:0.01585,(217:0.00016,338:0.03721)0.892:0.03778)0.770:0.00488,(392:0.00516,(1:0.00527,(240:0.01873,(51:0.02977,281:0.0106)0.492:0.01443)0.777:0.00831)0.772:0.00526)0.778:0.00519)0.833:0.00503,(406:0.01023,416:0.00515)0.865:0.00015)0.799:0.01576,68:0.01626)0.749:0.00507)0.757:0.00518,(87:0.02794,161:0.00014)0.233:0.00511)0.904:0.0159)0.896:0.02029)0.683:0.02168)0.833:0.01463)0.781:0.00532)0.723:0.00556)0.820:0.01376,((92:0.03867,((318:0.01724,(415:0.02669,148:0.00014)0.736:0.00422)0.837:0.01019,(261:0.00516,385:0.00502)0.967:0.02157)0.000:0.00015)0.895:0.01312,(6:0.04864,(((135:0.00901,(286:0.06254,105:0.01165)0.753:0.01766)0.580:0.0171,79:0.01655)0.632:0.00016,42:0.00015)0.829:0.00928)0.759:0.00636)0.758:0.01044)0.646:0.00165,299:0.00508)0.922:0.00016)0.860:0.01021)0.765:0.00517)0.776:0.00522);\n\\ No newline at end of file\n'

diff -r 000000000000 -r c11972e98d44 test-data/alpha_rarefaction/mapping_file.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alpha_rarefaction/mapping_file.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,11 @@
+#SampleID BarcodeSequence LinkerPrimerSequence Treatment DOB Description
+#Example mapping file for the QIIME analysis package. These 9 samples are from a study of the effects of exercise and diet on mouse cardiac physiology (Crawford, et al, PNAS, 2009).
+PC.354 AGCACGAGCCTA YATGCTGCCTCCCGTAGGAGT Control 20061218 Control_mouse_I.D._354
+PC.355 AACTCGTCGATG YATGCTGCCTCCCGTAGGAGT Control 20061218 Control_mouse_I.D._355
+PC.356 ACAGACCACTCA YATGCTGCCTCCCGTAGGAGT Control 20061126 Control_mouse_I.D._356
+PC.481 ACCAGCGACTAG YATGCTGCCTCCCGTAGGAGT Control 20070314 Control_mouse_I.D._481
+PC.593 AGCAGCACTTGT YATGCTGCCTCCCGTAGGAGT Control 20071210 Control_mouse_I.D._593
+PC.607 AACTGTGCGTAC YATGCTGCCTCCCGTAGGAGT Fast 20071112 Fasting_mouse_I.D._607
+PC.634 ACAGAGTCGGCT YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse_I.D._634
+PC.635 ACCGCAGAGTCA YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse_I.D._635
+PC.636 ACGGTGAGTGTC YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse_I.D._636

diff -r 000000000000 -r c11972e98d44 test-data/alpha_rarefaction/otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alpha_rarefaction/otu_table.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/alpha_rarefaction/rep_set.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alpha_rarefaction/rep_set.tre Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/assign_taxonomy/mothur_ref_seq_set.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/assign_taxonomy/mothur_ref_seq_set.fna Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,14 @@
+>X67228
+aacgaacgctggcggcaggcttaacacatgcaagtcgaacgctccgcaaggagagtggcagacgggtgagtaacgcgtgggaatctacccaaccctgcggaatagctctgggaaactggaattaataccgcatacgccctacgggggaaagatttatcggggatggatgagcccgcgttggattagctagttggtggggtaaaggcctaccaaggcgacgatccatagctggtctgagaggatgatcagccacattgggactgagacacggcccaaa
+>X73443
+nnnnnnngagatttgatcctggctcaggatgaacgctggccggccgtgcttacacatgcagtcgaacgaagcgcttaaactggatttcttcggattgaagtttttgctgactgagtggcggacgggtgagtaacgcgtgggtaacctgcctcatacagggggataacagttagaaatgactgctaataccnnataagcgcacagtgctgcatggcacagtgtaaaaactccggtggtatgagatggacccgcgtctgattagctagttggtggggt
+>AB004750
+acgctggcggcaggcctaacacatgcaagtcgaacggtagcagaaagaagcttgcttctttgctgacgagtggcggacgggtgagtaatgtctgggaaactgcccgatggagggggataactactggaaacggtagctaataccgcataacgtcttcggaccaaagagggggaccttcgggcctcttgccatcggatgtgcccagatgggattagctagtaggtggggtaacggctcacctaggcgacgatccctagctggtctgagaggatgaccagccacactggaactgagacacggtccagactcctacgggaggcagcagtggggaatattgca
+>xxxxxx
+ttgaacgctggcggcaggcctaacacatgcaagtcgagcggcagcannnncttcgggaggctggcgagcggcggacgggtgagtaacgcatgggaacttacccagtagtgggggatagcccggggaaacccggattaataccgcatacgccctgagggggaaagcgggctccggtcgcgctattggatgggcccatgtcggattagttagttggtggggtaatggcctaccaaggcgacgatccgtagctggtctgagaggatgatcagccacaccgggactgagacacggcccggactcctacgggaggcagcagtggggaatattggacaatgggggcaaccctgatccagccatgccg
+>AB004748
+acgctggcggcaggcctaacacatgcaagtcgaacggtagcagaaagaagcttgcttctttgctgacgagtggcggacgggtgagtaatgtctgggaaactgcccgatggagggggataactactggaaacggtagctaataccgcataacgtcttcggaccaaagagggggaccttcgggcctcttgccatcggatgtgcccagatgggattagctagtaggtggggtaacggctcacctaggcgacgatccctagctggtctgagaggatgaccagccacactggaactgagacacggtccagactcctacgggaggcagcagtggggaatattgcacaatgggcgcaagcctgatgcagccatgccgcgtgtatgaagaaggccttcgggttg
+>AB000278
+caggcctaacacatgcaagtcgaacggtaanagattgatagcttgctatcaatgctgacgancggcggacgggtgagtaatgcctgggaatataccctgatgtgggggataactattggaaacgatagctaataccgcataatctcttcggagcaaagagggggaccttcgggcctctcgcgtcaggattagcccaggtgggattagctagttggtggggtaatggctcaccaaggcgacgatccctagctggtctgagaggatgatcagccacactggaactgagacacggtccagactcctacgggaggcagcagtggggaatattgcacaatgggggaaaccctgatgcagccatgccgcgtgta
+>AB000390
+tggctcagattgaacgctggcggcaggcctaacacatgcaagtcgagcggaaacgantnntntgaaccttcggggnacgatnacggcgtcgagcggcggacgggtgagtaatgcctgggaaattgccctgatgtgggggataactattggaaacgatagctaataccgcataatgtctacggaccaaagagggggaccttcgggcctctcgcttcaggatatgcccaggtgggattagctagttggtgaggtaatggctcaccaaggcgacgatccctagctggtctgagaggatgatcagccacactggaactgag

diff -r 000000000000 -r c11972e98d44 test-data/assign_taxonomy/sortmerna_map.blast
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/assign_taxonomy/sortmerna_map.blast Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,28 @@
+X67228 152350 98.6 277 4 0 1 277 22 298 5.76e-129 464 277M 100
+X67228 558499 97.1 275 8 0 1 275 2 276 1.05e-122 443 275M2S 99.3
+X67228 553706 97.5 277 7 0 1 277 1 277 4.7e-125 451 277M 100
+X67228 553981 95.7 277 12 0 1 277 2 278 1.55e-118 429 277M 100
+X67228 4423084 98.6 277 4 0 1 277 21 297 5.76e-129 464 277M 100
+X73443 179865 96.3 269 2 8 8 276 2 268 2.31e-114 415 7S3M1I28M1I3M1I7M1D8M1D20M1I26M1I115M1D54M 97.5
+X73443 181718 96 269 3 8 8 276 2 268 4.66e-113 411 7S3M1I28M1I3M1I7M1D8M1D20M1I26M1I115M1D54M 97.5
+X73443 193551 96.3 269 2 8 8 276 2 268 2.31e-114 415 7S3M1I28M1I3M1I7M1D8M1D21M1I26M1I114M1D54M 97.5
+X73443 212341 96.3 269 2 8 8 276 2 268 2.31e-114 415 7S3M1I28M1I3M1I7M1D8M1D21M1I26M1I114M1D54M 97.5
+X73443 175883 96 269 3 8 8 276 2 268 4.66e-113 411 7S3M1I28M1I3M1I7M1D8M1D21M1I26M1I114M1D54M 97.5
+AB004750 3888577 100 339 0 0 1 339 26 364 1.61e-166 588 339M 100
+AB004750 581782 97.6 339 8 0 1 339 27 365 4.36e-156 554 339M 100
+AB004750 1108679 97.9 339 7 0 1 339 26 364 2.16e-157 558 339M 100
+AB004750 1109844 97.9 339 7 0 1 339 26 364 2.16e-157 558 339M 100
+AB004750 4418165 99.7 339 1 0 1 339 28 366 3.25e-165 584 339M 100
+xxxxxx 1102995 97.5 361 8 1 1 361 22 383 2.94e-166 588 174M1D187M 100
+xxxxxx 340031 95.6 361 13 3 1 361 23 386 1.07e-158 562 169M3D192M 100
+xxxxxx 340031 95.6 361 13 3 1 361 23 386 1.07e-158 562 169M3D192M 100
+AB004748 581782 98 396 8 0 1 396 27 422 8.13e-186 653 396M 100
+AB004748 1108679 98.2 396 7 0 1 396 26 421 4.04e-187 657 396M 100
+AB004748 1109844 98.2 396 7 0 1 396 26 421 4.04e-187 657 396M 100
+AB004748 3888577 100 396 0 0 1 396 26 421 3.01e-196 687 396M 100
+AB004748 561327 97.5 396 10 0 1 396 1 396 3.3e-183 644 396M 100
+AB000278 554346 98.6 368 5 0 1 368 6 373 4e-175 617 368M 100
+AB000278 160928 97 368 7 4 1 368 33 400 2.94e-166 588 33M1D5M1I8M1I2M1D318M 100
+AB000390 4433053 98.1 317 6 0 1 317 13 329 3.2e-147 524 317M 100
+AB000390 19456 94.4 317 14 4 1 317 12 328 4.28e-132 474 77M2D4M2I234M 100
+AB000390 4432126 94.4 317 14 4 1 317 13 329 4.28e-132 474 77M2D4M2I234M 100

diff -r 000000000000 -r c11972e98d44 test-data/assign_taxonomy/sortmerna_taxonomic_assignation.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/assign_taxonomy/sortmerna_taxonomic_assignation.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,8 @@
+#OTU ID taxonomy confidence num hits
+AB004750 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__; s__ 0.60 5
+AB000390 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Vibrionales; f__Vibrionaceae 1.00 3
+xxxxxx k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Alteromonadales; f__Alteromonadaceae; g__Marinobacter; s__ 1.00 3
+X67228 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhizobiales; f__Rhizobiaceae 0.60 5
+AB000278 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Vibrionales; f__Vibrionaceae; g__Photobacterium 1.00 2
+AB004748 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__; s__ 0.60 5
+X73443 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae 1.00 5

diff -r 000000000000 -r c11972e98d44 test-data/assign_taxonomy/uclust_input_seqs.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/assign_taxonomy/uclust_input_seqs.fasta Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,20 @@\n+>11472286\n+GATGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGGAACACTTTGTGTTTTGAGTTAATAGTTCGATAGTAGATAGTAAATAGTGAACACTATGAACTAGTAAACTATTTAACTAGAAACTCTTAAACGCAGAGCGTTTAGTGGCGAACGGGTGAGTAATACATTGGTATCTACCTCGGAGAAGGACATAGCCTGCCGAAAGGTGGGGTAATTTCCTATAGTCCCCGCACATATTTGTTCTTAAATCTGTTAAAATGATTATATGTTTTATGTTTATTTGATAAAAAGCAGCAAGACAAATGAGTTTTATATTGGTTATACAGCAGATTTAAAAAATAGAATTAGGTCTCATAATCAGGGAGAAAACAAATCAACTAAATCTAAAATACCTTGGGAATTGGTTTACTATGAAGCCTACAAAAACCAAACATCAGCAAGGGTTAGAGAATCAAAGTTGAAACATTATGGGCAATCATTAACTAGACTTAAGAGAAGAATTGGTTTTTGAGAACAAATATGTGCGGGGTAAAGCAGCAATGCGCTCCGAGAGGAACCTCTGTCCTATCAGCTTGTTGGTAAGGTAATGGCTTACCAAGGCGACGACGGGTAGCTGGTGTGAGAGCACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTCCACAATGGGCGCAAGCCTGATGGAGCAATGCCGCGTGAAGGATGAAGATTTTCGGATTGTAAACTTCTTTTAAGTAGGAAGATTATGACGGTACTACTTGAATAAGCATCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGATGCAAGCGTTATCCGGAATTACTGGGCGTAAAGCGTGTGTAGGTGGTTTATTAAGTTAAATGTTAAATTTTCAGGCTTAACTTGGAAACCGCATTTAATACTGGTAGACTTTGAGGACAAGAGAGGCAGGCGGAATTAGCGGAGTAGCGGTGAAATGCGTAGATATCGCTAAGAACACCAATGGCGAAGGCAGCCTGCTGGTTTGCACCTGACACTGAGATACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACGATGGTCACTAGCTGTTAGGGGCTCGACCCCTTTAGTAGCGAAGCTAACGCGTTAAGTGACCCGCCTGGGGAGTACGATCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAACGTGAGGTTTAATTCGTCTCTAAGCGAAAAACCTTACCGAGGCTTGACATCTCCGGAAGACCTTAGAAATAAGGTTGTGCCCGAAAGGGAGCCGGATGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTCGGTTAAGTCCGTTAACGAGCGCAACCCTTGCTGTGTGTTGTATTTTTCACACAGGACTATCCTGGTCAACAGGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCTCTTACGCCTCGGGCTACACTCGCGTTACAATGGCCGGTACAATGGGCTGCCAACTCGTAAGGGGGAGCTAATCCCATCAAAACCGGTCCCAGTTCGGATTGAGGGCTGCAATTCGCCCTCATGAAGTCGGAATCGCTAGTAACCGCGAATCAGCACGTCGCGGTGAATGCGTTCTCGGGTCTTGTACACACTGCCCGTCACACCACGAAAGTTAGTAACGCCCGAAGTGCCCTGTATGGGGTCCTAAGGTGGGGCTAGCGATTGGGGTG\n+>11472384\n+AGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGGGCAACCCTGGTGGCGAGTGGCGAACGGGTGAGTAATACATCGGAACGTGTCCTGTAGTGGGGGATAGCCCGGCGAAAGCCGGATTAATACCGCATACGCTCTACGGAGGAAAGGGGGGGATCTTAGGACCTCCCGCTACAGGGGCGGCCGATGGCAGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCTGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTTGTCCGGAAAGAAAACGCCGTGGTTAATACCCGTGGCGGATGACGGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTCCGCTAAGACAGATGTGAAATCCCCGGGCTTAACCTGGGAACTGCATTTGTGACTGGCGGGCTAGAGTATGGCAGAGGGGGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCCCCTGGGCCAATACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACTAGTTGTCGGGTCTTCATTGACTTGGTAACGTAGCTAACGCGTGAAGTTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAAAACCTTACCTACCCTTGACATGTATGGAATCCTGCTGAGAGGTGGGAGTGCCCGAAAGGGAGCCATAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCCTAGTTGCTACGCAAGAGCACTCTAGGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGGGTAGGGCTTCACACGTCATACAATGGTCGGAACAGAGGGTCGCCAACCCGCGAGGGGGAGCCAATCCCAGAAAACCGATCGTAGTCCGGATCGCACTCTGCAACTCGAGTGCGTGAAGCTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTTTACCAGAAGTGGCTAGTCTAACCGCAAGGAGGACGGTCACCACGGTAGGATTCATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTCTCGAGCGAACGTGTCGAACGTTGAGCGCTCACGCTTATCGGCTGTGAAATTAGGACAGTAAGTCAGACAGACTGAGGGGTCTGTAGCTCAGTCGGTTAGAGCACCGTCTTGATAAGGCGGGGGTCGATGGTTCGAATCCATCCAGACCCACCATTGTCT\n+>11468680\n+TAAACTGAAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGTGCTTGCACCTGGTGGCGAGTGGCGAACGGGTGAGTAATACATCGGAACATGTCCTGTAGTGGGGGATAGCCCGGCGAAAGCCGGATTAATACCGCATACGATCTACGGATGAAAGCGGGGGACCTTCGGGCCTCGCGCTATAGGGTTGGCCGATGGCTGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCAGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTTGTCCGGAAAGAAATCCTTGGCTCTAATACAGTCGGGGGATGACGGTACCGGAAG'..b'GGATTAGATACCCCGGTAGTCCTAGCTGTAAACGATGGATACTAGGTGTGGGAGGTATCGACCCCTTCTGTGCCGWCACTAACGCATTAAGTATCCCGCCTGGGGAGTACGGTCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGCAACGCGAAGAACCTTACCGGGGCTTGACATTGTCTTGCCCGTTTAAGAAATTAAATTTTCTTCCCTTTTAGGGAAGACAAGATAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCACAACGAGCGCAACCCTTATTCTTAGTTGCTAGTTTGTTTACAAACGCACTCTAAAGAGACTGCCGCAGATAATGCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTACGTCCCGGGCTACACACGTGCTACAATGGCCTGTACAGAGGGTAGCGAAAGAGCGATCTCAAGCTAATCCCTTAAAACAGGTCTCAGTTCGGATTGGAGGCTGCAACTCGCCTCCATGAAGTCGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGAAAGTTGGCGATACCTGAAGTTACTGTGCTAACCCGGCACTCAACTAAGTACATTAAGTCTTATTTTAAGCTATTGTATTTAGTTGAGTGCCGGGAGGCAGGTACCTAAGGTATGGCTAGCGATTGGGGTGAAGTCGTAACAAGGTAGCCG\n+>11480235\n+TGGTTTGATCCTGGCTCAGGATTAACGCTGGCGGCGCGCCTTATACATGCAAGTCGAACGAGCCTTGTGCTTCGCACAAGGAAATTCCAAGCACCAAGCACCAAATCTCAAACAAATCCCAATGACCAAAATTCCAAAAACCTAAACATTTTAAATGTTTAGAATTTGGAAAATTGGAATTTGGAATTTATTTGTTATTTGGAATTTATGATTTGGGATTTTCTCGCGCGGAGANCNTNAGTGGCGAACGGGTGAGTAATACGTTGGTATCTACCCCAAAGTAGAGAATAAGCCCGAGAAATCGGGGTTAATACTCTATGTGTTCGAAAGAACAAAGACTTCGGTTGCTTTGGGAAGAACCTGCGGCCTATCAGCTTGTTGGTAAGGTAACGGCTTACCAAGGCTTTGACGGGTAGCTGGTCTGGGAAGACGACCAGCCACAATGGGACTTAGACACGGCCCATACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGCCCGAAAGGTGACCGAGCGACGCCGCGTAGAGGAAGAAGATCTTTGGATTGTAAACTCTTTTTCTCCTAGACAAAGTTCTGATTGTATAGGAGGAATAAGGGGTTTCTAAACTCGTGCCAGCAGAAGCGGTAATACGAGTGCCCCAAGCGTTATCCGGAATCATTGGGCGTAGAGCGTTGTATAGGTGGTTTAAAAAGTCCAAAATTAAATCTTTAGGCTCAACCTAAAATCTGTTTTGGAAACTTTTAGACTTGAATAAAATCGACGSGAGTGGAACTTCCAGAGTAGGGGTTACATCCGTTGATACTGGAAGGAACGCCGAAGGCGAAAGCAACTCGCGAGATTTTATTGACGCCGCGTACACGAAAGCGTGGGGAGCGAAAAGTATTAGATACACTTGTAGTCCACGCCGTAAACTATGGATACTAGCAATTTGAAGCTTCGACCCTTCAAGTTGCGGACTAACGCGTTAAGTATCTCGCCTGGGAAGTACGGCCGCAAGGCTAAAACTCAAAGGAATAGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGATAAGCGTGGAACCTTACCAGGGCTTAGACGTACAGAGAATTCCTTGGAAACAAGGAAGTGCTTCGGGAACTCTGTACTCAGGTACTGCATGGCTGTCGTCAGTATGTACTGTGAAGCACTCCCTTAATTGGGGCAACATACGCAACCCCTATCCTAAGTTAGAAATGTCTTAGGAAACCGCTTCGATTCATCGGAGAGGAAGATGGGGACGACGTCAAGTCAGCATGGTCCTTGATGTCCTGGGCGACACACGTGCTACAATGGCTAGTATAACGGGATGCGTAGGTGCGAACCGAAGCTAATCCTTAAAAAACTAGTCTAAGTTCGGATTGAAGTCTGCAACTCGACTTCATGAAGCCGGAATCGCTAGTAACCGCAAATCAGCCACGTTGCGGTGAATACGTTCTCGGGCCTTGTACTCACTGCCCGTCACGTCAAAAAAGTCGGTAATACCCGAAGCACCCTTTTAAAGGGTTCTAAGGTAGGACCGATGATTGGGACGAAGTCGTAACAAGGTAGCCG\n+>11480408\n+AATTTAGCGGCCGCGAATTCGCCCTTGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGGGATATCCGAGCGGAAGGTTTCGGCCGGAAGGTTGGGTATTCGAGTGGCGGACGGGTGAGTAACGCGTGAGCAATCTGTCCCGGACAGGGGGATAACACTTGGAAACAGGTGCTAATACCGCATAAGACCACAGCATCGCATGGTGCAGGGGTAAAAGGAGCGATCCGGTCTGGGGTGAGCTCGCGTCCGATTAGATAGTTGGTGAGGTAACGGCCCACCAAGTCAACGATCGGTAGCCGACCTGAGAGGGTGATCGGCCACATTGGAACTGAGAGACGGTCCAAACTCCTACGGGAGGCAGCAGTGGGGAATATTGGGCAATGGGCGAAAGCCTGACCCAGCAACGCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTGTTATGCGAGACGAAGGAAGTGACGGTATCGCATAAGGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCGAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGTGTAGGCGGCCGTTTAAGTATGGAGTGAAAGTCCATTTTTCAAGGATGGAATTGCTTTGTAGACTGGATGGCTTGAGTGCGGAAGAGGTAAGTGGAATTCCCAGTGTAGCGGTGAAATGCGTAGAGATTGGGAGGAACACCAGTGGCGAAGGCGACTTACTGGGCCGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCGGTAAACGATGAATGCTAGGTGTTGCGGGTATCGACCCCTGCAGTGCCGGAGTAAACACAATAAGCATTCCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAGGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCATGTTGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATCCAGTTAAGCTCATAGAGATATGAGGTCCCTTCGGGGGAACTGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATGGTCAGTTACTAACGCGTGAAGGCGAGGACTCTGACGAGACTGCCGGGGACAACTCGGAGGAAGGTGGGGACGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACAAACGTGCTACAATGGTGACTACAAAGAGGAGCGAGACTGTAAAGTGGAGCGGATCTCAAAAAAGTCATCCCAGTTCGGATTGTGGGCTGCAACCCGCCCACATGAAGTTGGAGTTGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTTGGGAGCACCCGAAGTCAGTGAGGTAACCGGAAGGAGCCAGCTGCCGAAGGTGAGACCGATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTAAGGGCGAATTCGTTTAAACCTGCAGGACTAG\n'

diff -r 000000000000 -r c11972e98d44 test-data/assign_taxonomy/uclust_taxonomic_assignation.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/assign_taxonomy/uclust_taxonomic_assignation.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,10 @@
+11469739 k__Bacteria; p__OP9; c__JS1; o__SB-45; f__; g__; s__ 1.00 3
+11480235 k__Bacteria; p__OD1; c__; o__; f__; g__; s__ 1.00 1
+11460543 k__Bacteria; p__OP9; c__JS1; o__SB-45; f__; g__; s__ 1.00 3
+11460523 k__Bacteria; p__Proteobacteria; c__Deltaproteobacteria; o__Desulfobacterales; f__Desulfobulbaceae; g__; s__ 1.00 3
+11472286 k__Bacteria; p__WS5; c__; o__; f__; g__; s__ 1.00 1
+11458037 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Peptococcaceae; g__Desulfosporosinus; s__meridiei 1.00 3
+11472384 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__Burkholderia; s__ 0.67 3
+11469752 k__Bacteria; p__TM7; c__TM7-1; o__; f__; g__; s__ 1.00 3
+11480408 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__ 1.00 3
+11468680 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__Burkholderia; s__ 1.00 3

diff -r 000000000000 -r c11972e98d44 test-data/beta_diversity/otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_diversity/otu_table.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/beta_diversity/rep_set.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_diversity/rep_set.tre Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/beta_diversity_through_plots/map.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_diversity_through_plots/map.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/beta_diversity_through_plots/otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_diversity_through_plots/otu_table.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/beta_diversity_through_plots/rep_set.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_diversity_through_plots/rep_set.tre Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/beta_diversity_through_plots/unweighted_unifrac_dm.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_diversity_through_plots/unweighted_unifrac_dm.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,10 @@
+ PC.355 PC.607 PC.634 PC.635 PC.593 PC.636 PC.481 PC.354 PC.356
+PC.355 0.0 0.77062394744 0.753575681654 0.745509981365 0.660981656067 0.70062016649 0.647258584304 0.599541095803 0.615310834175
+PC.607 0.77062394744 0.0 0.726387392797 0.659269044234 0.713741192899 0.722772498498 0.686601452856 0.726258935536 0.735768463546
+PC.634 0.753575681654 0.726387392797 0.0 0.558850879936 0.763317384716 0.581124366673 0.663208945591 0.781832289452 0.788355481145
+PC.635 0.745509981365 0.659269044234 0.558850879936 0.0 0.745154628257 0.60737953696 0.655979250216 0.70672669146 0.72197480583
+PC.593 0.660981656067 0.713741192899 0.763317384716 0.745154628257 0.0 0.7377413135 0.657351659549 0.585097582096 0.718770654329
+PC.636 0.70062016649 0.722772498498 0.581124366673 0.60737953696 0.7377413135 0.0 0.669767446745 0.747947798007 0.748276547061
+PC.481 0.647258584304 0.686601452856 0.663208945591 0.655979250216 0.657351659549 0.669767446745 0.0 0.595087696488 0.697796152694
+PC.354 0.599541095803 0.726258935536 0.781832289452 0.70672669146 0.585097582096 0.747947798007 0.595087696488 0.0 0.610208881707
+PC.356 0.615310834175 0.735768463546 0.788355481145 0.72197480583 0.718770654329 0.748276547061 0.697796152694 0.610208881707 0.0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/beta_diversity_through_plots/unweighted_unifrac_pc.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_diversity_through_plots/unweighted_unifrac_pc.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,22 @@
+Eigvals 9
+0.512367260461 0.300719094427 0.267912066004 0.208988681078 0.19169895326 0.16054234528 0.15017695712 0.122457748167 0.0
+
+Proportion explained 9
+0.267573832777 0.15704469605 0.139911863774 0.109140272454 0.100111048503 0.0838401161912 0.0784269939011 0.0639511763509 0.0
+
+Species 0 0
+
+Site 9 9
+PC.355 -0.233482403212 0.225257974068 0.0188623096268 -0.107729981831 -0.177108999572 0.192905835151 -0.149819471408 0.0383549037465 0.0
+PC.607 0.0949631911323 -0.420974802495 0.154869454869 -0.0898427509281 -0.152618194488 0.0334232691501 -0.0251224777303 -0.0508988536409 0.0
+PC.634 0.359915158638 0.113822595435 -0.0662203444138 0.0297579972788 0.0572254078183 0.193133506163 0.145026331031 -0.149658611738 0.0
+PC.635 0.271001135391 -0.0185951319063 0.0864841926349 0.118064245315 0.198808358437 0.0211723599535 -0.191024027565 0.155646592377 0.0
+PC.593 -0.204636326241 -0.139361150932 -0.291513819623 -0.181566786821 0.159580132715 0.0246412130162 0.0866252404441 0.0996221476871 0.0
+PC.636 0.258465461183 0.173999546883 -0.0382875792552 -0.19447750562 -0.0831176020844 -0.262430333201 -0.0231636392235 -0.0184794039581 0.0
+PC.481 -0.0261407664325 -0.0111459676533 -0.147660603015 0.29087660853 -0.203945472801 -0.0619712384757 0.101641328709 0.105690998719 0.0
+PC.354 -0.285007552283 -0.0192549888483 -0.0623263375385 0.138126799852 0.104798602423 -0.0951720730628 -0.129636097542 -0.220687170372 0.0
+PC.356 -0.235077898175 0.0962519254489 0.345792726714 -0.00320862577619 0.0963777675519 -0.0457025386953 0.185472813286 0.0404093971793 0.0
+
+Biplot 0 0
+
+Site constraints 0 0

diff -r 000000000000 -r c11972e98d44 test-data/beta_diversity_through_plots/weighted_unifrac_dm.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_diversity_through_plots/weighted_unifrac_dm.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,10 @@
+ PC.355 PC.607 PC.634 PC.635 PC.593 PC.636 PC.481 PC.354 PC.356
+PC.355 0.0 0.324959266311 0.360463247619 0.301005982286 0.322882191481 0.367507936661 0.192866592582 0.237877518605 0.186403568707
+PC.607 0.324959266311 0.0 0.356951809843 0.221100536913 0.220838053691 0.367668532106 0.318716145536 0.396216241611 0.322076019239
+PC.634 0.360463247619 0.356951809843 0.0 0.240434181208 0.340061936913 0.207390851351 0.433075579909 0.510311668456 0.443208
+PC.635 0.301005982286 0.221100536913 0.240434181208 0.0 0.262879798658 0.275683407854 0.341452795348 0.411631543624 0.332995003579
+PC.593 0.322882191481 0.220838053691 0.340061936913 0.262879798658 0.0 0.316693638219 0.329334425393 0.395430805369 0.332624051454
+PC.636 0.367507936661 0.367668532106 0.207390851351 0.275683407854 0.316693638219 0.0 0.463169006849 0.530075154635 0.453169793694
+PC.481 0.192866592582 0.318716145536 0.433075579909 0.341452795348 0.329334425393 0.463169006849 0.0 0.168675520364 0.154091373516
+PC.354 0.237877518605 0.396216241611 0.510311668456 0.411631543624 0.395430805369 0.530075154635 0.168675520364 0.0 0.144798193736
+PC.356 0.186403568707 0.322076019239 0.443208 0.332995003579 0.332624051454 0.453169793694 0.154091373516 0.144798193736 0.0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/beta_diversity_through_plots/weighted_unifrac_pc.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_diversity_through_plots/weighted_unifrac_pc.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,22 @@
+Eigvals 9
+0.275632711048 0.0786886203713 0.0369532412336 0.0202873626005 0.0164214097718 0.0095529853755 0.00849733083443 0.0061010684167 0.0
+
+Proportion explained 9
+0.609625169162 0.174037991799 0.0817305966788 0.0448701709248 0.03631972661 0.0211286254937 0.0187938025486 0.0134939167832 0.0
+
+Species 0 0
+
+Site 9 9
+PC.355 -0.0884382226118 0.0974433877156 0.0141716969323 -0.0429717794866 -0.0614214470091 0.0454199392138 -0.0406570529076 -0.00439855709975 -0.0
+PC.607 0.0441929866994 -0.177254204339 -0.0524304712536 -0.0330076636585 -0.0546345821619 -0.0375978449419 -0.00834773861205 -0.0100272137195 -0.0
+PC.634 0.230087623733 0.0994209790973 -0.054816384248 0.0824577331281 -0.00869951929392 -0.0237567185329 -0.0255755782756 0.00926697365382 -0.0
+PC.635 0.114676368238 -0.0358646672493 -0.101513337225 -0.0274258689172 0.0618208970452 0.0490712037473 0.0117345304975 -0.00693612709856 -0.0
+PC.593 0.0667608134107 -0.133030890722 0.118738427104 0.0482906497896 0.0210996607504 0.0280044425392 -0.0172146599483 0.00665427864743 -0.0
+PC.636 0.251356816346 0.0844324162397 0.0796528445384 -0.058404756433 0.00424378531439 -0.0225573585917 0.0363606675627 -0.0108489168405 -0.0
+PC.481 -0.177236071394 0.0106671445069 -0.0126178848453 0.0507373988574 -0.0439794556539 0.0167250475345 0.0643606415736 0.00686733734311 -0.0
+PC.354 -0.261322740881 0.0369837477343 0.00951649282848 0.0155479065862 0.0453727490488 -0.0285802718687 -0.0124126338063 -0.0481739587353 -0.0
+PC.356 -0.180077573541 0.017202087016 -0.000701383830913 -0.0352236198661 0.03619791196 -0.0267284390995 -0.00824817608379 0.0575961838492 -0.0
+
+Biplot 0 0
+
+Site constraints 0 0

diff -r 000000000000 -r c11972e98d44 test-data/compare_categories/dbrda_plot.pdf

Binary file test-data/compare_categories/dbrda_plot.pdf has changed

diff -r 000000000000 -r c11972e98d44 test-data/compare_categories/map.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/compare_categories/map.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/compare_categories/unweighted_unifrac_dm.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/compare_categories/unweighted_unifrac_dm.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,10 @@
+ PC.354 PC.355 PC.356 PC.481 PC.593 PC.607 PC.634 PC.635 PC.636
+PC.354 0.0 0.595483768391 0.618074717633 0.582763100909 0.566949022108 0.714717232268 0.772001731764 0.690237118413 0.740681707488
+PC.355 0.595483768391 0.0 0.581427669668 0.613726772383 0.65945132763 0.745176523638 0.733836123821 0.720305073505 0.680785600439
+PC.356 0.618074717633 0.581427669668 0.0 0.672149021573 0.699416863323 0.71405573754 0.759178215168 0.689701276341 0.725100672826
+PC.481 0.582763100909 0.613726772383 0.672149021573 0.0 0.64756120797 0.666018240373 0.66532968784 0.650464714994 0.632524644216
+PC.593 0.566949022108 0.65945132763 0.699416863323 0.64756120797 0.0 0.703720200713 0.748240937349 0.73416971958 0.727154987937
+PC.607 0.714717232268 0.745176523638 0.71405573754 0.666018240373 0.703720200713 0.0 0.707316869557 0.636288883818 0.699880573956
+PC.634 0.772001731764 0.733836123821 0.759178215168 0.66532968784 0.748240937349 0.707316869557 0.0 0.565875193399 0.560605525642
+PC.635 0.690237118413 0.720305073505 0.689701276341 0.650464714994 0.73416971958 0.636288883818 0.565875193399 0.0 0.575788039321
+PC.636 0.740681707488 0.680785600439 0.725100672826 0.632524644216 0.727154987937 0.699880573956 0.560605525642 0.575788039321 0.0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/core_diversity_analyses/alpha_diversity_params.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/core_diversity_analyses/alpha_diversity_params.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,1 @@
+alpha_diversity:metrics chao1
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/core_diversity_analyses/map.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/core_diversity_analyses/map.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,10 @@
+#SampleID BarcodeSequence LinkerPrimerSequence SampleType year month day subject days_since_epoch Description
+f1 ACACTGTTCATG GTGCCAGCMGCCGCGGTAA feces 2008 10 22 1 14174 fecal1
+f2 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 14175 fecal2
+f3 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 14175 identical sequences to fecal2
+f4 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 14175 all sequences identical, map to GG 295053 at 97 percent id
+p1 AACGCACGCTAG GTGCCAGCMGCCGCGGTAA L_palm 2008 10 21 1 14173 palm1, contains one randomly generated sequence
+p2 ACACTGTTCATG GTGCCAGCMGCCGCGGTAA L_palm 2008 10 22 1 14174 palm2
+t1 AGTGAGAGAAGC GTGCCAGCMGCCGCGGTAA Tongue 2008 10 21 1 14173 tongue1, contains one randomly generated sequence
+t2 ATACTATTGCGC GTGCCAGCMGCCGCGGTAA Tongue 2008 10 22 1 14174 tongue2
+not16S.1 ATACTATTGCGC GTGCCAGCMGCCGCGGTAA Other 2008 10 22 1 14174 randomly generated sequence plus some variants, these should not map to 16S
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/core_diversity_analyses/otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/core_diversity_analyses/otu_table.biom Thu May 18 09:38:55 2017 -0400

[

@@ -0,0 +1,1 @@
+{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","type": "OTU table","generated_by": "QIIME 1.6.0-dev","date": "2013-02-09T09:30:11.550590","matrix_type": "sparse","matrix_element_type": "int","shape": [14, 9],"data": [[0,0,20],[0,1,18],[0,2,18],[0,3,22],[0,4,4],[1,4,1],[2,0,1],[2,4,1],[2,5,1],[3,6,1],[4,4,1],[5,7,20],[6,4,1],[7,4,1],[7,5,1],[8,4,1],[8,6,2],[8,8,3],[9,7,2],[10,5,1],[11,4,9],[11,5,20],[11,6,1],[11,8,4],[12,4,3],[12,6,19],[12,8,15],[13,0,1],[13,1,4],[13,2,4]],"rows": [{"id": "295053", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "42684", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria"]}},{"id": "None11", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None10", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None7", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None6", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None5", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "None4", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None3", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "None2", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "None1", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "879972", "metadata": {"taxonomy": ["k__Bacteria"]}},{"id": "None9", "metadata": {"taxonomy": ["Unclassified"]}},{"id": "None8", "metadata": {"taxonomy": ["k__Bacteria"]}}],"columns": [{"id": "f2", "metadata": null},{"id": "f1", "metadata": null},{"id": "f3", "metadata": null},{"id": "f4", "metadata": null},{"id": "p2", "metadata": null},{"id": "p1", "metadata": null},{"id": "t1", "metadata": null},{"id": "not16S.1", "metadata": null},{"id": "t2", "metadata": null}]}
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/core_diversity_analyses/rep_set.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/core_diversity_analyses/rep_set.tre Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,1 @@
+(None8:0.09606,((879972:0.05039,None3:0.00778)0.980:0.15948,((None11:0.07161,None4:0.06965)0.917:0.09643,(295053:0.06096,42684:0.15599)0.910:0.08898)0.899:0.09227)0.958:0.13976,(None7:0.10435,(None5:0.02626,None9:0.00014)1.000:0.25335)0.753:0.0465);
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/core_diversity_analyses/unweighted_unifrac_pc.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/core_diversity_analyses/unweighted_unifrac_pc.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,22 @@
+Eigvals 9
+1.06459336938 0.712030549144 0.29204442174 0.123841952918 0.0522627901636 0.0 0.0 0.0 0.0
+
+Proportion explained 9
+0.474254336565 0.317194889063 0.130099752134 0.0551690297058 0.0232819925324 0.0 0.0 0.0 0.0
+
+Species 0 0
+
+Site 9 9
+f2 -0.337382342185 0.0633507739971 0.167823623088 -0.0168909331792 0.112504055932 -0.0 0.0 0.0 0.0
+f1 -0.388873119352 0.0330785700332 -0.116515161486 0.000459982541288 0.0441156899615 -0.0 0.0 0.0 0.0
+f3 -0.388873119352 0.0330785700332 -0.116515161486 0.000459982541288 0.0441156899615 -0.0 -0.0 -0.0 0.0
+f4 -0.348412412671 0.0405169880579 -0.120000951389 0.0252062051453 -0.176886563099 -0.0 0.0 0.0 0.0
+p2 0.223595587648 0.168007799744 0.167052221863 -0.284063878547 -0.0395487094095 -0.0 0.0 0.0 0.0
+p1 0.142050547664 0.139597941737 0.356649453816 0.195582667916 -0.0373813212204 -0.0 0.0 0.0 0.0
+t1 0.461678348296 0.151817473226 -0.182389286903 0.044129246334 0.0270364210481 -0.0 -0.0 0.0 0.0
+not16S.1 0.174538161657 -0.781265590053 0.026284549398 -0.00901251908582 -0.000991684222 -0.0 0.0 0.0 0.0
+t2 0.461678348296 0.151817473226 -0.182389286903 0.044129246334 0.0270364210481 -0.0 0.0 0.0 0.0
+
+Biplot 0 0
+
+Site constraints 0 0

diff -r 000000000000 -r c11972e98d44 test-data/count_seqs/in.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count_seqs/in.fasta Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,12 @@
+>FLP3FBN01ELBSX length=250 xy=1766_0111 region=1 run=R_2008_12_09_13_51_01_
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGG
+CCGTTTACCCTCTCAGGCCGGCTACGCATCATCGCCTTGGTGGGCCGTTACCTCACCAAC
+TAGCTAATGCGCCGCAGGTCCATCCATGTTCACGCCTTGATGGGCGCTTTAATATACTGA
+GCATGCGCTCTGTATACCTATCCGGTTTTAGCTACCGTTTCCAGCAGTTATCCCGGACAC
+ATGGGCTAGG
+>FLP3FBN01EG8AX length=276 xy=1719_1463 region=1 run=R_2008_12_09_13_51_01_
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGG
+GGGCCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACA
+ACCTAATGGAACGCATCCCCATCGATGACCGAAGTTCTTTAATAGTTCTACCATGCGGAA
+GAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGG
+TTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCA

diff -r 000000000000 -r c11972e98d44 test-data/count_seqs/in1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count_seqs/in1.fasta Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,18 @@
+>FLP3FBN01ELBSX length=250 xy=1766_0111 region=1 run=R_2008_12_09_13_51_01_
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGG
+CCGTTTACCCTCTCAGGCCGGCTACGCATCATCGCCTTGGTGGGCCGTTACCTCACCAAC
+TAGCTAATGCGCCGCAGGTCCATCCATGTTCACGCCTTGATGGGCGCTTTAATATACTGA
+GCATGCGCTCTGTATACCTATCCGGTTTTAGCTACCGTTTCCAGCAGTTATCCCGGACAC
+ATGGGCTAGG
+>FLP3FBN01EG8AX length=276 xy=1719_1463 region=1 run=R_2008_12_09_13_51_01_
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGG
+GGGCCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACA
+ACCTAATGGAACGCATCCCCATCGATGACCGAAGTTCTTTAATAGTTCTACCATGCGGAA
+GAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGG
+TTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCA
+>FLP3FBN01EEWKD length=244 xy=1692_3531 region=1 run=R_2008_12_09_13_51_01_
+AGCACGAGCCTACATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGG
+CCGATCAGTCTCTTAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCTTACCAAC
+TAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGA
+CATGCGTCTAGTGTTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCT
+TGGG

diff -r 000000000000 -r c11972e98d44 test-data/count_seqs/in2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count_seqs/in2.fasta Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,36 @@
+>FLP3FBN01ELBSX length=250 xy=1766_0111 region=1 run=R_2008_12_09_13_51_01_
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGG
+CCGTTTACCCTCTCAGGCCGGCTACGCATCATCGCCTTGGTGGGCCGTTACCTCACCAAC
+TAGCTAATGCGCCGCAGGTCCATCCATGTTCACGCCTTGATGGGCGCTTTAATATACTGA
+GCATGCGCTCTGTATACCTATCCGGTTTTAGCTACCGTTTCCAGCAGTTATCCCGGACAC
+ATGGGCTAGG
+>FLP3FBN01EG8AX length=276 xy=1719_1463 region=1 run=R_2008_12_09_13_51_01_
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGG
+GGGCCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACA
+ACCTAATGGAACGCATCCCCATCGATGACCGAAGTTCTTTAATAGTTCTACCATGCGGAA
+GAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGG
+TTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCA
+>FLP3FBN01EEWKD length=244 xy=1692_3531 region=1 run=R_2008_12_09_13_51_01_
+AGCACGAGCCTACATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGG
+CCGATCAGTCTCTTAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCTTACCAAC
+TAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGA
+CATGCGTCTAGTGTTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCT
+TGGG
+>FLP3FBN01DEHK3 length=252 xy=1278_0245 region=1 run=R_2008_12_09_13_51_01_
+ACCAGCGACTAGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGG
+CCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAAC
+TATCTAATCAGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGGTATTCCGGCGATGC
+CGCCAAAATCATTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGC
+AGGTTGCTCACG
+>FLP3FBN01DGFYQ length=269 xy=1300_1344 region=1 run=R_2008_12_09_13_51_01_
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGG
+CCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTAGGCCGTTACCCTGCCAAC
+TGGCTAATCAGACGCGGGTCCATCTCACACCGATTAATCTTTTTCCAACCAGAGCATGCG
+CCCCTGTTGGCTTATGCGGTATTAGCGGTCGTTTCCAACTGTTATCCCCCTGTGTGAGGC
+AGGTTACCCACGCGTTACTCACCCGTCCG
+>FLP3FBN01A55WZ length=272 xy=0363_0481 region=1 run=R_2008_12_09_13_51_01_
+ACGGTGAGTGTCCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGG
+GGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTAC
+TATCTAATGGAACGCATCCCCATCTTATACCGGTAAACCTTTAATCATGAGAAAATGCTC
+ACTCATGATACCATCTTGTATTAATCTCCCTTTCAGAAGGCTATCCAAGAGTATAAGGCA
+GGTTGGATACGCGTTACTCACCCGTGCGCCGG

diff -r 000000000000 -r c11972e98d44 test-data/filter_alignment/alignment.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_alignment/alignment.fasta Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,122 @@\n+>r0 PC.634_176 RC:1..246\n+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G-AT--G--GC--G--AC-C-GG-C-GC-A--C-------------GGG-TGAGT-A--AC-AC-G-T-A-TC---CAA--C-CT-G--C-C-GAT--AA-C------------------------------------------------------------------T-CG----GGG-AT-AG-CCT-------------------------T-T-C-----------------------GAA-A---GAA-AGA-TTAA-TA---CC-C--G-AT-A----------G--------------------T-A--T-A-G--T--A-----------------TT---TC-C-----------------------------------------------------------------------------------------------------------------------G-CA-T--------------------------------------------------------------------------------------------------------------------------------------G-G-T--T-T---------------C--A-C-T-A-T-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAA--G-A----------------------------------------------------------------------------------------------------------------------------------------ATT------------------------------------------------------------------------------------------------------------------------------------T---C-G--------------G----T-T---A-TC-G---AT---G-G-----G-GAT-GCG--T-TCC--A------TT--A--G-AT-A----G---TTGG-C-G-GG-G-T----AAC-GG-C-C-C-ACCA--A-GT-C-A--A-CG-A------------TGG-A-T------AG-GG-G-T-TCT-G-AG----A--GG-AA--G-GT-C-CC-CCAC-A-TTGGA--A-C-TG-A-GA-C-AC-G-G-TCCAA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------'..b'--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n'

diff -r 000000000000 -r c11972e98d44 test-data/filter_fasta/inseqs.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_fasta/inseqs.fasta Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,12 @@
+>Seq1 some comment
+ACCTTGG
+>s2 some other comment
+TTGG
+>S3
+AAGGCCGG
+>S5 some comment
+CGT
+>seq6 some other comment
+AA
+>S7
+T
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/filter_fasta/inseqs.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_fasta/inseqs.fastq Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,24 @@
+@Seq1 some comment
+ACCTTGG
++
+BBBBBBB
+@s2 some other comment
+TTGG
++
+BBBB
+@S3
+AAGGCCGG
++
+BBBBBBBB
+@S5 some comment
+CGT
++
+BBB
+@seq6 some other comment
+AA
++
+BB
+@S7
+T
++
+B
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/filter_fasta/map.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_fasta/map.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,2 @@
+S5
+S3
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/filter_fasta/otu_map.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_fasta/otu_map.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,2 @@
+0 Seq1 s2
+qiime_otu_1 S3

diff -r 000000000000 -r c11972e98d44 test-data/filter_fasta/otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_fasta/otu_table.biom Thu May 18 09:38:55 2017 -0400

[

@@ -0,0 +1,1 @@
+{"rows": [{"id": "0", "metadata": null}, {"id": "qiime_otu_1", "metadata": null}], "format": "Biological Observation Matrix 0.9.1-dev", "data": [[0, 0, 1.0], [0, 1, 1.0], [1, 2, 1.0]], "columns": [{"id": "Seq1", "metadata": null}, {"id": "s2", "metadata": null}, {"id": "S3", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2813", "matrix_type": "sparse", "shape": [2, 3], "format_url": "http://biom-format.org", "date": "2012-03-14T12:47:52.091830", "type": "OTU table", "id": null, "matrix_element_type": "int"}
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/filter_fasta/seqs_to_keep.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_fasta/seqs_to_keep.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,3 @@
+S7
+S3
+s99
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/filter_fasta/sl_inseqs.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_fasta/sl_inseqs.fasta Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,12 @@
+>Sample1_0 some comment
+ACCTTGG
+>Sample2_1 some other comment
+TTGG
+>Sample1_2
+AAGGCCGG
+>Sample3_3 some comment
+CGT
+>Sample2_4 some other comment
+AA
+>S7
+T

diff -r 000000000000 -r c11972e98d44 test-data/filter_otus_from_otu_table/chimera_filtered_otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_otus_from_otu_table/chimera_filtered_otu_table.biom Thu May 18 09:38:55 2017 -0400

[

b'@@ -0,0 +1,1 @@\n+{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by": "QIIME 1.9.1","date": "2017-05-15T17:21:30.352786","matrix_element_type": "float","shape": [416, 9],"type": "OTU table","matrix_type": "sparse","data": 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diff -r 000000000000 -r c11972e98d44 test-data/filter_otus_from_otu_table/chimera_picked_otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_otus_from_otu_table/chimera_picked_otu_table.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/filter_otus_from_otu_table/chimeric_otus.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_otus_from_otu_table/chimeric_otus.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,1 @@
+352

diff -r 000000000000 -r c11972e98d44 test-data/filter_otus_from_otu_table/filtered_otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_otus_from_otu_table/filtered_otu_table.biom Thu May 18 09:38:55 2017 -0400

[

@@ -0,0 +1,1 @@
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\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/filter_otus_from_otu_table/otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_otus_from_otu_table/otu_table.biom Thu May 18 09:38:55 2017 -0400

[

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"int"}\n\\ No newline at end of file\n'

diff -r 000000000000 -r c11972e98d44 test-data/filter_samples_from_otu_table/abundance_max.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples_from_otu_table/abundance_max.biom Thu May 18 09:38:55 2017 -0400

[

b'@@ -0,0 +1,1 @@\n+{"id": "No Table ID","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-04-20T10:38:52.535023","type": "OTU table","matrix_element_type": "float","shape": [421, 7],"data": 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"397", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "398", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "399", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes"]}},{"id": "400", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "401", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Bacilli\\"", "\\"Lactobacillales\\"", "Lactobacillaceae", "Lactobacillus"]}},{"id": "402", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "403", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\"", "Ruminococcus"]}},{"id": "404", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "405", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "406", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "407", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\"", "\\"Ruminococcaceae Incertae Sedis\\""]}},{"id": "408", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "409", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "410", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "411", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "412", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Lachnospiraceae\\""]}},{"id": "413", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "414", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "415", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "416", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "417", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "418", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\""]}},{"id": "419", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Lachnospiraceae\\""]}},{"id": "420", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}}],"columns": [{"id": "PC.354", "metadata": null},{"id": "PC.355", "metadata": null},{"id": "PC.481", "metadata": null},{"id": "PC.593", "metadata": null},{"id": "PC.607", "metadata": null},{"id": "PC.635", "metadata": null},{"id": "PC.636", "metadata": null}]}\n\\ No newline at end of file\n'

diff -r 000000000000 -r c11972e98d44 test-data/filter_samples_from_otu_table/abundance_min.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples_from_otu_table/abundance_min.biom Thu May 18 09:38:55 2017 -0400

[

b'@@ -0,0 +1,1 @@\n+{"id": "No Table ID","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-04-20T10:38:30.892686","type": "OTU table","matrix_element_type": "float","shape": [421, 2],"data": [[2,1,1.0],[5,0,2.0],[7,0,2.0],[7,1,1.0],[9,1,4.0],[10,1,1.0],[14,0,1.0],[14,1,1.0],[15,1,1.0],[16,1,5.0],[18,0,2.0],[18,1,1.0],[19,1,1.0],[29,0,1.0],[29,1,3.0],[31,1,2.0],[33,1,1.0],[34,1,1.0],[39,0,2.0],[40,0,5.0],[41,0,1.0],[42,0,1.0],[45,1,9.0],[46,0,2.0],[47,1,1.0],[48,1,1.0],[51,0,1.0],[52,1,13.0],[55,0,2.0],[57,0,1.0],[62,1,2.0],[67,0,2.0],[67,1,2.0],[69,1,1.0],[73,0,1.0],[73,1,2.0],[74,0,10.0],[75,0,1.0],[76,0,1.0],[80,1,1.0],[82,0,1.0],[82,1,1.0],[84,0,1.0],[87,1,1.0],[88,0,2.0],[91,0,1.0],[92,1,3.0],[95,0,2.0],[100,0,1.0],[102,1,2.0],[104,1,5.0],[105,0,1.0],[106,1,1.0],[108,0,1.0],[112,1,5.0],[115,1,1.0],[116,0,1.0],[122,0,3.0],[123,1,1.0],[125,0,1.0],[130,1,1.0],[131,1,1.0],[133,1,1.0],[135,0,1.0],[142,0,1.0],[144,0,1.0],[145,0,7.0],[153,0,1.0],[154,0,1.0],[158,1,1.0],[159,1,1.0],[161,1,1.0],[167,0,2.0],[169,1,1.0],[170,1,1.0],[172,0,10.0],[175,0,1.0],[178,0,1.0],[180,0,2.0],[185,0,1.0],[187,0,2.0],[188,0,1.0],[191,0,1.0],[192,0,1.0],[198,0,1.0],[208,0,2.0],[211,0,1.0],[214,1,1.0],[218,1,21.0],[224,0,2.0],[243,1,1.0],[245,0,1.0],[247,0,1.0],[248,1,1.0],[254,1,1.0],[260,1,1.0],[262,0,3.0],[263,0,1.0],[271,0,1.0],[275,0,1.0],[278,0,5.0],[281,0,1.0],[284,0,1.0],[287,1,5.0],[288,1,1.0],[292,1,1.0],[293,1,2.0],[295,1,1.0],[297,0,2.0],[298,1,1.0],[302,1,1.0],[303,0,1.0],[308,1,1.0],[310,0,1.0],[312,0,1.0],[315,0,2.0],[320,1,1.0],[325,0,1.0],[326,1,1.0],[331,0,1.0],[342,1,3.0],[344,1,2.0],[345,1,1.0],[346,1,2.0],[349,1,1.0],[352,1,2.0],[354,0,1.0],[355,0,1.0],[357,0,1.0],[358,1,1.0],[364,1,4.0],[365,0,1.0],[366,0,1.0],[367,0,1.0],[368,0,1.0],[377,1,3.0],[378,1,1.0],[379,0,1.0],[382,0,1.0],[383,1,1.0],[388,1,2.0],[389,0,1.0],[392,0,1.0],[393,1,1.0],[398,0,3.0],[401,0,14.0],[402,0,1.0],[404,0,1.0],[409,1,2.0],[413,0,1.0],[414,0,1.0],[419,0,1.0]],"rows": [{"id": "0", "metadata": {"taxonomy": ["Root", "Bacteria", "Actinobacteria", "Actinobacteria", "Coriobacteridae", "Coriobacteriales", "Coriobacterineae", "Coriobacteriaceae"]}},{"id": "1", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "2", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "3", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "4", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}},{"id": "5", "metadata": {"taxonomy": ["Root"]}},{"id": "6", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "7", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}},{"id": "8", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "9", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}},{"id": "10", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}},{"id": "11", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Bacilli\\"", "Bacillales", "\\"Staphylococcaceae\\"", "Staphylococcus"]}},{"id": "12", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}},{"id": "13", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "14", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}},{"id": "15", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "16", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes", "Bacteroidetes", "Bacteroidales", "Rikenellaceae", "Alistipes"]}},{"id": "17", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}},{"id": "18", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes", "Bacteroidetes", "Bacteroidales", "Rikenellaceae", "Alistipes"]}},{"id": "19", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes", "Bacteroidetes", "Bacteroidales"]}},{"id": "20", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes"]}},{"id": "'..b'", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "388", "metadata": {"taxonomy": ["Root", "Bacteria", "Proteobacteria", "Deltaproteobacteria"]}},{"id": "389", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "390", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Bacilli\\"", "\\"Lactobacillales\\"", "Streptococcaceae", "Streptococcus"]}},{"id": "391", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Lachnospiraceae\\""]}},{"id": "392", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "393", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "394", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "395", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "396", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "397", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "398", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "399", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes"]}},{"id": "400", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "401", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Bacilli\\"", "\\"Lactobacillales\\"", "Lactobacillaceae", "Lactobacillus"]}},{"id": "402", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "403", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\"", "Ruminococcus"]}},{"id": "404", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "405", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "406", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "407", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\"", "\\"Ruminococcaceae Incertae Sedis\\""]}},{"id": "408", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "409", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "410", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "411", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "412", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Lachnospiraceae\\""]}},{"id": "413", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "414", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "415", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "416", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "417", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "418", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\""]}},{"id": "419", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Lachnospiraceae\\""]}},{"id": "420", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}}],"columns": [{"id": "PC.356", "metadata": null},{"id": "PC.634", "metadata": null}]}\n\\ No newline at end of file\n'

diff -r 000000000000 -r c11972e98d44 test-data/filter_samples_from_otu_table/id_negative.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples_from_otu_table/id_negative.biom Thu May 18 09:38:55 2017 -0400

[

b'@@ -0,0 +1,1 @@\n+{"id": "No Table ID","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-04-20T10:45:54.864405","type": "OTU table","matrix_element_type": "float","shape": [421, 7],"data": [[1,2,1.0],[1,6,1.0],[2,3,2.0],[2,4,2.0],[2,5,1.0],[2,6,5.0],[5,1,2.0],[5,6,1.0],[6,6,1.0],[7,0,1.0],[7,1,2.0],[7,3,9.0],[7,4,1.0],[7,5,1.0],[7,6,1.0],[9,2,1.0],[9,5,4.0],[9,6,8.0],[10,0,2.0],[10,2,2.0],[10,3,1.0],[10,4,6.0],[10,5,1.0],[10,6,2.0],[12,0,1.0],[12,4,3.0],[12,6,1.0],[13,2,1.0],[13,6,1.0],[14,1,1.0],[14,5,1.0],[14,6,1.0],[15,5,1.0],[15,6,3.0],[16,5,5.0],[17,4,5.0],[18,0,2.0],[18,1,2.0],[18,2,4.0],[18,4,5.0],[18,5,1.0],[18,6,5.0],[19,5,1.0],[19,6,1.0],[20,6,1.0],[21,6,2.0],[23,6,1.0],[25,6,1.0],[27,4,1.0],[28,0,1.0],[29,0,1.0],[29,1,1.0],[29,2,1.0],[29,3,1.0],[29,5,3.0],[30,3,9.0],[30,4,1.0],[31,5,2.0],[31,6,1.0],[32,4,2.0],[33,5,1.0],[34,5,1.0],[35,4,1.0],[38,6,1.0],[39,1,2.0],[39,2,1.0],[40,1,5.0],[40,3,1.0],[41,1,1.0],[42,0,1.0],[42,1,1.0],[43,3,1.0],[44,3,2.0],[45,4,5.0],[45,5,9.0],[45,6,5.0],[46,0,1.0],[46,1,2.0],[47,5,1.0],[48,5,1.0],[49,3,3.0],[51,1,1.0],[52,5,13.0],[53,4,2.0],[54,0,1.0],[55,1,2.0],[55,6,1.0],[56,6,1.0],[57,1,1.0],[58,3,1.0],[60,3,2.0],[60,6,6.0],[61,0,2.0],[61,2,1.0],[61,6,1.0],[62,5,2.0],[63,0,1.0],[64,0,9.0],[64,2,3.0],[64,6,2.0],[65,0,2.0],[65,4,1.0],[66,0,1.0],[67,0,1.0],[67,1,2.0],[67,3,3.0],[67,5,2.0],[68,4,1.0],[69,4,1.0],[69,5,1.0],[70,4,1.0],[71,2,1.0],[71,6,1.0],[72,6,1.0],[73,0,16.0],[73,1,1.0],[73,3,1.0],[73,5,2.0],[74,0,1.0],[74,1,10.0],[74,2,2.0],[74,3,24.0],[74,6,1.0],[75,1,1.0],[75,4,2.0],[75,6,1.0],[76,1,1.0],[76,3,1.0],[77,0,1.0],[78,2,1.0],[79,4,7.0],[80,2,1.0],[80,5,1.0],[80,6,2.0],[81,2,2.0],[82,0,1.0],[82,1,1.0],[82,2,2.0],[82,5,1.0],[82,6,1.0],[83,0,1.0],[84,1,1.0],[85,3,1.0],[87,5,1.0],[88,0,4.0],[88,1,2.0],[88,3,1.0],[88,4,2.0],[88,6,1.0],[89,2,1.0],[90,3,1.0],[91,1,1.0],[92,2,1.0],[92,5,3.0],[92,6,1.0],[93,6,1.0],[94,6,1.0],[95,1,2.0],[96,6,2.0],[97,4,1.0],[98,4,1.0],[99,6,1.0],[100,0,1.0],[100,1,1.0],[101,2,1.0],[102,5,2.0],[102,6,1.0],[103,0,1.0],[104,5,5.0],[105,1,1.0],[106,5,1.0],[107,2,2.0],[108,1,1.0],[109,4,6.0],[109,6,3.0],[110,4,1.0],[110,6,1.0],[111,2,5.0],[111,3,17.0],[111,4,14.0],[112,4,3.0],[112,5,5.0],[112,6,2.0],[113,0,4.0],[113,2,1.0],[113,4,2.0],[115,5,1.0],[116,0,3.0],[116,1,1.0],[117,0,1.0],[117,3,1.0],[118,0,1.0],[118,2,5.0],[118,4,1.0],[119,0,1.0],[119,2,4.0],[119,6,1.0],[120,0,1.0],[121,0,1.0],[121,2,1.0],[121,3,1.0],[122,1,3.0],[122,4,4.0],[123,5,1.0],[125,0,1.0],[125,1,1.0],[125,2,3.0],[126,0,2.0],[127,0,1.0],[128,3,1.0],[129,2,1.0],[130,5,1.0],[131,5,1.0],[132,4,1.0],[133,5,1.0],[134,2,1.0],[135,1,1.0],[136,4,1.0],[138,2,2.0],[139,0,1.0],[140,4,1.0],[142,1,1.0],[143,2,2.0],[143,3,4.0],[144,0,2.0],[144,1,1.0],[145,0,4.0],[145,1,7.0],[145,3,1.0],[146,4,4.0],[149,6,1.0],[150,2,1.0],[153,1,1.0],[153,2,1.0],[154,0,3.0],[154,1,1.0],[154,3,1.0],[155,6,1.0],[156,2,1.0],[157,6,1.0],[158,5,1.0],[159,5,1.0],[160,0,1.0],[160,2,3.0],[160,6,1.0],[161,5,1.0],[162,3,9.0],[163,4,1.0],[164,2,1.0],[165,2,1.0],[166,3,1.0],[167,0,4.0],[167,1,2.0],[167,2,6.0],[168,4,1.0],[169,5,1.0],[170,5,1.0],[171,4,2.0],[171,6,1.0],[172,0,1.0],[172,1,10.0],[173,3,1.0],[174,3,1.0],[175,1,1.0],[176,6,1.0],[177,2,1.0],[178,1,1.0],[179,0,1.0],[180,1,2.0],[180,2,1.0],[182,2,4.0],[183,3,10.0],[184,3,1.0],[185,1,1.0],[186,2,1.0],[186,6,1.0],[187,1,2.0],[188,1,1.0],[189,2,1.0],[190,2,1.0],[191,1,1.0],[192,1,1.0],[193,4,1.0],[194,6,1.0],[195,4,1.0],[196,4,1.0],[197,6,1.0],[198,1,1.0],[199,6,1.0],[200,4,1.0],[201,3,1.0],[202,0,1.0],[203,4,1.0],[205,4,1.0],[206,4,2.0],[207,2,1.0],[208,1,2.0],[209,2,1.0],[210,4,1.0],[211,1,1.0],[212,2,1.0],[213,6,1.0],[214,4,7.0],[214,5,1.0],[214,6,2.0],[215,6,2.0],[217,4,1.0],[217,6,1.0],[218,0,18.0],[218,2,1.0],[218,5,21.0],[218,6,4.0],[219,3,1.0],[220,3,1.0],[221,6,1.0],[222,3,1.0],[223,2,1.0],[223,4,2.0],[223,6,1.0],[224,1,2.0],[226,4,1.0],[227,6,1.0],[228,'..b'oteobacteria"]}},{"id": "389", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "390", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Bacilli\\"", "\\"Lactobacillales\\"", "Streptococcaceae", "Streptococcus"]}},{"id": "391", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Lachnospiraceae\\""]}},{"id": "392", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "393", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "394", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "395", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "396", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "397", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "398", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "399", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes"]}},{"id": "400", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "401", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Bacilli\\"", "\\"Lactobacillales\\"", "Lactobacillaceae", "Lactobacillus"]}},{"id": "402", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "403", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\"", "Ruminococcus"]}},{"id": "404", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "405", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "406", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "407", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\"", "\\"Ruminococcaceae Incertae Sedis\\""]}},{"id": "408", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "409", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "410", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "411", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "412", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Lachnospiraceae\\""]}},{"id": "413", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "414", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "415", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "416", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "417", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "418", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\""]}},{"id": "419", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Lachnospiraceae\\""]}},{"id": "420", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}}],"columns": [{"id": "PC.355", "metadata": null},{"id": "PC.356", "metadata": null},{"id": "PC.481", "metadata": null},{"id": "PC.593", "metadata": null},{"id": "PC.607", "metadata": null},{"id": "PC.634", "metadata": null},{"id": "PC.635", "metadata": null}]}\n\\ No newline at end of file\n'

diff -r 000000000000 -r c11972e98d44 test-data/filter_samples_from_otu_table/id_positive.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples_from_otu_table/id_positive.biom Thu May 18 09:38:55 2017 -0400

[

b'@@ -0,0 +1,1 @@\n+{"id": "No Table ID","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-04-20T10:45:39.580517","type": "OTU table","matrix_element_type": "float","shape": [421, 2],"data": [[0,1,1.0],[2,1,1.0],[3,1,1.0],[4,1,1.0],[7,1,3.0],[8,1,1.0],[9,1,29.0],[10,0,1.0],[10,1,4.0],[11,1,2.0],[12,1,1.0],[19,1,1.0],[21,1,3.0],[22,1,1.0],[24,1,1.0],[25,1,1.0],[26,1,5.0],[29,1,4.0],[36,1,1.0],[37,1,1.0],[40,0,6.0],[42,0,1.0],[45,1,3.0],[50,1,1.0],[59,1,1.0],[64,0,5.0],[68,0,1.0],[74,0,2.0],[74,1,1.0],[77,1,2.0],[80,1,19.0],[82,1,1.0],[86,1,1.0],[88,1,1.0],[93,1,1.0],[96,1,2.0],[100,1,1.0],[111,0,1.0],[112,1,5.0],[114,0,1.0],[116,0,1.0],[118,0,2.0],[120,1,1.0],[121,1,3.0],[122,0,1.0],[123,1,1.0],[124,0,1.0],[137,0,1.0],[141,0,1.0],[142,0,1.0],[143,0,1.0],[145,0,2.0],[146,0,1.0],[147,1,1.0],[148,0,1.0],[151,0,1.0],[152,1,1.0],[153,0,1.0],[162,0,16.0],[166,0,1.0],[167,0,1.0],[172,0,29.0],[174,0,5.0],[176,1,1.0],[178,0,1.0],[180,0,2.0],[181,0,1.0],[183,0,1.0],[201,0,1.0],[204,1,1.0],[208,0,1.0],[214,1,2.0],[216,1,1.0],[218,0,2.0],[218,1,4.0],[220,0,1.0],[223,1,1.0],[225,0,1.0],[226,1,1.0],[232,0,1.0],[234,0,1.0],[237,0,1.0],[241,0,1.0],[249,0,1.0],[250,1,1.0],[251,0,1.0],[257,0,1.0],[258,1,1.0],[259,0,1.0],[260,1,2.0],[262,0,1.0],[265,1,1.0],[266,0,2.0],[270,0,1.0],[271,0,1.0],[272,1,1.0],[278,0,9.0],[281,0,2.0],[287,1,3.0],[291,0,1.0],[303,0,1.0],[306,0,1.0],[314,0,1.0],[317,1,2.0],[319,1,1.0],[323,1,1.0],[327,1,1.0],[332,0,1.0],[341,1,1.0],[343,0,1.0],[344,1,1.0],[349,1,1.0],[351,0,1.0],[352,0,1.0],[352,1,3.0],[375,1,1.0],[376,0,1.0],[381,1,1.0],[388,1,1.0],[394,0,1.0],[396,1,1.0],[398,1,3.0],[401,0,14.0],[403,0,1.0],[412,1,1.0],[414,0,1.0],[417,0,1.0],[419,0,1.0]],"rows": [{"id": "0", "metadata": {"taxonomy": ["Root", "Bacteria", "Actinobacteria", "Actinobacteria", "Coriobacteridae", "Coriobacteriales", "Coriobacterineae", "Coriobacteriaceae"]}},{"id": "1", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "2", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "3", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "4", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}},{"id": "5", "metadata": {"taxonomy": ["Root"]}},{"id": "6", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "7", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}},{"id": "8", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "9", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}},{"id": "10", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}},{"id": "11", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Bacilli\\"", "Bacillales", "\\"Staphylococcaceae\\"", "Staphylococcus"]}},{"id": "12", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}},{"id": "13", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "14", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}},{"id": "15", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "16", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes", "Bacteroidetes", "Bacteroidales", "Rikenellaceae", "Alistipes"]}},{"id": "17", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}},{"id": "18", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes", "Bacteroidetes", "Bacteroidales", "Rikenellaceae", "Alistipes"]}},{"id": "19", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes", "Bacteroidetes", "Bacteroidales"]}},{"id": "20", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes"]}},{"id": "21", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}},{"id": "22", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Bacilli\\"", "Bacillales", "\\"Staphylococcaceae\\"", "Staphylococcus"]}},{"id": "23", "metadata": {"taxonomy": ["Root", "Bacteria", "B'..b'", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "388", "metadata": {"taxonomy": ["Root", "Bacteria", "Proteobacteria", "Deltaproteobacteria"]}},{"id": "389", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "390", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Bacilli\\"", "\\"Lactobacillales\\"", "Streptococcaceae", "Streptococcus"]}},{"id": "391", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Lachnospiraceae\\""]}},{"id": "392", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "393", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "394", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "395", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "396", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "397", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "398", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "399", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes"]}},{"id": "400", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "401", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Bacilli\\"", "\\"Lactobacillales\\"", "Lactobacillaceae", "Lactobacillus"]}},{"id": "402", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "403", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\"", "Ruminococcus"]}},{"id": "404", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "405", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "406", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "407", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\"", "\\"Ruminococcaceae Incertae Sedis\\""]}},{"id": "408", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "409", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "410", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "411", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "412", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Lachnospiraceae\\""]}},{"id": "413", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "414", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "415", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "416", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "417", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "418", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\""]}},{"id": "419", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Lachnospiraceae\\""]}},{"id": "420", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}}],"columns": [{"id": "PC.354", "metadata": null},{"id": "PC.636", "metadata": null}]}\n\\ No newline at end of file\n'

diff -r 000000000000 -r c11972e98d44 test-data/filter_samples_from_otu_table/ids.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples_from_otu_table/ids.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,4 @@
+#SampleID BarcodeSequence LinkerPrimerSequence Treatment DOB Description
+#Example mapping file for the QIIME analysis package. These 9 samples are from a study of the effects of exercise and diet on mouse cardiac physiology (Crawford, et al, PNAS, 2009).
+PC.354 AGCACGAGCCTA YATGCTGCCTCCCGTAGGAGT Control 20061218 Control_mouse__I.D._354
+PC.636 ACGGTGAGTGTC YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse__I.D._636

diff -r 000000000000 -r c11972e98d44 test-data/filter_samples_from_otu_table/map.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples_from_otu_table/map.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,11 @@
+#SampleID BarcodeSequence LinkerPrimerSequence Treatment DOB Description
+#Example mapping file for the QIIME analysis package. These 9 samples are from a study of the effects of exercise and diet on mouse cardiac physiology (Crawford, et al, PNAS, 2009).
+PC.354 AGCACGAGCCTA YATGCTGCCTCCCGTAGGAGT Control 20061218 Control_mouse__I.D._354
+PC.355 AACTCGTCGATG YATGCTGCCTCCCGTAGGAGT Control 20061218 Control_mouse__I.D._355
+PC.356 ACAGACCACTCA YATGCTGCCTCCCGTAGGAGT Control 20061126 Control_mouse__I.D._356
+PC.481 ACCAGCGACTAG YATGCTGCCTCCCGTAGGAGT Control 20070314 Control_mouse__I.D._481
+PC.593 AGCAGCACTTGT YATGCTGCCTCCCGTAGGAGT Control 20071210 Control_mouse__I.D._593
+PC.607 AACTGTGCGTAC YATGCTGCCTCCCGTAGGAGT Fast 20071112 Fasting_mouse__I.D._607
+PC.634 ACAGAGTCGGCT YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse__I.D._634
+PC.635 ACCGCAGAGTCA YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse__I.D._635
+PC.636 ACGGTGAGTGTC YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse__I.D._636

diff -r 000000000000 -r c11972e98d44 test-data/filter_samples_from_otu_table/metadata_negative.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples_from_otu_table/metadata_negative.biom Thu May 18 09:38:55 2017 -0400

[

b'@@ -0,0 +1,1 @@\n+{"id": "No Table ID","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-04-20T10:45:16.902666","type": "OTU table","matrix_element_type": "float","shape": [421, 4],"data": [[0,3,1.0],[1,2,1.0],[2,0,2.0],[2,1,1.0],[2,2,5.0],[2,3,1.0],[3,3,1.0],[4,3,1.0],[5,2,1.0],[6,2,1.0],[7,0,1.0],[7,1,1.0],[7,2,1.0],[7,3,3.0],[8,3,1.0],[9,1,4.0],[9,2,8.0],[9,3,29.0],[10,0,6.0],[10,1,1.0],[10,2,2.0],[10,3,4.0],[11,3,2.0],[12,0,3.0],[12,2,1.0],[12,3,1.0],[13,2,1.0],[14,1,1.0],[14,2,1.0],[15,1,1.0],[15,2,3.0],[16,1,5.0],[17,0,5.0],[18,0,5.0],[18,1,1.0],[18,2,5.0],[19,1,1.0],[19,2,1.0],[19,3,1.0],[20,2,1.0],[21,2,2.0],[21,3,3.0],[22,3,1.0],[23,2,1.0],[24,3,1.0],[25,2,1.0],[25,3,1.0],[26,3,5.0],[27,0,1.0],[29,1,3.0],[29,3,4.0],[30,0,1.0],[31,1,2.0],[31,2,1.0],[32,0,2.0],[33,1,1.0],[34,1,1.0],[35,0,1.0],[36,3,1.0],[37,3,1.0],[38,2,1.0],[45,0,5.0],[45,1,9.0],[45,2,5.0],[45,3,3.0],[47,1,1.0],[48,1,1.0],[50,3,1.0],[52,1,13.0],[53,0,2.0],[55,2,1.0],[56,2,1.0],[59,3,1.0],[60,2,6.0],[61,2,1.0],[62,1,2.0],[64,2,2.0],[65,0,1.0],[67,1,2.0],[68,0,1.0],[69,0,1.0],[69,1,1.0],[70,0,1.0],[71,2,1.0],[72,2,1.0],[73,1,2.0],[74,2,1.0],[74,3,1.0],[75,0,2.0],[75,2,1.0],[77,3,2.0],[79,0,7.0],[80,1,1.0],[80,2,2.0],[80,3,19.0],[82,1,1.0],[82,2,1.0],[82,3,1.0],[86,3,1.0],[87,1,1.0],[88,0,2.0],[88,2,1.0],[88,3,1.0],[92,1,3.0],[92,2,1.0],[93,2,1.0],[93,3,1.0],[94,2,1.0],[96,2,2.0],[96,3,2.0],[97,0,1.0],[98,0,1.0],[99,2,1.0],[100,3,1.0],[102,1,2.0],[102,2,1.0],[104,1,5.0],[106,1,1.0],[109,0,6.0],[109,2,3.0],[110,0,1.0],[110,2,1.0],[111,0,14.0],[112,0,3.0],[112,1,5.0],[112,2,2.0],[112,3,5.0],[113,0,2.0],[115,1,1.0],[118,0,1.0],[119,2,1.0],[120,3,1.0],[121,3,3.0],[122,0,4.0],[123,1,1.0],[123,3,1.0],[130,1,1.0],[131,1,1.0],[132,0,1.0],[133,1,1.0],[136,0,1.0],[140,0,1.0],[146,0,4.0],[147,3,1.0],[149,2,1.0],[152,3,1.0],[155,2,1.0],[157,2,1.0],[158,1,1.0],[159,1,1.0],[160,2,1.0],[161,1,1.0],[163,0,1.0],[168,0,1.0],[169,1,1.0],[170,1,1.0],[171,0,2.0],[171,2,1.0],[176,2,1.0],[176,3,1.0],[186,2,1.0],[193,0,1.0],[194,2,1.0],[195,0,1.0],[196,0,1.0],[197,2,1.0],[199,2,1.0],[200,0,1.0],[203,0,1.0],[204,3,1.0],[205,0,1.0],[206,0,2.0],[210,0,1.0],[213,2,1.0],[214,0,7.0],[214,1,1.0],[214,2,2.0],[214,3,2.0],[215,2,2.0],[216,3,1.0],[217,0,1.0],[217,2,1.0],[218,1,21.0],[218,2,4.0],[218,3,4.0],[221,2,1.0],[223,0,2.0],[223,2,1.0],[223,3,1.0],[226,0,1.0],[226,3,1.0],[227,2,1.0],[228,0,2.0],[230,2,1.0],[231,2,1.0],[233,2,1.0],[235,2,1.0],[242,0,1.0],[243,0,1.0],[243,1,1.0],[244,2,1.0],[248,1,1.0],[250,3,1.0],[254,1,1.0],[255,0,1.0],[256,0,1.0],[258,3,1.0],[259,0,1.0],[260,1,1.0],[260,2,5.0],[260,3,2.0],[261,2,1.0],[264,0,1.0],[265,3,1.0],[269,0,2.0],[272,3,1.0],[273,0,2.0],[274,0,1.0],[286,2,2.0],[287,1,5.0],[287,2,4.0],[287,3,3.0],[288,1,1.0],[292,1,1.0],[293,1,2.0],[295,1,1.0],[298,1,1.0],[301,0,1.0],[302,1,1.0],[306,2,1.0],[308,1,1.0],[309,2,1.0],[311,2,1.0],[316,0,1.0],[317,3,2.0],[318,0,1.0],[319,3,1.0],[320,1,1.0],[321,2,1.0],[323,3,1.0],[326,1,1.0],[327,3,1.0],[330,2,1.0],[333,0,1.0],[335,2,1.0],[338,2,1.0],[339,0,1.0],[340,0,2.0],[340,2,1.0],[341,3,1.0],[342,1,3.0],[342,2,6.0],[344,1,2.0],[344,2,3.0],[344,3,1.0],[345,1,1.0],[346,1,2.0],[347,0,1.0],[349,1,1.0],[349,3,1.0],[350,2,1.0],[352,1,2.0],[352,3,3.0],[353,0,1.0],[358,1,1.0],[361,0,1.0],[362,2,1.0],[364,1,4.0],[366,2,1.0],[368,2,1.0],[371,0,1.0],[373,0,1.0],[374,0,1.0],[375,3,1.0],[377,1,3.0],[378,1,1.0],[380,2,1.0],[381,3,1.0],[383,1,1.0],[384,2,1.0],[385,0,1.0],[386,0,1.0],[388,1,2.0],[388,3,1.0],[389,2,1.0],[390,0,1.0],[393,1,1.0],[395,0,1.0],[396,3,1.0],[397,0,1.0],[398,2,1.0],[398,3,3.0],[399,0,1.0],[400,0,1.0],[403,2,2.0],[406,0,1.0],[408,0,1.0],[409,1,2.0],[410,2,1.0],[411,0,1.0],[412,3,1.0],[413,2,1.0],[415,2,1.0],[418,2,1.0],[419,2,1.0]],"rows": 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{"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "395", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "396", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "397", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "398", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "399", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes"]}},{"id": "400", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "401", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Bacilli\\"", "\\"Lactobacillales\\"", "Lactobacillaceae", "Lactobacillus"]}},{"id": "402", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "403", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\"", "Ruminococcus"]}},{"id": "404", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "405", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "406", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "407", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\"", "\\"Ruminococcaceae Incertae Sedis\\""]}},{"id": "408", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "409", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "410", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "411", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "412", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Lachnospiraceae\\""]}},{"id": "413", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "414", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "415", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "416", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "417", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "418", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\""]}},{"id": "419", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Lachnospiraceae\\""]}},{"id": "420", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}}],"columns": [{"id": "PC.607", "metadata": null},{"id": "PC.634", "metadata": null},{"id": "PC.635", "metadata": null},{"id": "PC.636", "metadata": null}]}\n\\ No newline at end of file\n'

diff -r 000000000000 -r c11972e98d44 test-data/filter_samples_from_otu_table/metadata_positive.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples_from_otu_table/metadata_positive.biom Thu May 18 09:38:55 2017 -0400

[

b'@@ -0,0 +1,1 @@\n+{"id": "No Table ID","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-04-20T10:41:21.150841","type": "OTU table","matrix_element_type": "float","shape": [421, 5],"data": [[1,3,1.0],[2,4,2.0],[5,2,2.0],[7,1,1.0],[7,2,2.0],[7,4,9.0],[9,3,1.0],[10,0,1.0],[10,1,2.0],[10,3,2.0],[10,4,1.0],[12,1,1.0],[13,3,1.0],[14,2,1.0],[18,1,2.0],[18,2,2.0],[18,3,4.0],[28,1,1.0],[29,1,1.0],[29,2,1.0],[29,3,1.0],[29,4,1.0],[30,4,9.0],[39,2,2.0],[39,3,1.0],[40,0,6.0],[40,2,5.0],[40,4,1.0],[41,2,1.0],[42,0,1.0],[42,1,1.0],[42,2,1.0],[43,4,1.0],[44,4,2.0],[46,1,1.0],[46,2,2.0],[49,4,3.0],[51,2,1.0],[54,1,1.0],[55,2,2.0],[57,2,1.0],[58,4,1.0],[60,4,2.0],[61,1,2.0],[61,3,1.0],[63,1,1.0],[64,0,5.0],[64,1,9.0],[64,3,3.0],[65,1,2.0],[66,1,1.0],[67,1,1.0],[67,2,2.0],[67,4,3.0],[68,0,1.0],[71,3,1.0],[73,1,16.0],[73,2,1.0],[73,4,1.0],[74,0,2.0],[74,1,1.0],[74,2,10.0],[74,3,2.0],[74,4,24.0],[75,2,1.0],[76,2,1.0],[76,4,1.0],[77,1,1.0],[78,3,1.0],[80,3,1.0],[81,3,2.0],[82,1,1.0],[82,2,1.0],[82,3,2.0],[83,1,1.0],[84,2,1.0],[85,4,1.0],[88,1,4.0],[88,2,2.0],[88,4,1.0],[89,3,1.0],[90,4,1.0],[91,2,1.0],[92,3,1.0],[95,2,2.0],[100,1,1.0],[100,2,1.0],[101,3,1.0],[103,1,1.0],[105,2,1.0],[107,3,2.0],[108,2,1.0],[111,0,1.0],[111,3,5.0],[111,4,17.0],[113,1,4.0],[113,3,1.0],[114,0,1.0],[116,0,1.0],[116,1,3.0],[116,2,1.0],[117,1,1.0],[117,4,1.0],[118,0,2.0],[118,1,1.0],[118,3,5.0],[119,1,1.0],[119,3,4.0],[120,1,1.0],[121,1,1.0],[121,3,1.0],[121,4,1.0],[122,0,1.0],[122,2,3.0],[124,0,1.0],[125,1,1.0],[125,2,1.0],[125,3,3.0],[126,1,2.0],[127,1,1.0],[128,4,1.0],[129,3,1.0],[134,3,1.0],[135,2,1.0],[137,0,1.0],[138,3,2.0],[139,1,1.0],[141,0,1.0],[142,0,1.0],[142,2,1.0],[143,0,1.0],[143,3,2.0],[143,4,4.0],[144,1,2.0],[144,2,1.0],[145,0,2.0],[145,1,4.0],[145,2,7.0],[145,4,1.0],[146,0,1.0],[148,0,1.0],[150,3,1.0],[151,0,1.0],[153,0,1.0],[153,2,1.0],[153,3,1.0],[154,1,3.0],[154,2,1.0],[154,4,1.0],[156,3,1.0],[160,1,1.0],[160,3,3.0],[162,0,16.0],[162,4,9.0],[164,3,1.0],[165,3,1.0],[166,0,1.0],[166,4,1.0],[167,0,1.0],[167,1,4.0],[167,2,2.0],[167,3,6.0],[172,0,29.0],[172,1,1.0],[172,2,10.0],[173,4,1.0],[174,0,5.0],[174,4,1.0],[175,2,1.0],[177,3,1.0],[178,0,1.0],[178,2,1.0],[179,1,1.0],[180,0,2.0],[180,2,2.0],[180,3,1.0],[181,0,1.0],[182,3,4.0],[183,0,1.0],[183,4,10.0],[184,4,1.0],[185,2,1.0],[186,3,1.0],[187,2,2.0],[188,2,1.0],[189,3,1.0],[190,3,1.0],[191,2,1.0],[192,2,1.0],[198,2,1.0],[201,0,1.0],[201,4,1.0],[202,1,1.0],[207,3,1.0],[208,0,1.0],[208,2,2.0],[209,3,1.0],[211,2,1.0],[212,3,1.0],[218,0,2.0],[218,1,18.0],[218,3,1.0],[219,4,1.0],[220,0,1.0],[220,4,1.0],[222,4,1.0],[223,3,1.0],[224,2,2.0],[225,0,1.0],[229,3,1.0],[232,0,1.0],[233,3,4.0],[234,0,1.0],[236,4,1.0],[237,0,1.0],[238,3,1.0],[239,1,1.0],[240,4,1.0],[241,0,1.0],[245,2,1.0],[246,3,1.0],[247,2,1.0],[248,1,1.0],[249,0,1.0],[251,0,1.0],[251,1,1.0],[252,3,1.0],[253,1,1.0],[257,0,1.0],[258,1,1.0],[259,0,1.0],[259,3,1.0],[260,3,1.0],[262,0,1.0],[262,1,4.0],[262,2,3.0],[262,3,2.0],[263,2,1.0],[266,0,2.0],[266,1,2.0],[266,3,1.0],[267,4,1.0],[268,3,1.0],[268,4,5.0],[269,3,1.0],[270,0,1.0],[271,0,1.0],[271,2,1.0],[273,4,5.0],[275,2,1.0],[276,1,1.0],[277,3,2.0],[278,0,9.0],[278,1,11.0],[278,2,5.0],[278,3,13.0],[278,4,1.0],[279,1,1.0],[280,3,1.0],[281,0,2.0],[281,1,2.0],[281,2,1.0],[282,3,1.0],[283,1,1.0],[284,2,1.0],[285,3,1.0],[289,3,3.0],[290,3,1.0],[291,0,1.0],[294,3,1.0],[296,3,1.0],[297,2,2.0],[298,3,8.0],[299,4,1.0],[300,3,1.0],[303,0,1.0],[303,2,1.0],[304,4,1.0],[305,3,1.0],[306,0,1.0],[307,4,2.0],[308,4,2.0],[310,1,2.0],[310,2,1.0],[312,2,1.0],[313,3,1.0],[314,0,1.0],[314,1,1.0],[315,2,2.0],[317,4,4.0],[322,4,1.0],[324,3,1.0],[325,2,1.0],[328,3,1.0],[329,3,1.0],[331,2,1.0],[332,0,1.0],[332,1,1.0],[334,4,1.0],[336,3,1.0],[337,1,1.0],[343,0,1.0],[348,1,1.0],[351,0,1.0],[352,0,1.0],[352,4,2.0],[354,2,1.0],[355,2,1.0],[356,1,1.0],[357,2,1.0],[359,1,1.0],[360,3,1.0],[363,4,1.0],[365,2,1.0],[366,2,1.0],'..b'etadata": {"taxonomy": ["Root", "Bacteria", "Proteobacteria", "Deltaproteobacteria"]}},{"id": "389", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "390", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Bacilli\\"", "\\"Lactobacillales\\"", "Streptococcaceae", "Streptococcus"]}},{"id": "391", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Lachnospiraceae\\""]}},{"id": "392", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "393", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "394", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "395", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "396", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "397", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "398", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "399", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes"]}},{"id": "400", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "401", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Bacilli\\"", "\\"Lactobacillales\\"", "Lactobacillaceae", "Lactobacillus"]}},{"id": "402", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "403", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\"", "Ruminococcus"]}},{"id": "404", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "405", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "406", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "407", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\"", "\\"Ruminococcaceae Incertae Sedis\\""]}},{"id": "408", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "409", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Ruminococcaceae\\""]}},{"id": "410", "metadata": {"taxonomy": ["Root", "Bacteria"]}},{"id": "411", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "412", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Lachnospiraceae\\""]}},{"id": "413", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "414", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "415", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "416", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "417", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}},{"id": "418", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\""]}},{"id": "419", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales", "\\"Lachnospiraceae\\""]}},{"id": "420", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}}],"columns": [{"id": "PC.354", "metadata": null},{"id": "PC.355", "metadata": null},{"id": "PC.356", "metadata": null},{"id": "PC.481", "metadata": null},{"id": "PC.593", "metadata": null}]}\n\\ No newline at end of file\n'

diff -r 000000000000 -r c11972e98d44 test-data/filter_samples_from_otu_table/metadata_positive.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples_from_otu_table/metadata_positive.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,6 @@
+#SampleID BarcodeSequence DOB Description
+PC.354 AGCACGAGCCTA 20061218 Control_mouse__I.D._354
+PC.355 AACTCGTCGATG 20061218 Control_mouse__I.D._355
+PC.356 ACAGACCACTCA 20061126 Control_mouse__I.D._356
+PC.481 ACCAGCGACTAG 20070314 Control_mouse__I.D._481
+PC.593 AGCAGCACTTGT 20071210 Control_mouse__I.D._593
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/filter_samples_from_otu_table/otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples_from_otu_table/otu_table.biom Thu May 18 09:38:55 2017 -0400

[

b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "0", "metadata": {"taxonomy": ["Root", "Bacteria", "Actinobacteria", "Actinobacteria", "Coriobacteridae", "Coriobacteriales", "Coriobacterineae", "Coriobacteriaceae"]}}, {"id": "1", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}}, {"id": "2", "metadata": {"taxonomy": ["Root", "Bacteria"]}}, {"id": "3", "metadata": {"taxonomy": ["Root", "Bacteria"]}}, {"id": "4", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}}, {"id": "5", "metadata": {"taxonomy": ["Root"]}}, {"id": "6", "metadata": {"taxonomy": ["Root", "Bacteria"]}}, {"id": "7", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}}, {"id": "8", "metadata": {"taxonomy": ["Root", "Bacteria"]}}, {"id": "9", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}}, {"id": "10", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}}, {"id": "11", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Bacilli\\"", "Bacillales", "\\"Staphylococcaceae\\"", "Staphylococcus"]}}, {"id": "12", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}}, {"id": "13", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Clostridia\\"", "Clostridiales"]}}, {"id": "14", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}}, {"id": "15", "metadata": {"taxonomy": ["Root", "Bacteria"]}}, {"id": "16", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes", "Bacteroidetes", "Bacteroidales", "Rikenellaceae", "Alistipes"]}}, {"id": "17", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}}, {"id": "18", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes", "Bacteroidetes", "Bacteroidales", "Rikenellaceae", "Alistipes"]}}, {"id": "19", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes", "Bacteroidetes", "Bacteroidales"]}}, {"id": "20", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes"]}}, {"id": "21", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}}, {"id": "22", "metadata": {"taxonomy": ["Root", "Bacteria", "Firmicutes", "\\"Bacilli\\"", "Bacillales", "\\"Staphylococcaceae\\"", "Staphylococcus"]}}, {"id": "23", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}}, {"id": "24", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}}, {"id": "25", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}}, {"id": "26", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}}, {"id": "27", "metadata": {"taxonomy": ["Root", "Bacteria"]}}, {"id": "28", "metadata": {"taxonomy": ["Root", "Bacteria"]}}, {"id": "29", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes"]}}, {"id": "30", "metadata": {"taxonomy": ["Root", "Bacteria"]}}, {"id": "31", "metadata": {"taxonomy": ["Root", "Bacteria", "Bacteroidetes", "Bacteroidetes", "Bacteroidales", "Bacteroidaceae", "Bacteroides"]}}, {"id": "32", "metadata": {"taxonomy": ["Root", "Bacteria", 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"matrix_element_type": "float"}\n\\ No newline at end of file\n'

diff -r 000000000000 -r c11972e98d44 test-data/filter_taxa_from_otu_table/negative_taxa.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_taxa_from_otu_table/negative_taxa.biom Thu May 18 09:38:55 2017 -0400

[

@@ -0,0 +1,1 @@
+{"id": "No Table ID","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-04-20T12:00:08.953521","type": "OTU table","matrix_element_type": "float","shape": [53, 9],"data": [[0,4,1.0],[1,8,1.0],[2,8,1.0],[3,3,2.0],[4,3,1.0],[5,8,2.0],[6,3,1.0],[7,7,2.0],[8,7,1.0],[9,7,1.0],[10,7,1.0],[11,0,6.0],[11,3,2.0],[11,7,3.0],[11,8,5.0],[12,2,1.0],[13,3,1.0],[14,6,1.0],[15,1,1.0],[16,5,1.0],[17,8,1.0],[18,0,1.0],[19,2,1.0],[20,7,1.0],[21,2,1.0],[22,0,1.0],[23,0,2.0],[23,4,4.0],[24,1,1.0],[25,3,1.0],[26,5,1.0],[27,5,1.0],[28,8,1.0],[29,1,5.0],[29,2,1.0],[29,4,17.0],[29,7,20.0],[30,7,1.0],[31,7,1.0],[32,0,1.0],[33,0,1.0],[33,8,2.0],[34,0,1.0],[35,4,5.0],[35,7,2.0],[36,8,1.0],[37,8,1.0],[38,5,1.0],[39,4,1.0],[40,6,1.0],[41,7,1.0],[42,7,1.0],[43,3,1.0],[44,7,1.0],[45,5,1.0],[46,3,1.0],[47,0,1.0],[48,7,1.0],[49,8,4.0],[50,4,1.0],[51,1,1.0],[52,1,1.0]],"rows": [{"id": "9", "metadata": 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\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/filter_taxa_from_otu_table/otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_taxa_from_otu_table/otu_table.biom Thu May 18 09:38:55 2017 -0400

[

b'@@ -0,0 +1,1 @@\n+{"rows": [{"id": "0", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "1", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Staphylococcaceae"]}}, {"id": "2", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "3", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "4", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "5", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Lactobacillaceae"]}}, {"id": "6", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, 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"int"}\n\\ No newline at end of file\n'

diff -r 000000000000 -r c11972e98d44 test-data/filter_taxa_from_otu_table/positive_negative_taxa.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_taxa_from_otu_table/positive_negative_taxa.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/filter_taxa_from_otu_table/positive_taxa.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_taxa_from_otu_table/positive_taxa.biom Thu May 18 09:38:55 2017 -0400

[

b'@@ -0,0 +1,1 @@\n+{"id": "No Table ID","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-04-20T11:59:42.375968","type": "OTU table","matrix_element_type": "float","shape": [365, 9],"data": 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"f__Ruminococcaceae"]}},{"id": "387", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}},{"id": "388", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}},{"id": "389", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}},{"id": "390", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}},{"id": "391", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}},{"id": "392", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae"]}},{"id": "393", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}},{"id": "394", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}},{"id": "396", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__"]}},{"id": "397", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}},{"id": "398", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Porphyromonadaceae"]}},{"id": "399", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}},{"id": "400", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}},{"id": "401", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}},{"id": "402", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}},{"id": "403", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}},{"id": "404", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}},{"id": "405", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}},{"id": "406", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}},{"id": "408", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}},{"id": "409", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Turicibacterales", "f__Turicibacteraceae"]}},{"id": "411", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}},{"id": "412", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}},{"id": "413", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}},{"id": "414", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}},{"id": "415", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}],"columns": [{"id": "PC.636", "metadata": null},{"id": "PC.481", "metadata": null},{"id": "PC.354", "metadata": null},{"id": "PC.635", "metadata": null},{"id": "PC.593", "metadata": null},{"id": "PC.356", "metadata": null},{"id": "PC.355", "metadata": null},{"id": "PC.607", "metadata": null},{"id": "PC.634", "metadata": null}]}\n\\ No newline at end of file\n'

diff -r 000000000000 -r c11972e98d44 test-data/jackknifed_beta_diversity/map.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/jackknifed_beta_diversity/map.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/jackknifed_beta_diversity/otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/jackknifed_beta_diversity/otu_table.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/jackknifed_beta_diversity/rep_set.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/jackknifed_beta_diversity/rep_set.tre Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/make_emperor/map.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/make_emperor/map.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/make_emperor/unweighted_unifrac_pc.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/make_emperor/unweighted_unifrac_pc.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/make_otu_heatmap/basic_heatmap.pdf

Binary file test-data/make_otu_heatmap/basic_heatmap.pdf has changed

diff -r 000000000000 -r c11972e98d44 test-data/make_otu_heatmap/basic_heatmap.png

Binary file test-data/make_otu_heatmap/basic_heatmap.png has changed

diff -r 000000000000 -r c11972e98d44 test-data/make_otu_heatmap/basic_heatmap.svg
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diff -r 000000000000 -r c11972e98d44 test-data/make_otu_heatmap/mapping_file.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/make_otu_heatmap/mapping_file.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/make_otu_heatmap/otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/make_otu_heatmap/otu_table.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/make_otu_heatmap/rep_set.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/make_otu_heatmap/rep_set.tre Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/make_otu_heatmap/sample_otu_sorted_heatmap.pdf

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diff -r 000000000000 -r c11972e98d44 test-data/make_otu_heatmap/sample_sorted_heatmap.pdf

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diff -r 000000000000 -r c11972e98d44 test-data/make_otu_heatmap/treatment_sample_sorted_heatmap.pdf

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diff -r 000000000000 -r c11972e98d44 test-data/make_phylogeny/aligned.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r c11972e98d44 test-data/make_phylogeny/clustalw.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/make_phylogeny/clustalw.tre Thu May 18 09:38:55 2017 -0400

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diff -r 000000000000 -r c11972e98d44 test-data/make_phylogeny/fasttree_midpoint.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r c11972e98d44 test-data/make_phylogeny/fasttree_tree_method_default.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/make_phylogeny/fasttree_tree_method_default.tre Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,1 @@
+(((((((New.0.ReferenceOTU5:0.05067,(New.0.ReferenceOTU33:0.10526,(New.0.ReferenceOTU39:0.00016,r129:0.04665)0.993:0.09542)0.988:0.14134)0.978:0.13902,(New.0.ReferenceOTU36:0.12367,((r148:0.16175,New.0.CleanUp.ReferenceOTU9:0.00016)0.999:0.17786,r47:0.023)0.779:0.07434)0.993:0.14975)0.907:0.09058,(r78:0.26492,(New.0.ReferenceOTU22:0.11636,New.0.ReferenceOTU34:0.04549)0.703:0.01733)0.880:0.05224)0.832:0.08021,New.0.ReferenceOTU51:0.14487)0.433:0.02668,(New.0.ReferenceOTU26:0.03188,New.0.ReferenceOTU42:0.21485)0.341:0.01962)0.371:0.08711,r28:0.63554)0.650:0.03085,((r158:0.19778,(r96:0.12601,(r38:0.24145,r92:0.297)0.943:0.16926)0.999:0.19538)0.892:0.12716,(r146:0.26593,((((r181:0.15944,((New.0.ReferenceOTU32:0.06939,((New.0.CleanUp.ReferenceOTU33:0.23266,New.0.CleanUp.ReferenceOTU29:0.067)0.209:0.05032,New.0.ReferenceOTU14:0.39581)0.817:0.04969)0.897:0.07762,((New.0.ReferenceOTU7:0.07948,r59:0.04644)0.627:0.02639,(New.0.ReferenceOTU17:0.16137,New.0.ReferenceOTU28:0.04686)0.999:0.17798)0.944:0.08501)0.400:0.02682)0.089:0.00611,((New.0.ReferenceOTU30:0.11078,New.0.ReferenceOTU52:0.06277)0.497:0.03057,(((((r70:0.3363,(r0:0.00116,r143:1.2314)0.081:0.50764)0.425:0.15912,New.0.ReferenceOTU49:0.00016)0.855:0.09762,New.0.ReferenceOTU13:0.04006)0.255:0.01316,r74:0.20638)0.999:0.4103,New.0.ReferenceOTU38:0.54196)0.000:0.00016)0.260:0.05949)0.831:0.14971,(New.0.ReferenceOTU57:0.25477,r84:0.10524)0.998:0.40986)0.959:0.21713,(((New.0.ReferenceOTU48:0.09656,New.0.CleanUp.ReferenceOTU7:0.03314)0.989:0.20998,(r153:0.2175,((r102:0.0974,r175:0.40572)0.964:0.2358,(New.0.CleanUp.ReferenceOTU19:0.17636,r111:0.07083)0.841:0.14281)0.591:0.20414)0.373:0.15365)0.823:0.09797,(New.0.ReferenceOTU29:0.28773,(r39:0.19166,r63:0.12122)0.878:0.08664)0.744:0.06053)0.781:0.07918)0.915:0.14771)0.629:0.05893)0.749:0.05953,((New.0.ReferenceOTU15:0.36885,(New.0.ReferenceOTU41:0.4242,r192:0.06058)0.764:0.09601)0.809:0.10529,(New.0.ReferenceOTU9:0.22154,(((r162:0.45819,(New.0.CleanUp.ReferenceOTU12:0.44102,New.0.ReferenceOTU6:0.75725)0.299:0.1103)0.089:0.00015,r49:0.17029)0.973:0.22038,(New.0.ReferenceOTU54:0.18481,(New.0.CleanUp.ReferenceOTU17:0.16433,r178:0.48934)0.949:0.23612)0.807:0.16454)0.478:0.02748)0.230:0.11348)0.966:0.16346);

diff -r 000000000000 -r c11972e98d44 test-data/make_phylogeny/muscle.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/make_phylogeny/muscle.tre Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,1 @@
+('seq_31':1.12732,('seq_48':1.10277,((('seq_25':0.504624,('seq_36':0.467309,('seq_2':0.46,'seq_41':0.46):0.00730872):0.0373152):0.454956,(('seq_56':0.327907,'seq_7':0.327907):0.58686,(('seq_3':0.760137,('seq_38':0.698401,(('seq_50':0.626629,('seq_32':0.587397,('seq_14':0.561323,('seq_53':0.53139,'seq_16':0.53139):0.0299327):0.0260743):0.0392315):0.0128615,('seq_4':0.649129,('seq_54':0.609292,('seq_15':0.595946,(('seq_28':0.410256,'seq_55':0.410256):0.146957,('seq_46':0.514344,('seq_10':0.23617,'seq_13':0.23617):0.278173):0.0428695):0.0387327):0.0133457):0.0398378):-0.00963926):0.0589107):0.0617365):0.111034,('seq_35':0.818076,(('seq_24':0.47973,'seq_5':0.47973):0.302398,(('seq_34':0.389121,'seq_8':0.389121):0.259124,('seq_30':0.424779,'seq_58':0.424779):0.223466):0.133883):0.0359485):0.053095):0.0435957):0.0448129):0.0823335,('seq_43':1.01997,('seq_52':0.978471,('seq_0':0.988378,('seq_22':0.934682,(('seq_20':0.859155,'seq_47':0.859155):0.0247327,(('seq_9':0.880572,('seq_29':0.687912,('seq_27':0.648512,(('seq_57':0.518891,('seq_23':0.373538,('seq_11':0.338389,('seq_18':0.265086,'seq_12':0.265086):0.0733024):0.0351499):0.145352):0.0792318,(('seq_26':0.551948,'seq_59':0.551948):0.0299734,(('seq_6':0.381362,('seq_60':0.339565,('seq_19':0.320288,(('seq_40':0.163043,'seq_42':0.163043):0.143088,('seq_51':0.271452,('seq_33':0.225346,('seq_21':0.0829493,'seq_37':0.0829493):0.142396):0.046106):0.0346796):0.0141571):0.0192771):0.0417971):0.172122,('seq_49':0.532258,'seq_17':0.532258):0.0212262):0.0284371):0.016201):0.0503898):0.0393994):0.192661):-0.0101835,('seq_44':0.869437,('seq_39':0.824699,('seq_1':0.794118,'seq_45':0.794118):0.0305815):0.0447375):0.000952303):0.0134987):0.0507939):0.0536962):-0.00990623):0.0415013):0.0219407):0.0608518):0.0245566);

diff -r 000000000000 -r c11972e98d44 test-data/map.tsv.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/map.tsv.html Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,68 @@\n+<html>\n+<head>\n+\n+<script type="text/javascript" src="./overlib.js"></script>\n+</head>\n+<body bgcolor="white"> <h1>No errors or warnings detected.<br></h1><h1>Mapping file error and warning details.</h1>\n+Notes for interpreting this report:\n+<ul>\n+ <li>Errors will be listed in red, warnings in yellow.\n+ <li>Mouse over an error or warning in a cell for more details.\n+ <li>Errors in the header row may mask other errors, so these should be corrected first.\n+ <li>Modifications to your mapping file to fix certain issues may result in different errors. You should run <tt>validate_mapping_file.py</tt> until no errors (nor warnings, ideally) are found.\n+</ul>\n+<p>\n+Some general rules about formatting mapping files (see <a href="http://qiime.org/documentation/file_formats.html#metadata-mapping-files">here</a> for additional details):\n+<ul>\n+ <li>Header characters should only contain alphanumeric and <tt>_</tt> characters only.\n+ <li>Valid characters for SampleID fields are alphanumeric and <tt>.</tt> only.<br>\n+ <li>Other fields allow alphanumeric and <tt>+-%./ :,;_</tt> characters.\n+</ul>\n+General issues with your mapping file (i.e., those that do not pertain to a particular cell) will be listed here, if any:<table border="1" cellspacing="0" cellpadding="7"><tr></tr></table><br>\n+<table border="2" cellspacing="0" cellpadding="5">\n+\n+<tr></tr>\n+<tr>\n+<th>SampleID</th><th>BarcodeSequence</th><th>LinkerPrimerSequence</th><th>SampleType</th><th>Year</th><th>Month</th><th>Day</th><th>Subject</th><th>ReportedAntibioticUsage</th><th>DaysSinceExperimentStart</th><th>Description</th>\n+</tr>\n+\n+<tr>\n+<tr><th><tt>L1S8</tt></th><th><tt>AGCTGACTAGTC</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>gut</tt></th><th><tt>2008</tt></th><th><tt>10</tt></th><th><tt>28</tt></th><th><tt>1</tt></th><th><tt>Yes</tt></th><th><tt>0</tt></th><th><tt>1_Fece_10_28_2008\n+</tt></th></tr><tr><th><tt>L1S140</tt></th><th><tt>ATGGCAGCTCTA</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>gut</tt></th><th><tt>2008</tt></th><th><tt>10</tt></th><th><tt>28</tt></th><th><tt>2</tt></th><th><tt>Yes</tt></th><th><tt>0</tt></th><th><tt>2_Fece_10_28_2008\n+</tt></th></tr><tr><th><tt>L1S57</tt></th><th><tt>ACACACTATGGC</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>gut</tt></th><th><tt>2009</tt></th><th><tt>1</tt></th><th><tt>20</tt></th><th><tt>1</tt></th><th><tt>No</tt></th><th><tt>84</tt></th><th><tt>1_Fece_1_20_2009\n+</tt></th></tr><tr><th><tt>L1S208</tt></th><th><tt>CTGAGATACGCG</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>gut</tt></th><th><tt>2009</tt></th><th><tt>1</tt></th><th><tt>20</tt></th><th><tt>2</tt></th><th><tt>No</tt></th><th><tt>84</tt></th><th><tt>2_Fece_1_20_2009\n+</tt></th></tr><tr><th><tt>L1S76</tt></th><th><tt>ACTACGTGTGGT</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>gut</tt></th><th><tt>2009</tt></th><th><tt>2</tt></th><th><tt>17</tt></th><th><tt>1</tt></th><th><tt>No</tt></th><th><tt>112</tt></th><th><tt>1_Fece_2_17_2009\n+</tt></th></tr><tr><th><tt>L1S105</tt></th><th><tt>AGTGCGATGCGT</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>gut</tt></th><th><tt>2009</tt></th><th><tt>3</tt></th><th><tt>17</tt></th><th><tt>1</tt></th><th><tt>No</tt></th><th><tt>140</tt></th><th><tt>1_Fece_3_17_2009\n+</tt></th></tr><tr><th><tt>L1S257</tt></th><th><tt>CCGACTGAGATG</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>gut</tt></th><th><tt>2009</tt></th><th><tt>3</tt></th><th><tt>17</tt></th><th><tt>2</tt></th><th><tt>No</tt></th><th><tt>140</tt></th><th><tt>2_Fece_3_17_2009\n+</tt></th></tr><tr><th><tt>L1S281</tt></th><th><tt>CCTCTCGTGATC</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>gut</tt></th><th><tt>2009</tt></th><th><tt>4</tt></th><th><tt>14</tt></th><th><tt>2</tt></th><th><tt>No</tt></th><th><tt>168</tt></th><th><tt>2_Fece_4_14_2009\n+</tt></th></tr><tr><th><tt>L2S240</tt></th><th><tt>CATATCGCAGTT</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>left palm</tt></th><th><tt>'..b'h><th><tt>AGTGTCACGGTG</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>right palm</tt></th><th><tt>2009</tt></th><th><tt>2</tt></th><th><tt>17</tt></th><th><tt>1</tt></th><th><tt>No</tt></th><th><tt>112</tt></th><th><tt>1_R_Palm_2_17_2009\n+</tt></th></tr><tr><th><tt>L3S341</tt></th><th><tt>CAAGTGAGAGAG</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>right palm</tt></th><th><tt>2009</tt></th><th><tt>3</tt></th><th><tt>17</tt></th><th><tt>1</tt></th><th><tt>No</tt></th><th><tt>140</tt></th><th><tt>1_R_Palm_3_17_2009\n+</tt></th></tr><tr><th><tt>L4S112</tt></th><th><tt>GCGTTACACACA</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>right palm</tt></th><th><tt>2009</tt></th><th><tt>3</tt></th><th><tt>17</tt></th><th><tt>2</tt></th><th><tt>No</tt></th><th><tt>140</tt></th><th><tt>2_R_Palm_3_17_2009\n+</tt></th></tr><tr><th><tt>L3S360</tt></th><th><tt>CATCGTATCAAC</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>right palm</tt></th><th><tt>2009</tt></th><th><tt>4</tt></th><th><tt>14</tt></th><th><tt>1</tt></th><th><tt>No</tt></th><th><tt>168</tt></th><th><tt>1_R_Palm_4_14_2009\n+</tt></th></tr><tr><th><tt>L4S137</tt></th><th><tt>GAACTGTATCTC</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>right palm</tt></th><th><tt>2009</tt></th><th><tt>4</tt></th><th><tt>14</tt></th><th><tt>2</tt></th><th><tt>No</tt></th><th><tt>168</tt></th><th><tt>2_R_Palm_4_14_2009\n+</tt></th></tr><tr><th><tt>L5S104</tt></th><th><tt>CAGTGTCAGGAC</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>tongue</tt></th><th><tt>2008</tt></th><th><tt>10</tt></th><th><tt>28</tt></th><th><tt>1</tt></th><th><tt>Yes</tt></th><th><tt>0</tt></th><th><tt>1_Tong_10_28_2008\n+</tt></th></tr><tr><th><tt>L5S240</tt></th><th><tt>CTGGACTCATAG</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>tongue</tt></th><th><tt>2008</tt></th><th><tt>10</tt></th><th><tt>28</tt></th><th><tt>2</tt></th><th><tt>Yes</tt></th><th><tt>0</tt></th><th><tt>2_Tong_10_28_2008\n+</tt></th></tr><tr><th><tt>L5S155</tt></th><th><tt>ATCTTAGACTGC</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>tongue</tt></th><th><tt>2009</tt></th><th><tt>1</tt></th><th><tt>20</tt></th><th><tt>1</tt></th><th><tt>No</tt></th><th><tt>84</tt></th><th><tt>1_Tong_1_20_2009\n+</tt></th></tr><tr><th><tt>L6S20</tt></th><th><tt>GAGGCTCATCAT</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>tongue</tt></th><th><tt>2009</tt></th><th><tt>1</tt></th><th><tt>20</tt></th><th><tt>2</tt></th><th><tt>No</tt></th><th><tt>84</tt></th><th><tt>2_Tong_1_20_2009\n+</tt></th></tr><tr><th><tt>L5S174</tt></th><th><tt>CAGACATTGCGT</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>tongue</tt></th><th><tt>2009</tt></th><th><tt>2</tt></th><th><tt>17</tt></th><th><tt>1</tt></th><th><tt>No</tt></th><th><tt>112</tt></th><th><tt>1_Tong_2_17_2009\n+</tt></th></tr><tr><th><tt>L5S203</tt></th><th><tt>CGATGCACCAGA</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>tongue</tt></th><th><tt>2009</tt></th><th><tt>3</tt></th><th><tt>17</tt></th><th><tt>1</tt></th><th><tt>No</tt></th><th><tt>140</tt></th><th><tt>1_Tong_3_17_2009\n+</tt></th></tr><tr><th><tt>L6S68</tt></th><th><tt>GATACGTCCTGA</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>tongue</tt></th><th><tt>2009</tt></th><th><tt>3</tt></th><th><tt>17</tt></th><th><tt>2</tt></th><th><tt>No</tt></th><th><tt>140</tt></th><th><tt>2_Tong_3_17_2009\n+</tt></th></tr><tr><th><tt>L5S222</tt></th><th><tt>CTAGAGACTCTT</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>tongue</tt></th><th><tt>2009</tt></th><th><tt>4</tt></th><th><tt>14</tt></th><th><tt>1</tt></th><th><tt>No</tt></th><th><tt>168</tt></th><th><tt>1_Tong_4_14_2009\n+</tt></th></tr><tr><th><tt>L6S93</tt></th><th><tt>GATTAGCACTCT</tt></th><th><tt>GTGCCAGCMGCCGCGGTAA</tt></th><th><tt>tongue</tt></th><th><tt>2009</tt></th><th><tt>4</tt></th><th><tt>14</tt></th><th><tt>2</tt></th><th><tt>No</tt></th><th><tt>168</tt></th><th><tt>2_Tong_4_14_2009</tt></th></tr>\n+</tr>\n+</table>\n+\n+</body>\n+</html>\n\\ No newline at end of file\n'

diff -r 000000000000 -r c11972e98d44 test-data/map.tsv_corrected.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/map.tsv_corrected.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,35 @@
+#SampleID BarcodeSequence LinkerPrimerSequence SampleType Year Month Day Subject ReportedAntibioticUsage DaysSinceExperimentStart Description
+L1S8 AGCTGACTAGTC GTGCCAGCMGCCGCGGTAA gut 2008 10 28 1 Yes 0 1_Fece_10_28_2008
+L1S140 ATGGCAGCTCTA GTGCCAGCMGCCGCGGTAA gut 2008 10 28 2 Yes 0 2_Fece_10_28_2008
+L1S57 ACACACTATGGC GTGCCAGCMGCCGCGGTAA gut 2009 1 20 1 No 84 1_Fece_1_20_2009
+L1S208 CTGAGATACGCG GTGCCAGCMGCCGCGGTAA gut 2009 1 20 2 No 84 2_Fece_1_20_2009
+L1S76 ACTACGTGTGGT GTGCCAGCMGCCGCGGTAA gut 2009 2 17 1 No 112 1_Fece_2_17_2009
+L1S105 AGTGCGATGCGT GTGCCAGCMGCCGCGGTAA gut 2009 3 17 1 No 140 1_Fece_3_17_2009
+L1S257 CCGACTGAGATG GTGCCAGCMGCCGCGGTAA gut 2009 3 17 2 No 140 2_Fece_3_17_2009
+L1S281 CCTCTCGTGATC GTGCCAGCMGCCGCGGTAA gut 2009 4 14 2 No 168 2_Fece_4_14_2009
+L2S240 CATATCGCAGTT GTGCCAGCMGCCGCGGTAA left palm 2008 10 28 2 Yes 0 2_L_Palm_10_28_2008
+L2S155 ACGATGCGACCA GTGCCAGCMGCCGCGGTAA left palm 2009 1 20 1 No 84 1_L_Palm_1_20_2009
+L2S309 CGTGCATTATCA GTGCCAGCMGCCGCGGTAA left palm 2009 1 20 2 No 84 2_L_Palm_1_20_2009
+L2S175 AGCTATCCACGA GTGCCAGCMGCCGCGGTAA left palm 2009 2 17 1 No 112 1_L_Palm_2_17_2009
+L2S204 ATGCAGCTCAGT GTGCCAGCMGCCGCGGTAA left palm 2009 3 17 1 No 140 1_L_Palm_3_17_2009
+L2S357 CTAACGCAGTCA GTGCCAGCMGCCGCGGTAA left palm 2009 3 17 2 No 140 2_L_Palm_3_17_2009
+L2S222 CACGTGACATGT GTGCCAGCMGCCGCGGTAA left palm 2009 4 14 1 No 168 1_L_Palm_4_14_2009
+L2S382 CTCAATGACTCA GTGCCAGCMGCCGCGGTAA left palm 2009 4 14 2 No 168 2_L_Palm_4_14_2009
+L3S242 ACAGTTGCGCGA GTGCCAGCMGCCGCGGTAA right palm 2008 10 28 1 Yes 0 1_R_Palm_10_28_2008
+L3S378 ATCGATCTGTGG GTGCCAGCMGCCGCGGTAA right palm 2008 10 28 2 Yes 0 2_R_Palm_10_28_2008
+L3S294 CACGACAGGCTA GTGCCAGCMGCCGCGGTAA right palm 2009 1 20 1 No 84 1_R_Palm_1_20_2009
+L4S63 CTCGTGGAGTAG GTGCCAGCMGCCGCGGTAA right palm 2009 1 20 2 No 84 2_R_Palm_1_20_2009
+L3S313 AGTGTCACGGTG GTGCCAGCMGCCGCGGTAA right palm 2009 2 17 1 No 112 1_R_Palm_2_17_2009
+L3S341 CAAGTGAGAGAG GTGCCAGCMGCCGCGGTAA right palm 2009 3 17 1 No 140 1_R_Palm_3_17_2009
+L4S112 GCGTTACACACA GTGCCAGCMGCCGCGGTAA right palm 2009 3 17 2 No 140 2_R_Palm_3_17_2009
+L3S360 CATCGTATCAAC GTGCCAGCMGCCGCGGTAA right palm 2009 4 14 1 No 168 1_R_Palm_4_14_2009
+L4S137 GAACTGTATCTC GTGCCAGCMGCCGCGGTAA right palm 2009 4 14 2 No 168 2_R_Palm_4_14_2009
+L5S104 CAGTGTCAGGAC GTGCCAGCMGCCGCGGTAA tongue 2008 10 28 1 Yes 0 1_Tong_10_28_2008
+L5S240 CTGGACTCATAG GTGCCAGCMGCCGCGGTAA tongue 2008 10 28 2 Yes 0 2_Tong_10_28_2008
+L5S155 ATCTTAGACTGC GTGCCAGCMGCCGCGGTAA tongue 2009 1 20 1 No 84 1_Tong_1_20_2009
+L6S20 GAGGCTCATCAT GTGCCAGCMGCCGCGGTAA tongue 2009 1 20 2 No 84 2_Tong_1_20_2009
+L5S174 CAGACATTGCGT GTGCCAGCMGCCGCGGTAA tongue 2009 2 17 1 No 112 1_Tong_2_17_2009
+L5S203 CGATGCACCAGA GTGCCAGCMGCCGCGGTAA tongue 2009 3 17 1 No 140 1_Tong_3_17_2009
+L6S68 GATACGTCCTGA GTGCCAGCMGCCGCGGTAA tongue 2009 3 17 2 No 140 2_Tong_3_17_2009
+L5S222 CTAGAGACTCTT GTGCCAGCMGCCGCGGTAA tongue 2009 4 14 1 No 168 1_Tong_4_14_2009
+L6S93 GATTAGCACTCT GTGCCAGCMGCCGCGGTAA tongue 2009 4 14 2 No 168 2_Tong_4_14_2009

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/output_with_barcode/forward_1/fastqjoin.un1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/output_with_barcode/forward_1/fastqjoin.un1.fastq Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,8 @@
+@HWI-ST753:99:C038WACXX:4:1101:1252:1987 1:N:0:
+NACGGAGGGTGCGAGCGTTGTCCGGAATCATTGGGCGTAAAGGGCGCGTAGGTGGCCCGGTCAGCGTGCGGTGACAGCTCGGCGCTCAACCACGAGTAGG
++
+#1=DDBDFHCFHHIIJGDHIJJJJIFGGHCGGGGEGIEGCHHHEDB@B8?;@AAB?<?7<75;CCB##################################
+@HWI-ST753:99:C038WACXX:4:1101:1357:1989 1:N:0:
+NACGGGGGGGGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGGGTTCGTAGGTGGCCTACTAAGTCAGACGAGAGCTCACTCAGCATATCTGGCGCACTG
++
+#1=DDFFFDDD@6@BBB8?B?BCBDBBDDCDCDD?BB79?ACC?+8?:8??B@@B#############################################
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/output_with_barcode/forward_1/fastqjoin.un2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/output_with_barcode/forward_1/fastqjoin.un2.fastq Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,8 @@
+@HWI-ST753:99:C038WACXX:4:1101:1252:1987 2:N:0:
+TCGTCGATAATCA
++
+====ADDDHFHHF
+@HWI-ST753:99:C038WACXX:4:1101:1357:1989 2:N:0:
+ACGTGTACCCAAA
++
+@CCFFFDEHHHGF
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/output_with_barcode/forward_2/fastqjoin.join.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/output_with_barcode/forward_2/fastqjoin.join.fastq Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,4 @@
+@HWI-ST753:99:C038WACXX:4:1101:1252:1987 1:N:0:
+NACGGAGGGTGCGAGCGTTGTCCGGAATCATTGGGCGTAAAGGGCGCGTAGGTGGCCCGGTCAGCGTGCGGTGACAGCTCGGCGCTCAACCACGAGTAGGAAATCTGGTAACTCTTTCTCTCTGGGTATATCTCTGGTCTAATCTCGTTAAAACTTCTCTGGTATTGTCGGT
++
+#1=DDBDFHCFHHIIJGDHIJJJJIFGGHCGGGGEGIEGCHHHEDB@B8?;@AAB?<?7<75;CCB########################################BCC;57<7?<?BAA@;?8B@BDEHHHCGEIGEGGGGCHGGFIJJJJIHDGJIIHHFCHFDBDD=1#

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/output_with_barcode/forward_2/fastqjoin.join_barcodes.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/output_with_barcode/forward_2/fastqjoin.join_barcodes.fastq Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,4 @@
+@HWI-ST753:99:C038WACXX:4:1101:1252:1987 1:N:0:
+TCGTCGATAATCA
++
+====ADDDHFHHF

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/output_with_barcode/forward_2/fastqjoin.un1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/output_with_barcode/forward_2/fastqjoin.un1.fastq Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,4 @@
+@HWI-ST753:99:C038WACXX:4:1101:1357:1989 1:N:0:
+NACGGGGGGGGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGGGTTCGTAGGTGGCCTACTAAGTCAGACGAGAGCTCACTCAGCATATCTGGCGCACTG
++
+#1=DDFFFDDD@6@BBB8?B?BCBDBBDDCDCDD?BB79?ACC?+8?:8??B@@B#############################################
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/output_with_barcode/forward_2/fastqjoin.un2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/output_with_barcode/forward_2/fastqjoin.un2.fastq Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,4 @@
+@HWI-ST753:99:C038WACXX:4:1101:1357:1989 2:N:0:
+NACGGGGGGGGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGGGTTCGTAGGTGGCCTACTAAGTCAGACGAGAGCTCACTCAGCATATCTGGCGCACTG
++
+#1=DDFFFDDD@6@BBB8?B?BCBDBBDDCDCDD?BB79?ACC?+8?:8??B@@B#############################################
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/output_without_barcode/forward_1/fastqjoin.un1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/output_without_barcode/forward_1/fastqjoin.un1.fastq Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/output_without_barcode/forward_1/fastqjoin.un2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/output_without_barcode/forward_1/fastqjoin.un2.fastq Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/output_without_barcode/forward_2/fastqjoin.un1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/output_without_barcode/forward_2/fastqjoin.un1.fastq Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/output_without_barcode/forward_2/fastqjoin.un2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/output_without_barcode/forward_2/fastqjoin.un2.fastq Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/output_without_barcode/forward_3/fastqjoin.un1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/output_without_barcode/forward_3/fastqjoin.un1.fastq Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/output_without_barcode/forward_3/fastqjoin.un2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/output_without_barcode/forward_3/fastqjoin.un2.fastq Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,8 @@
+@HWI-ST753:99:C038WACXX:4:1101:1252:1987 2:N:0:
+TCGTCGATAATCA
++
+====ADDDHFHHF
+@HWI-ST753:99:C038WACXX:4:1101:1357:1989 2:N:0:
+ACGTGTACCCAAA
++
+@CCFFFDEHHHGF

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/qiime_parameters.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/qiime_parameters.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,1 @@
+join_paired_ends:pe_join_method SeqPrep
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/with_barcode/barcode_1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/with_barcode/barcode_1.fastq Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/with_barcode/barcode_2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/with_barcode/barcode_2.fastq Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,8 @@
+@HWI-ST753:99:C038WACXX:4:1101:1252:1987 1:N:0:
+TCGTCGATAATCA
++
+====ADDDHFHHF
+@HWI-ST753:99:C038WACXX:4:1101:1357:1989 1:N:0:
+ACGTGTACCCAAA
++
+@CCFFFDEHHHGF
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/with_barcode/forward_1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/with_barcode/forward_1.fastq Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/with_barcode/forward_2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/with_barcode/forward_2.fastq Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/with_barcode/reverse_1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/with_barcode/reverse_1.fastq Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/with_barcode/reverse_2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/with_barcode/reverse_2.fastq Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,8 @@
+@HWI-ST753:99:C038WACXX:4:1101:1252:1987 2:N:0:
+ACCGACAATACCAGAGAAGTTTTAACGAGATTAGACCAGAGATATACCCAGAGAGAAAGAGTTACCAGATTTCCTACTCGTGGTTGAGCGCCGAGCTGTC
++
+#1=DDBDFHCFHHIIJGDHIJJJJIFGGHCGGGGEGIEGCHHHEDB@B8?;@AAB?<?7<75;CCB##################################
+@HWI-ST753:99:C038WACXX:4:1101:1357:1989 2:N:0:
+NACGGGGGGGGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGGGTTCGTAGGTGGCCTACTAAGTCAGACGAGAGCTCACTCAGCATATCTGGCGCACTG
++
+#1=DDFFFDDD@6@BBB8?B?BCBDBBDDCDCDD?BB79?ACC?+8?:8??B@@B#############################################
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/without_barcode/forward_1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/without_barcode/forward_1.fastq Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/without_barcode/forward_2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/without_barcode/forward_2.fastq Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/without_barcode/reverse_1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/without_barcode/reverse_1.fastq Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/multiple_join_paired_ends/without_barcode/reverse_2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_join_paired_ends/without_barcode/reverse_2.fastq Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/multiple_split_libraries_fastq/input/barcodes_1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_split_libraries_fastq/input/barcodes_1.fastq Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,8 @@
+@HWI-ST753:99:C038WACXX:4:1101:1252:1987 2:N:0:
+TCGTCGATAATC
++
+====ADDDHFHH
+@HWI-ST753:99:C038WACXX:4:1101:1357:1989 2:N:0:
+ACGTGTACCCAA
++
+@CCFFFDEHHHG
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/multiple_split_libraries_fastq/input/barcodes_2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_split_libraries_fastq/input/barcodes_2.fastq Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/multiple_split_libraries_fastq/input/mapping_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_split_libraries_fastq/input/mapping_1.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,3 @@
+#SampleID BarcodeSequence LinkerPrimerSequence Description
+test1 TCGTCGATAATC GTGCCAGCMGCCGCGGTAA SB1
+test2 ACGTGTACCCAA GTGCCAGCMGCCGCGGTAA TA1.1
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/multiple_split_libraries_fastq/input/mapping_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_split_libraries_fastq/input/mapping_2.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,3 @@
+#SampleID BarcodeSequence LinkerPrimerSequence Description
+test1 TCGTCGATAATC GTGCCAGCMGCCGCGGTAA SB1
+test2 ACGTGTACCCAA GTGCCAGCMGCCGCGGTAA TA1.1
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/multiple_split_libraries_fastq/input/reads_1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_split_libraries_fastq/input/reads_1.fastq Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,8 @@
+@HWI-ST753:99:C038WACXX:4:1101:1252:1987 1:N:0:
+AACGGAGGGTGCGAGCGTTGTCCGGAATCATTGGGCGTAAAGGGCGCGTAGGTGGCCCGGTCAGCGTGCGGTGACAGCTCGGCGCTCAACCACGAGTAGGAACGGAGGGTGCGAGCGTTGTCCGGAATCATTGGGCGTAAAGGGCGCGTAGGTGGCCCGGTCAGCGTGCGGTGACAGCTCGGCGCTCAACCACGAGTAGG
++
+ADADDBDFHCFHHIIJGDHIJJJJIFGGHCGGGGEGIEGCHHHEDBDDBDFHCFHHIIJGDHIJJJJIFGGHCGGGGEGIEGCHHHDDBDFHCFHHIIJGDHIJJJJIFGGHCGGGGEGIEGCHHHGGEGIEGCHHHDDBDFHCFHHIIJGDHIJJJJIFGGHCGGGGEGIEGCHHHGGEGIEGCHHHDDBDFHCFHHII
+@HWI-ST753:99:C038WACXX:4:1101:1357:1989 1:N:0:
+CACGGGGGGGGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGGGTTCGTAGGTGGCCTACTAAGTCAGACGAGAGCTCACTCAGCATATCTGGCGCACTGCACGGGGGGGGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGGGTTCGTAGGTGGCCTACTAAGTCAGACGAGAGCTCACTCAGCATATCTGGCGCACTG
++
+#1=DDFFFDDD@6@BBB8?B?BCBDBBDDCDCDD?BB79?ACC?+8?:8??B@@B##############################################1=DDFFFDDD@6@BBB8?B?BCBDBBDDCDCDD?BB79?ACC?+8?:8??B@@B#############################################
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/multiple_split_libraries_fastq/input/reads_2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_split_libraries_fastq/input/reads_2.fastq Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/multiple_split_libraries_fastq/qiime_parameters.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_split_libraries_fastq/qiime_parameters.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,1 @@
+split_libraries_fastq:barcode_type 12
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/pick_closed_reference_otus/assign_taxonomy_otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_closed_reference_otus/assign_taxonomy_otu_table.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/pick_closed_reference_otus/basic_otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_closed_reference_otus/basic_otu_table.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/pick_closed_reference_otus/refseqs.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_closed_reference_otus/refseqs.fna Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,10 @@
+>r1
+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTTACCCTCTCAGGCCGGCTACGCATCATCGCCTTGGTGGGCCGTTACCTCACCAACTAGCTAATGCGCCGCAGGTCCATCCATGTTCACGCCTTGATGGGCGCTTTAATATACTGAGCATGCGCTCTGTATACCTATCCGGTTTTAGCTACCGTTTCCAGCAGTTATCCCGGACACATGGGCTAGG
+>r2
+TTGGACCGTGTCTCAGTTCCAATGTGGGGGCCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACAACCTAATGGAACGCATCCCCATCGATGACCGAAGTTCTTTAATAGTTCTACCATGCGGAAGAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCA
+>r3
+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTTAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCTTACCAACTAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGACATGCGTCTAGTGTTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCTTGGG
+>r4
+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCAGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGGTATTCCGGCGATGCCGCCAAAATCATTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTGCTCACG
+>r5
+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTAGGCCGTTACCCTGCCAACTGGCTAATCAGACGCGGGTCCATCTCACACCGATTAATCTTTTTCCAACCAGAGCATGCGCCCCTGTTGGCTTATGCGGTATTAGCGGTCGTTTCCAACTGTTATCCCCCTGTGTGAGGCAGGTTACCCACGCGTTACTCACCCGTCCG

diff -r 000000000000 -r c11972e98d44 test-data/pick_closed_reference_otus/seqs.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_closed_reference_otus/seqs.fna Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,2668 @@\n+>PC.634_1 FLP3FBN01ELBSX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTTACCCTCTCAGGCCGGCTACGCATCATCGCCTTGGTGGGCCGTTACCTCACCAACTAGCTAATGCGCCGCAGGTCCATCCATGTTCACGCCTTGATGGGCGCTTTAATATACTGAGCATGCGCTCTGTATACCTATCCGGTTTTAGCTACCGTTTCCAGCAGTTATCCCGGACACATGGGCTAGG\n+>PC.634_2 FLP3FBN01EG8AX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGCCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACAACCTAATGGAACGCATCCCCATCGATGACCGAAGTTCTTTAATAGTTCTACCATGCGGAAGAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCA\n+>PC.354_3 FLP3FBN01EEWKD orig_bc=AGCACGAGCCTA new_bc=AGCACGAGCCTA bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTTAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCTTACCAACTAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGACATGCGTCTAGTGTTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCTTGGG\n+>PC.481_4 FLP3FBN01DEHK3 orig_bc=ACCAGCGACTAG new_bc=ACCAGCGACTAG bc_diffs=0\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCAGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGGTATTCCGGCGATGCCGCCAAAATCATTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTGCTCACG\n+>PC.634_5 FLP3FBN01DGFYQ orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTAGGCCGTTACCCTGCCAACTGGCTAATCAGACGCGGGTCCATCTCACACCGATTAATCTTTTTCCAACCAGAGCATGCGCCCCTGTTGGCTTATGCGGTATTAGCGGTCGTTTCCAACTGTTATCCCCCTGTGTGAGGCAGGTTACCCACGCGTTACTCACCCGTCCG\n+>PC.636_6 FLP3FBN01A55WZ orig_bc=ACGGTGAGTGTC new_bc=ACGGTGAGTGTC bc_diffs=0\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCTTATACCGGTAAACCTTTAATCATGAGAAAATGCTCACTCATGATACCATCTTGTATTAATCTCCCTTTCAGAAGGCTATCCAAGAGTATAAGGCAGGTTGGATACGCGTTACTCACCCGTGCGCCGG\n+>PC.634_7 FLP3FBN01D7O1S orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGATAACCGAAATTCTTTAATAGTGAAACCATGCGGAAATACTATACTATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTTATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCATC\n+>PC.634_8 FLP3FBN01CV5ZU orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+TTGGTCCGTGTCTCAGTACCAATGTGGGGGGTTAACCTCTCAGTCCCCCTATGTATCGTCGCCTTGGTAAGCCGTTACCTTACCAACCAGCTAATACAACGCATGCCCATCTGTAACCGCCGAAACTTTCAACCACAAGAGATGCCTCTCATAGTGTTATGCGGTATTAGTACCGATTTCTCAGTGTTATCCCCCTGTTACAGGTAGGTTGCATACGCGTTACGCACCCGTGCGCCGGTCG\n+>PC.634_9 FLP3FBN01DQ783 orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCCG\n+>PC.634_10 FLP3FBN01DDPFF orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTCCCTTTCAGAAGGCTATCCAAGAGTATAAGGCAGGTTGGGTACGCGTTACTC\n+>PC.634_11 FLP3FBN01CPD70 orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+CTGGACCGTGTCTCAGTTCCAATGTGGGGGGCCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACAACCTAATGGAACGCATCCCCATCGATGACCGAAGTTCTTTAATAGTTCTACCATGCGGAAGAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCG\n+>PC.593_12 FLP3FBN01BBAE6 orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCCCGCCGACTAGCTAATGCGCCGCATGCCCATCCGCCACCGGTAATCCCTTTGGCGGCACCGGGATGCCCCGATGCCGCGTCACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGTGGCGGGCAGGTTGCATACGTGTTACTCACCCGTGCG\n+>PC.355_13 FLP3FBN01AWYZD orig_bc=AACTCGTCGATG new_bc=AACTCGTCGATG bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTCAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCTTACCAACTAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGACATG'..b'GTCCGCCCTCTCAGGCCGGCTATGCATCATCGTCTTGGTGGGCCTTTACCCCGCCAACCAACTAATGCACCGCAGGTCCATCCGCGCCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTCCTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTT\n+>PC.593_1323 FLP3FBN01DBF9Z orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGACCGTGTCTCAGTTCCAGTGTGTCCGATCACCCTCTCAGGCCGGATACCCGTCATAGCCTTGGTGAGCCATTACCTCACCAACAAGCTGATAGGACATAGGCTGATCCTTTAGCGAAAAACTTTCCCCCGTAGGGAGTATCCAGTATTAATCACCGTTTCCAGTGGCTATCCCAGACTAAAGGGCACATAACCTATGCATTACTCACCCGTGCGCC\n+>PC.593_1324 FLP3FBN01APHXO orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTATGCATCATCGTCTTGGTGGGCCTTTACCCCGCCAACCAACTAATGCACCGCAGGTCCATCCGCGCCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTCCTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTTACT\n+>PC.593_1325 FLP3FBN01C0GRI orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTGGGCCGTTACCCCGCCAACTGGCTAATCAGACGCGGATCCATCGTATACCACCGGAGTTTTTCACACTGTTCCATGCGGAACCGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCGGTATACGGCAGGTTATCCACGCGTTACTCACCCGTCCG\n+>PC.593_1326 FLP3FBN01CEZZE orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTATGCATCATCGTCTTGGTGGGCCTTTACCCCGCCAACAAACTAATGCACCGCAGGTCCATCCGCGCCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTCCTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTT\n+>PC.593_1327 FLP3FBN01AGO5G orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGGTTAGGTGGGCCTTTACCCCGCCAACAAACTAATGCACCGCAGGTCCATCCGCGCCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTCCTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTTACTCACCCGTTCGCC\n+>PC.593_1328 FLP3FBN01A9WKI orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTATGCATCATCGTCTTGGTGGGCCTTTACCCCGCCAACAAACTAATGCACCGCAGGTCCATCCGCACCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTCCTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTT\n+>PC.593_1329 FLP3FBN01AMKUE orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCCCGCCGACTAGCTAATGCGCCGCATGGCCATCCGCAGCCGATAAATCTTTAAACATCGGGAGATGCCTCCCAACGTTGTTACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTGCGGGCAGGTTCCATACGTGTTACTCACCCGTGCG\n+>PC.593_1330 FLP3FBN01CD50B orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTTGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCGGGTCCATCTTACACCACCGGAGTTTTCAAGTAAAAGACATGCGTCTCCTACTGTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTGCAAGGCAGGTTACCCACGCGTTACTCACCCGTCCGCC\n+>PC.593_1331 FLP3FBN01CXEQE orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCCCGCCAACAAGCTAATCAGACGCGGATCCATCGTATACCACCAAAAGCTTTAGCTTTTTGTTTTCCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTATACGGCAGGTT\n+>PC.593_1332 FLP3FBN01C6MIF orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGGCCGTGTCTCAGTCCCAGTGTGGCCGTCCGCCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTAGGCCGTTACCCTGCCAACTGGCTAATCAGACGCGGGCCCATCCTGTACCACCGGAGTTTTCAGGGAAAAGCCATGCGGCTTCCCCCGTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCTGTACAGGCCAGGTTGCCCACGCGTTACTCACCCGTCCGCC\n+>PC.593_1333 FLP3FBN01CKQYM orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCCCGCCGACTAGCTAATGCGCCGCATGGCCATCCGCAGCCGATAAATCTTTAAACATCGGGAGATGCCTCCCAACGTTGTTACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTGCGGGCAGGTTCCATACGTGTTACTCACCCGTGCG\n+>PC.593_1334 FLP3FBN01A68AG orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCCCGCCGACTAGCTAATGCGCCGCATGGCCATCCGCAGCCGGTAAACCTTTAAACCACCGGAGATGCCTCCAACGGTTGTTACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTGCGGGCAGGTTCCATACGTGTTACTCACCCGTGCGCCGGTCGCCGG\n'

diff -r 000000000000 -r c11972e98d44 test-data/pick_closed_reference_otus/sortmerna_otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_closed_reference_otus/sortmerna_otu_table.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/pick_closed_reference_otus/sortmerna_params.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_closed_reference_otus/sortmerna_params.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,2 @@
+pick_otus:otu_picking_method sortmerna
+pick_otus:threads 1
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/pick_closed_reference_otus/suppress_taxonomy_assignment_otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_closed_reference_otus/suppress_taxonomy_assignment_otu_table.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/pick_closed_reference_otus/taxa.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_closed_reference_otus/taxa.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,5 @@
+r1 k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Escherichia;s__
+r2 k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Escherichia;s__
+r3 k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Escherichia;s__
+r4 k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Escherichia;s__
+r5 k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Escherichia;s__

diff -r 000000000000 -r c11972e98d44 test-data/pick_open_reference_otus/1_final_otu_map.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_open_reference_otus/1_final_otu_map.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,30 @@
+4374484 L1S8_76 L1S281_24 L1S105_1
+New.CleanUp.ReferenceOTU0 L1S76_65
+New.CleanUp.ReferenceOTU1 L1S208_79
+New.CleanUp.ReferenceOTU2 L1S257_85
+New.CleanUp.ReferenceOTU3 L1S257_80
+New.CleanUp.ReferenceOTU4 L1S76_81 L1S140_70 L1S8_6 L1S76_31 L1S208_60 L1S208_83
+New.CleanUp.ReferenceOTU5 L1S8_28
+New.CleanUp.ReferenceOTU6 L1S208_7 L1S281_19 L1S208_57 L1S257_55 L1S281_8
+New.CleanUp.ReferenceOTU7 L1S281_37
+New.CleanUp.ReferenceOTU8 L1S76_40
+New.CleanUp.ReferenceOTU9 L1S281_59
+New.CleanUp.ReferenceOTU10 L1S8_17
+New.CleanUp.ReferenceOTU11 L1S8_49
+New.CleanUp.ReferenceOTU12 L1S76_39
+New.CleanUp.ReferenceOTU13 L1S57_33
+New.CleanUp.ReferenceOTU14 L1S76_11
+New.CleanUp.ReferenceOTU15 L1S140_44
+New.CleanUp.ReferenceOTU16 L1S76_13 L1S257_63 L1S105_35 L1S8_84
+New.CleanUp.ReferenceOTU17 L1S208_46 L1S257_36
+New.CleanUp.ReferenceOTU18 L1S105_75
+New.CleanUp.ReferenceOTU19 L1S105_10 L1S105_56
+New.CleanUp.ReferenceOTU20 L1S8_4 L1S8_23 L1S76_21 L1S8_53 L1S140_18 L1S57_41 L1S281_78 L1S76_25 L1S76_73 L1S281_43 L1S140_9
+New.CleanUp.ReferenceOTU21 L1S140_45 L1S208_48 L1S105_50 L1S257_5 L1S257_27 L1S257_54 L1S281_2 L1S105_16 L1S140_47 L1S57_30 L1S105_34
+New.CleanUp.ReferenceOTU22 L1S208_15 L1S257_22 L1S140_67 L1S140_69 L1S57_52 L1S57_62 L1S281_64 L1S140_26 L1S105_71 L1S76_82 L1S208_58 L1S208_14 L1S140_32 L1S208_3 L1S281_12 L1S57_68 L1S76_74 L1S76_61 L1S8_38 L1S105_29
+New.CleanUp.ReferenceOTU23 L1S281_72
+New.CleanUp.ReferenceOTU24 L1S76_51
+New.CleanUp.ReferenceOTU25 L1S57_77 L1S57_42
+New.CleanUp.ReferenceOTU26 L1S8_20
+New.CleanUp.ReferenceOTU27 L1S281_66
+New.CleanUp.ReferenceOTU28 L1S140_0

diff -r 000000000000 -r c11972e98d44 test-data/pick_open_reference_otus/1_final_otu_map_mc.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_open_reference_otus/1_final_otu_map_mc.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,10 @@
+4374484 L1S8_76 L1S281_24 L1S105_1
+New.CleanUp.ReferenceOTU4 L1S76_81 L1S140_70 L1S8_6 L1S76_31 L1S208_60 L1S208_83
+New.CleanUp.ReferenceOTU6 L1S208_7 L1S281_19 L1S208_57 L1S257_55 L1S281_8
+New.CleanUp.ReferenceOTU16 L1S76_13 L1S257_63 L1S105_35 L1S8_84
+New.CleanUp.ReferenceOTU17 L1S208_46 L1S257_36
+New.CleanUp.ReferenceOTU19 L1S105_10 L1S105_56
+New.CleanUp.ReferenceOTU20 L1S8_4 L1S8_23 L1S76_21 L1S8_53 L1S140_18 L1S57_41 L1S281_78 L1S76_25 L1S76_73 L1S281_43 L1S140_9
+New.CleanUp.ReferenceOTU21 L1S140_45 L1S208_48 L1S105_50 L1S257_5 L1S257_27 L1S257_54 L1S281_2 L1S105_16 L1S140_47 L1S57_30 L1S105_34
+New.CleanUp.ReferenceOTU22 L1S208_15 L1S257_22 L1S140_67 L1S140_69 L1S57_52 L1S57_62 L1S281_64 L1S140_26 L1S105_71 L1S76_82 L1S208_58 L1S208_14 L1S140_32 L1S208_3 L1S281_12 L1S57_68 L1S76_74 L1S76_61 L1S8_38 L1S105_29
+New.CleanUp.ReferenceOTU25 L1S57_77 L1S57_42

diff -r 000000000000 -r c11972e98d44 test-data/pick_open_reference_otus/1_rep_set_tree.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_open_reference_otus/1_rep_set_tree.tre Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,1 @@
+((New.CleanUp.ReferenceOTU6:0.13597,((4374484:0.03298,New.CleanUp.ReferenceOTU19:0.00653)0.990:0.22089,(New.CleanUp.ReferenceOTU25:0.13896,(New.CleanUp.ReferenceOTU17:0.00014,New.CleanUp.ReferenceOTU4:0.08814)0.473:0.04881)0.689:0.03524)0.970:0.13853)0.985:0.16118,New.CleanUp.ReferenceOTU20:0.02491,(New.CleanUp.ReferenceOTU22:0.0388,(New.CleanUp.ReferenceOTU21:0.02398,New.CleanUp.ReferenceOTU16:0.00821)0.154:0.00746)0.348:0.0136);

diff -r 000000000000 -r c11972e98d44 test-data/pick_open_reference_otus/2_final_otu_map.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_open_reference_otus/2_final_otu_map.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/pick_open_reference_otus/2_final_otu_map_mc.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_open_reference_otus/2_final_otu_map_mc.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,7 @@
+4374484 L1S8_76 L1S281_24 L1S105_1
+New.CleanUp.ReferenceOTU4 L1S76_81 L1S140_70 L1S8_6 L1S76_31 L1S208_60 L1S208_83
+New.CleanUp.ReferenceOTU6 L1S208_7 L1S281_19 L1S208_57 L1S257_55 L1S281_8
+New.CleanUp.ReferenceOTU16 L1S76_13 L1S257_63 L1S105_35 L1S8_84
+New.CleanUp.ReferenceOTU20 L1S8_4 L1S8_23 L1S76_21 L1S8_53 L1S140_18 L1S57_41 L1S281_78 L1S76_25 L1S76_73 L1S281_43 L1S140_9
+New.CleanUp.ReferenceOTU21 L1S140_45 L1S208_48 L1S105_50 L1S257_5 L1S257_27 L1S257_54 L1S281_2 L1S105_16 L1S140_47 L1S57_30 L1S105_34
+New.CleanUp.ReferenceOTU22 L1S208_15 L1S257_22 L1S140_67 L1S140_69 L1S57_52 L1S57_62 L1S281_64 L1S140_26 L1S105_71 L1S76_82 L1S208_58 L1S208_14 L1S140_32 L1S208_3 L1S281_12 L1S57_68 L1S76_74 L1S76_61 L1S8_38 L1S105_29

diff -r 000000000000 -r c11972e98d44 test-data/pick_open_reference_otus/3_final_otu_map.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_open_reference_otus/3_final_otu_map.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/pick_open_reference_otus/3_final_otu_map_mc.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_open_reference_otus/3_final_otu_map_mc.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,3 @@
+New.CleanUp.ReferenceOTU20 L1S8_4 L1S8_23 L1S76_21 L1S8_53 L1S140_18 L1S57_41 L1S281_78 L1S76_25 L1S76_73 L1S281_43 L1S140_9
+New.CleanUp.ReferenceOTU21 L1S140_45 L1S208_48 L1S105_50 L1S257_5 L1S257_27 L1S257_54 L1S281_2 L1S105_16 L1S140_47 L1S57_30 L1S105_34
+New.CleanUp.ReferenceOTU22 L1S208_15 L1S257_22 L1S140_67 L1S140_69 L1S57_52 L1S57_62 L1S281_64 L1S140_26 L1S105_71 L1S76_82 L1S208_58 L1S208_14 L1S140_32 L1S208_3 L1S281_12 L1S57_68 L1S76_74 L1S76_61 L1S8_38 L1S105_29

diff -r 000000000000 -r c11972e98d44 test-data/pick_open_reference_otus/3_rep_set_tree.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_open_reference_otus/3_rep_set_tree.tre Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,1 @@
+(New.CleanUp.ReferenceOTU20:0.05104,New.CleanUp.ReferenceOTU21:0.02296,New.CleanUp.ReferenceOTU22:0.03307);

diff -r 000000000000 -r c11972e98d44 test-data/pick_open_reference_otus/gg_13_8_79_otus.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_open_reference_otus/gg_13_8_79_otus.fasta Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,2330 @@\n+>1109493\n+AGAGTTTGATCATGGCTCAGAATGAACGCTGGCGGCGTGGATTAGGCATGCAAGTCGAACGAGAAAATACCTTCGGGTATGAGTACAGTGGCGAAAGGGTTAGTAATACATGAACAACCTGCCTTTAAGACGGGGATAACTCGAAGAAATTCGGGCTAATACCCGATGATATCATGTGTCTCAGGGCACATGATCAAATGGTGGTTTTATAATTTCTGCTTAGAGAGGGGTTCATGGCCTACTAGTTTGTTGGTGAGGTAATGGCTCACCAAGACGATGATGGGTAGCCGGGCTGAGAGGCCGATCGGCAACACTGGGACTGAGACACTGCCCAGACTCCTACGGGAGGCTGCAGTCGAGAATCTTCTGCAATGCGCGAAAGCGTGACAGAGCGACGCCGCGTGCGGGATGAAGGCCTACGGGTTGTAAACCGCTGTCAGAGGCTATAAAACGTTGGAGTAACGATCCAACTTGATGTTAGCCTCAAAGGAAGTCATGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGTGGCAAGCGTTATTCGGAATCATTGGGCATAAAGGGCCTGTAGGCGGTCTGTTAAGTTAATTGTGAAATCCCTCGGCTTAACCGGGGAATTGCAGTTAAAACTGGCAGACTTGAGTGTTGGAGGGGTAAGTGGAATTCTTGGTGGAGCGGTGGAATGCGTAGATATCAAGAGGAACGCCGGAGGCGAAAGCGACTTACTGGACAACTACTGACGCTGAGGGGCGAAAGCTAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTAGCCGCTAACTATGAGCACTAGGCGATGGACGTTCCGATACGTTCGTCGCTATAGATAATTCATTAAGTGCTCCGCCTGGGGAGTATAAGCGCAAGCTTGAAACTCAAAGGAATTGACGGGGACTCACACAAGCGGTGGAGGACGTTCTTTAATTCGAAACAACGCGAAGAACCTTACCCAGACTTGACATGCACTTGACCGTCTGTGAAAGCAGATTTCCACTTCGGTGGCGGGTGCACAGGTGTTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTCGGGTTAAGTCCCTTAACGAGCGCAACCCTTGCCACTAATTGCCAACAGGTAAAGCTGGGGACTTTAGTGGGACTGCCGGTGTTAAACCGGAGGAAGGTGGGGACGACGTCAAGTCATCATGGCCCTTACGTCTGGGGCTAGAAACGTCCTACAATGGGTTGAACAATGAGTTGCAAGACCGCGAGGTGGAGCAAATCTCTCAAATCAACCCCAAGTTCGGATAGCAGGCTGAAATTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATATGTTCCTGAGTCTTGTACACACCGCCCGTCAAGCCACCCGAATTGGGAGTATCCTAAGGCATGTACCTAACCGCAAGGAAGGAAGTGCCAAAGGTAAGTCCAGTGAGGGGGACTAAGTCGTAACAAGGTA\n+>1109328\n+ACATGCAAGTCGGGCGGGAAGCGTACTTTCGGGTGCGTGGAGAGTGGCGAACGGGTGAGTAACACGTAGATGACCTGCCTTAGAGAGGGGGACAACTGATGGAAACGTCAGCTAATACCCTATGGACTTGATATAGTTAGAGAGTATTGAGTAAAGGAGCAATCCGCTTTAAGAGGGGTCTGCGGTCTATCAGCTAGTTGGTGGGGTAACGGCGTACCAAGGCGAAGACGGATAGGGGGCGTGAGAGCGCGATCCCCCACAATGGGACTGAGACACGGCCCATACTCCTACGGGAGGCAGCAGTGAGGAATATTGCACAATGGGGGCAACCCTGATGCAGCAATGCCGCGTGGGTGATGAAGGTTTTCGGATTGTAAAGCCCTTTTCTGCGAGAAGAGAGAGGACGGTATCGCAGGAATAAGTCCCGGCTAACTACGTGCCAGCAGCCGCGGTAAAACGTAGGGGGCGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCATGTAGGCGGTAGGGTAAGATAGGCGTGAAAGCTCTCGGCTTAACCGGGAGAGGACGTTTGTGACTGCCGTACTTGAGTGGAGTAGAGGAGAGCGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAAGCGGCTCTCTGGGCTTTAACTGACGTTGAGATGCGAAAGCGTGGGTAGCGAACGGGATTAGATACCCCGGTAGTCCACGCTGTAAACGATGGATGCTAGGTGTAGCGGGTGTAGACCCCTGCTGTGCCGCAGCTAACGCGATAAGCATCCCGCCTGGGGACTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCGTGTGGTTTAATTCGATGATACGCGAAGAACCTTACCTGGGTTTGACATCACCGTGGTAGCGAGGCGAAAGCCGAGTGACCCTTCGGGGAGCGGAGACAGGTGTTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCACGTCGTTAGTTACAAGTGTCTAGCGAGACAGCCGTTATCAAAGCGGAGGAAGGTGTGGACGACGTCAAGTCAGCATGACCTTTATATCCAGGGCGACACACACGCTACAATGGCCGGTACAATGGGCAGCGACCCTGCGAAGGGGAGCGAATCCTGAAAGCCGGTCTCAGTTCGGATAGCAGTCTGCAACTCGACTGCTTGAAGGTGGAGTTGCTAGTAACCGTGCGTCAGCCATAGCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGGAAGCCGGCAACACTTGAAGAGGGTGACCGAACCGCGAGGTAGGAGCTTTCTAGGGTGGGGCTGGTAACTGGGACGAAGTCGTAACAAGGTAGCC\n+>1104783\n+AGCGGCGGACGGGTGAGTAACGCGTGGGTGACCTACCCGGAAGAGGCGGACAACCTGGGGAAACTCAGGCTAATCCGCCATGTGGTCCTATTCTGTGGGGTAGGACTAAAGGGGCGACCCGCTTCCGGATGGGCCCGCGTCCCATCAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGACGGGTAGCCGGTCTGAGAGGATGGCCGGCCACAGGGGCACTGAGACACGGGCCCCACTCCTACGGGAGGCAGCAGTTAGGAATCTTCCGCAATGGACGGAAGTCTGACGGAGCGACGCCGCTTGGAGGAGGAAGCCCTTCGGGGTGTAAACTCCTGAACTGGGGACGAAAGCCCTGGAGAGGGGGATGACGGTACCCAGGTAATAGCGCCGGCCAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGCGCGAGCGTTACCCGGATTTACTGGGCGTAAAGGGCGTGTAGGCGGTTTGGGGCGTCCCATGTGAAAGGCCACGGCTCAACCGTGGAGGAGCGTGGGATACGCTCAAGCTAGAGGGTGGGAGAGGGTGGTGGAATTCCCGGAGTAGCGGTGAAATGCGCAGATACCGGGAGGAACGCCGATGGCGAAGGCAGCCACCTGGCCCATTTCTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACCGGATTAGATACCCGGGTAGTCCACGCCCTAAACGATGCGCGCTAGGTTTTCTGGGTTTACTTGGGGGCGGAAGCCAACGCGTTAAGCGCGCCGCCTGGGGAGTACGGCCGCAAAGGCTGAAACTCAAAGGAAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTTGTTTAAATTTGAAAGCAACGCGAAGAACCTTACCAGGCCTTGACCATGCTAGGGGGACCTAGGGGAAAGCCTGGGGGTGCCCTCCGAGGGGGAGCCCTTAGCACCAGGTGGTGCATGGCCGTCGTCAGCCTCCGTGTTCGTGAGGATGTTTGGGGTTAAAGTTCCCCGCCAAACGAGCGGCA'..b'CGCGAAACCTCCGCAATGCACGCAAGTGTGACGGGGCCATCCCGAGTGCCTTCGGGCTTTTCTACAGTGTAAGAAGCTGTAGGAATAAGGGGAGGGCAAGGCTGGTGCCAGCCGCCGCGGTAAAACCAGCTCCTCAAGTGATTCGGACTTTTACTGGGCCTAAAGCGTCCGTAGCCGGGCCTGCAAGTCTTCGGTTAAATCCGGCAGCTTAACTGTCGGCCCGCTGGAGATACTACAGGTCTAGGAGGCGGAAGAGGTAGAGGGTACTCCTTGGGTAGGGGTGAAATCCGATAATCCAAGGGGGACCACCAGTGGCGAAGCGCTCTACTGGGACGCGCTCGACGGTGAGGGACGAAAGCCAGGGGAGCGAACCGGATTAGATACATGTTTGCATGTTTAGCATTATGCTAAATACCCGGGTAGTCCTGTGCTGTAAACGATGCGAGCTAGGTGTTGGTCCAGCCACGAGCTGGATCAGTGCCGAAGGGAAGCCGTTAAGCTCGCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCACCACAAGGGGTGAAGCCTGCGGTTTAATTGGACTCAACGCCGTGAAGCTTACCAGGGGCGACGACAGAATGAAGGTCAGGCTGACGACCTTACCAGACAAGTCGAGAGGAGGTGCATGGCCGTCGTCAGTTCGTGCCGTGAGGTGTCCTGTTAAGTCAGGCAACGAACGAAACCCACGCCCACAGTTGCGAGCAGATTCCTTCGGGGATGCTGGGCACTCTGTGGGGACTGCCAGCGATAAGTTGGATGAAGGTGTGGGCCACGGCAGGTCAGTATGCCCCGAATCCCCTGGGCCACACGCGGGCTGCAATGGCGAGTACAATGGGTTGCTACACCGAAAGGTGACGCTAATCCCGAAACCTCGTCGTAGTTAGGATCGAGGGTTGCAACTCACCCTCGTGAATATGGAATCCCTAGTAATCGCGTGTCATCATCGCGCGGTGAATACGTCCCTGCTCCTTGCACAC\n+>4455990\n+GATGCTGGAATGCCCTGTAATCCAAAGTTCCGACGCCCTAGGATGGATCTGCGGCCGATTAGGTTGTTGTTGGGGTAATGGCCCAACAAGCCCGTAATCGGTACGGGTTGTGGGAGCAAGAGCCCGGAGTTGGATTCTGAGACACGAATCCAGGCCCTACGGGGCGCAGCAGGCGCGAAAACTTTACAATGCGGGCAACCGTGATAAGGGAACCTCGAGTGCCTGTAAATGCAGGCTGTTCAGGTGCCTAAAACACACCTGAATAAAGGGCCGGGCAAGACCGGTGCCANGCCGCCGTCGGTAATACCGGCGGCTCGAGTGGTGGCCGCTTTTATTGGGCTTAAAGCGTTCGTAGCTGGGTTGTTAAGTCTCTTGGGAAATCTGGCGTGCTTAACCGTCAGGCGTCTAACGGGATACTGGCAATCTTGGAACCTCGGCTCGAGTGGTGGCCGCTTTTATTGGGCTTAAAGCGTTCGTAGCTGGGTTGTTAAGTCTCTTGGGAAATCTGGCGGCTTAACCGTCAGGCGTCTAAGGGATACTGGCAATCTTGGAACCGGGAGAGGTGAGGGGTACTTCGGGGGTAGGAGTGAAATCCTGTAATCCTCGAGGGACCACCTGTGGCGAAGGCGCCTCACCAGAACGGCTTCGACAGTGAGGGACGAAAGCTGGGGGAGCAAACCGGATTAGATACCCGGGTAGTCCCAGCCGTAAACTATGCGCGTTAGGTGTATCGGTGACCACGAGTTACCGAGGTGCCGAAGGGAAACCGTGAAACGTGCCGCCTGGGAAGTACGGTCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCACCACAACAGGTGGAGCCTGCGGTTTAATTGGACTCAACGCCGGGAAGCTCACCGGATAAGACAGCAGAATGATTGCCGGGCTGAAGACTCTGCATGACTAGCTGAGAGGAGGTGCATGGCCGTCGTCAGTTCGTACTGTGAAGCATCCTGTTAAGTCAGGCAACGAGCAAGACCCACGCCAACAGTTGCCAGCATGGTCTCCGGACTGATGGGGACACTGTTGGGACCGCCTCTGCTAAAGAGGAGGAAGGAATGGGCAACGGTAGGTCAGCATGCCCTGAATTATCCGGGCTACACGCGGGCTACAATGGGCAGGACAATGGGCATCGACACCGAAAGGTGAAGGCAATCTCCTAAACCTGTCCTTAGTTCGGATTGTGGGCTGCAACTCGCCCACATGAAGCTGGAATCTGTAGTAATCGCGTTTCAAAATAACGCGGTGAATTTGTCCCTGCTCCTTGCACACACCGCCCGTCAAACCACCCGAGTGGGGTTTGGATGAGGTTGCGGTTGTTGCCGCAGTCGAATCTAGGTTCCGCAAGGGGGGTTAAGTCGTAACAAGGTAGCCGTAGGGGAATCTGC\n+>4479984\n+TTCCGGTTTGATCCTGCCGGAGGTCACTGCTATTGGAGTCCGACTAAGCCATGCGAGTGCTTTGGGTATCCTCTTCTGAGGAGACCTGAAGTGCGAACTGCTCAGTAACACATAGTCAATCTGCCCTTAGGTTCACCATAATCTCAGGAAACTGAGGATAAAGGGGGATAGGATAGGTGTTCTGGAAAGAGCCTATCTGAATCTTACCTAAGGATGAGACTATGTCTGATTAGGTTGTTGTTGGGGTAACGGCCCAACAAGCCGATAATCAGTACGGGCCATGAGAGTGGGAGCCCGGAGATGAACTCTGAGACATGAGTTCAGGCCCTACGGGGCGCAGCAGGCGCGAAACCTTTACAATGCACGCAAGTGTGATAGGGGGTCTCCAAGTGCTTTCTCTTAAACAGAGACAGCTTTTGCTGAGTGAAAAAAGCTCAGCGAATAAGTGGTGGGTAATAAACTGCTGAGTCAAGGAATTAATAATACACTTGGTTCACAGTTTACCAAACGGGTGGCAGCCGCCGCGGTAATACCCGAGCCACAAGTGGTGACCACTTTTATTGGGTTTAAAGCATCCGTAGCCGGCCAGGTAAGTTTCTGGTTAAATCCCTTGTTAACCAAGGAACTGCCAGAAATACTATCTTGCTTGAGACCGGGAGAGGCTGGAGGTACTCTTAGGGTAGGGGTGAAATCCGTTGATCCTAAGGGGACCACCAATGGTGAAGGCATCCAGCCAGAACGGCTCTGACGGTGAGGGATGAAAGCTAGGGGAGCGATCGGGATTAGATACCCCGGTAGTCCTAGCCGTAAACGATGCCCGCTAGGTGTTGGCTGGTTTGTAGGAATCAGTCAGTGCCGAAGGGAAACCATTAAGCGGGCCACCTGGGGAGTACGGTCGCAAGGCCGAAACTTAAAGGAATTGGCGGGGRAGCACATAAGGGGTGAGGTGTGCSGWTTAATTGGACTCAACACCGAGGRTCTTACCAGCGGAGACAGCAGGATGAAGGTCAGGCTAAAGACCTTACCAGACAAGCTGAGAGGAGTTGCATGGCCGTCGTCAGCTCGTGCTGTGAAGTGTCCGGTTAAGTCCGGCAACGAGCGAGACCCACACTGCTAGTTGCTATCTTCATAAGAAGCACTCTAACAGGACTGCCTGCGTAAGCAGGAGGAAAGTTTTACAGTTTGATTATTATATAGCAAGCTGTAAAGCCTTTAAGGAGTGGGCGACGGCAGGTCAGTATAGCCCGAATCCGCTGGGCTACACGCGCGCAACAATGGCTAAAACAGAGGGTTGCAACGCCGAAAGGCGAAGCTAATCCCTAAATTTAGCCTCAGTTCAGATCGAGGGCTGAAACTCGCCCTCGTGACGACGGAATCCCTAGTAATCGAACGTCAGCATCGTTCGATGAATATATCCCTGCTCCTTGCACACACTGCCCGTCAAGCCATCCGAGTAGAGTCTTGAGGAAGCTTGCTCCATATGGAGTAATCAACCTTGGGCTTTGCGAGGAGGGCTAAGTCGTAACAAGGTAGC\n'

diff -r 000000000000 -r c11972e98d44 test-data/pick_open_reference_otus/sequences.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_open_reference_otus/sequences.fasta Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,172 @@\n+>L1S140_0 HWI-EAS440_0386:1:25:1851:1463#0/1 orig_bc=ATGGCAGCTCTA new_bc=ATGGCAGCTCTA bc_diffs=0\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGACATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATA\n+>L1S105_1 HWI-EAS440_0386:1:25:4646:1592#0/1 orig_bc=AGTGCGATGCGT new_bc=AGTGCGATGCGT bc_diffs=0\n+AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTG\n+>L1S281_2 HWI-EAS440_0386:1:25:4380:1628#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTA\n+>L1S208_3 HWI-EAS440_0386:1:25:1510:1668#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAG\n+>L1S8_4 HWI-EAS440_0386:1:25:3929:1715#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTG\n+>L1S257_5 HWI-EAS440_0386:1:25:2639:1894#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTAGAGGCAG\n+>L1S8_6 HWI-EAS440_0386:1:25:6139:2018#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGTACTAGAGTGT\n+>L1S208_7 HWI-EAS440_0386:1:25:3109:2059#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n+TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATTTCGGGGCTCAACCCTGAACGTGCCTCTAATACTGTTGAGCTAGAGAGTAGTTGCGGTAGG\n+>L1S281_8 HWI-EAS440_0386:1:25:7669:2080#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n+TACGGAGGATCCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATTTCGGGGCTCGACCCTGAACGTGCCTCTAATACTGTTGAGCTAGAGAGTAG\n+>L1S140_9 HWI-EAS440_0386:1:25:3922:2110#0/1 orig_bc=ATGGCAGCTCTA new_bc=ATGGCAGCTCTA bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACAGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTT\n+>L1S105_10 HWI-EAS440_0386:1:25:3806:2202#0/1 orig_bc=AGTGCGATGCGT new_bc=AGTGCGATGCGT bc_diffs=0\n+AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGTGTAAAGGGAGCGCAGGCGGGAGAACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAG\n+>L1S76_11 HWI-EAS440_0386:1:25:6540:2228#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGAAGGCTAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGGTCATCTA\n+>L1S281_12 HWI-EAS440_0386:1:25:2668:2254#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTT\n+>L1S76_13 HWI-EAS440_0386:1:25:5054:2329#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACAGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCTG\n+>L1S208_14 HWI-EAS440_0386:1:25:8482:2380#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAG\n+>L1S208_15 HWI-EAS440_0386:1:25:8261:2388#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAG\n+>L1S105_16 HWI-EAS440_0386:1:25:9735:2401#0/1 orig_bc=AGTGCGATGCGT new_bc=AGTGCGATGCGT bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAG\n+>L1S8_17 HWI-EAS440_0386:1:25:8948:2437#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n+TACG'..b'GATACTGGATATCTTGAGTGCAGTTGAGGCAGG\n+>L1S140_69 HWI-EAS440_0386:1:25:4994:3354#0/1 orig_bc=ATGGCAGCTCTA new_bc=ATGGCAGCTCTA bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAG\n+>L1S140_70 HWI-EAS440_0386:1:25:12091:3381#0/1 orig_bc=ATGGCAGCTCTA new_bc=ATGGCAGCTCTA bc_diffs=0\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGTACTAGAGTGTCGG\n+>L1S105_71 HWI-EAS440_0386:1:25:8594:3395#0/1 orig_bc=AGTGCGATGCGT new_bc=AGTGCGATGCGT bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTT\n+>L1S281_72 HWI-EAS440_0386:1:25:2052:3400#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTTTTGCAAGTCTGAAGTGAAAGCCCGGGGCTTAACCCCGGGACTGCTTTGGAAACTGTAGGAC\n+>L1S76_73 HWI-EAS440_0386:1:25:11776:3405#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAG\n+>L1S76_74 HWI-EAS440_0386:1:25:11052:3431#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGA\n+>L1S105_75 HWI-EAS440_0386:1:25:9796:3444#0/1 orig_bc=AGTGCGATGCGT new_bc=AGTGCGATGCGT bc_diffs=0\n+TACGTATGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGTGTAGGTGGCCATGCAAGTCAGAAGTGAAAATCCGGGGCTCAACCCCGGAACTGCTTTTGAAACTGTGAGGCTAGAGTGCAGGAGGGGTGAGTGGAATTCCTAGTG\n+>L1S8_76 HWI-EAS440_0386:1:25:2235:3462#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n+AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAGTCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCA\n+>L1S57_77 HWI-EAS440_0386:1:25:6708:3509#0/1 orig_bc=ACACACTATGGC new_bc=ACACACTATGGC bc_diffs=0\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAAGGCAAGTCTGATGTGAAAACCCAGGGCTTAACCCTGGGACTGCATTGGAAACTGTCTGGCTCGAG\n+>L1S281_78 HWI-EAS440_0386:1:25:13919:3507#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGG\n+>L1S208_79 HWI-EAS440_0386:1:25:7788:3570#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGTCTGAAGTGAAATGCGGGGGCTCAACCCCTGAACTGCTTTGGAAACTGTCATGCTAGAGTGCAGGAGGGGTGAGCGGAATTCCTAGTG\n+>L1S257_80 HWI-EAS440_0386:1:25:14850:3657#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTGGTAATTTAAGTCAGCGGTGAAAGTTTGTGGCTCAACCATAAAATTGCCGTTGAAACTGGGTTACTTGAGTG\n+>L1S76_81 HWI-EAS440_0386:1:25:11581:3662#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGTACTAGAGTGTCGGAGGG\n+>L1S76_82 HWI-EAS440_0386:1:25:16965:3660#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAGTTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAG\n+>L1S208_83 HWI-EAS440_0386:1:25:8197:3691#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGGACTAGAGTGTCG\n+>L1S8_84 HWI-EAS440_0386:1:25:11617:3701#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACAGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCTGTCTTGAG\n+>L1S257_85 HWI-EAS440_0386:1:25:15484:3705#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n+TACGGAGGATCCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTAGTAAGTCAGCGGTGAAATTTTGGTGCTTAACACCAAACGTGCCGTTGATACTGCTGGGCTAGAGAGTAGTTGCGG\n'

diff -r 000000000000 -r c11972e98d44 test-data/pick_otus/refseqs.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_otus/refseqs.fasta Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,300 @@\n+>378462\n+GATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGAACAGATAAGGAGCTTGCTCCTTTGACGTTAGCGGCGGACGGGTGAGTAACACGTGGGTAACCTACCTATAAGACTGGAATAACTCCGGGAAACCGGGGCTAATGCCGGATAACATGTTGAACCGCATGGTTCTACAGTGAAAGGCGGCTTTGCTGTCACTTATAGATGGACCCGCGCCGTATTAGCTAGTTGGTGAGGTGACGGCTCACCAAGGCAACGATACGTAGCCGACCTGAGAGGGTGATCGGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACAAATGCGTAAGTAACTGTGCGCGTCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGGAGGGTCATTGGAAACTGAAAAAACTTGAGTGCAGAGAGGGAAAGTGGAAATCCATGTGTAGCGGTGAAATGCGCAGAGATATGGGAGGAACTCCAGTGGCGAAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGGCCGCAAGGCTTAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAAATCTTGACATCCTTTGACCGCTCTAGAGATAGAGTCTTCCCCTTCGGGGGACAAAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTAAGCTTAGTTGCCATCATTCAGTTGGGCACTCTAAGTTGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGATTTGGGCTACACACGTGCTACAATGGACAATACAAAGGGCAGCGAAACCGCGAGGTCAAGCAAATCCCATAAAGTTGTTCTCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGTAGATCAGCATGCTACGGTGAATACGTTCCCGGGTCT\n+>186233\n+AGAGTTTGATCCTGGCTCAGGATGAACACTAGCTACAGGCTTAACACATGCAAGTCGAGGGGCATCAGTTTGGTTTGCTTGCAAACCAAAGCTGGCGACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCGACAACACTGGGATAGCCTTTCGAAAGAAAGATTAATACCGCATGAAGCAGGGATCCCGCATGGGAATATTTGCTAAAGATTCATCGCTGATAGATAGGCATGCGTTCCATTAGGCAGTTGGCGGGGTAACGGCCCACCAAACCGACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGTACTGAGACACGGACCAAACTCCTACGGGAGGCAGCAGTGAGGAATATTGGTCAATGGCCGAGAGGCTGAACCAGCCAAGTCGCGTGAGGGATGAAGGTTCTATGGATCGTAAACCTCTTTTATAAGGGAATAAAGTGCGGGACGTGTCCCGTTTTGTATGTACCTTATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCCCTTAAGTCAGCGGTGAAAGTCTGTGGCTCAACCATAGAATTGCCGTTGAAACTGGGAGGCTTGAGTATGTTTGAGGCAGGTGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTGCCAAGCCATTACTGACGCTGATGCACGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCAGTAAACGATGATCACTAGCTGTCTGCGATACACTGTAAGCGGCACAGCGAAAGCGTTAAGTGATCCACCTGGGGAGTACGCCGGCAACGGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGAGGAACATGTGGTTTAATTCGATGATACGCGAGGAACCTTACCCGGGTTTGAACGCATTTCGACAGCTCTGGAAACAGAGTCTCTAGCGATAGCGATTTGCGAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTGCCACTAGTTACTAACAGGTAAAGCTGAGGACTCTGGTGGGACTGCCAGCGTAAGCTGCGAGGAAGGCGGGGATGACGTCAAATCAGCACGGCCCTTACATCCGGGGCGACACACGTGTTACAATGGCGTGGACAAAGGGAGGCCACCTGGTGACAGGGAGCGAATCCCCAAACCACGTCTCAGTTCGGATCGGAGTCTGCAACCCGACTCCGTGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCATGGCGCGGTGAATACGTTCCCGGGCCTTGCACACACAGCCCGTCAAG\n+>260529\n+AGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGAAGCATAAGGGAAGGAAGATTCGTCTGACGGAACTTATGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCCCATACCGGGGGATAACATTCAGAAATGAGTGCTAATACCGCATAAGACCACAGTGCCGCATGGCACAGGGGTCAAAACTCCGGTGGTATGGGATGGACCCGCGTCTGATTAGGTAGTTGGCGGGGTAACGGCCCACCAAGCCGACGATCAGTAGCCGACCTGAGAGGGTGACCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGTGAGGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAAATGACGGTACCTGACTAAGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTCCTGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTAAGGCTAGAGTGTCGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGACTACTAGGTGTCGGGTGGCAAAGCCATTCGGTGCCGCAGCCAACGCAATAAGTAGTCCACCTGGGGAGTACGTTCGCAAGAATGAAACTCAAGGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCTGGCCTTGACATCCCCCTGACGTAGGGGCAATGCCCTATTTCTTTCGGGACAGGGGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTTGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTATCTTCAGTAGCCAGCATTACGGATGGGAACTCTGGAGAGACTGCCAGGGACAACCTGGAGGAAGGTGGG'..b'AGCAACGCCGCGTGAAGGAAGAAGGCTTTCGGGTCGTAAACTTTTGTCTGGAGGGACGAATACTGACGGTACCTCCGGAGGAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCGAGCGTTGTCCGGAATTACTGGGTGTAAAGGGCGCGTAGACGGGCATGTAAGTCAGATGTGAAATACCGGGGCTCAACTCCGGGGCTGCATTTGAAACTGCAAGTCTTGAGTGCAGGAGAGGGAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACGATGGGTACTAGGTGTAGGAGGTATCGACCCCTTCTGTGCCGGAGTTAACGCAATAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGGCTTGACATCCAACTAACGAAGCAGAGATGCATTAGGTGCCCTTCGGGGAAAGTTGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTGATTAGTTGCTACGCAAGAGCACTCTAATCAGACTGCCGTTGACAAAACGGAGGAAGGTGGGGACGACGTCAAATCATCATGCCCTTTATGACCTGGGCTACACACGTACTACAATGGTCGTTAACAGAGGGAAGCAATACCGCGAGGTGGAGCAAAACCCTAAAAACGGTCTCAGTTCAGATTGTAGGCTGCAACTCGCCTACATGAAGTTGGAATTGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGCACTCACCGCCCGTCA\n+>81732\n+AGAGTTTGATCCTGGCTCAGAACGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGAGAAAGTCCTGCTTGCAGGATGAGTAAAGTGGCGCACGGGTGAGTAACACGTGGATAATCTGCCTTTAAGCGAGGAATAACACTTCGAAAGGAGTGCTAATACCTCATAATGTTATTTTCTCTTCGGAGAGAATAGCCAAAGGTGACCTCTGTCTCAAGTTGCCGCTTAGAGATGAGTCCGCGGCCCATTAGCTAGTTGGTAGGGTAAAAGCTTACCAAGGCGACGATGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGAGATACGGTCCAGACTCCTACGGGAGGCAGCAGTGAGGAATCTTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGTGTGAGTGATGAAGGTCTTCGGGTCGTAAAGCTCTGTTTGAAGGGACGAAACGTATTTGATTAATACTCAAATAACTTGACGGTACCTTCAGAGGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTGTTCGGAATCACTGGGCGTAAAGGGCGTGTAGGTGGCTAATTAAGTCAGGTGTGAAATCCTTCCGCTTAACGGGAGAAGTGCACTTGAAACTGCTTAGCTAGAGTACGGGAGAGGAAGGTGGAATTCCTGGTGTAGAGGTGAAATTCATAGATATCGGGAAGAACACCGGTGGCGAAGGCGGCCTTCTGGCCCGATACTGACGCTGAGACGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGTTGGGCACTAGGTGTGGGAGGTTTTTATTCCTTCTTTGCCGAAGCTAACGCATTAAGTGCCCCGCCTGGGGAGTACGGTCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGCAACGCGAAAAACCTTACCTGGGCTTGACATGCTGGTAGTAGTGAACCGAAAGGGAAACGATCCTGAGCAATCAGGAAGCCAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGTAACGAGCGCAACCCCTACCTTTATTTGCCATCATTTAGTTGGGCACTCTAAAGGAACCGCCTCGGTCAACGGGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCTTTATGCCCAGGGCTACACACGTGCTACAATGGCCAGTACAAAGGGCCGCGAACCCGCGAGGGTAAGCAAATCCCAAAAACCTGGTCTCAGTTCGGATTGGAGTCTGCAACTCGACTCCATGGAGTCGGAATCGCTAGTAATCGCAGATCAGCGTGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAAAGTCGATTATACCAGAAGTCGCTGGTTTAACCCCCGATTTATCTCGGGGGAGATAAGCGCCTAAGGTATGGTTGGTAATTGGGGTGAAGTCGTAACAAGGTAGCCGTAGGGAACCTGCGGCTGGATCACCTC\n+>151679\n+AACGCTGGCGGCGTGCTTAACACATGCAAGTCGAGCGACGCTCTCCCTTCGGGGGGATGACGGAGCGGCGAACGGGTGAGTAACACGTGGGCAACCTGCCCCTCGCTCTGGGACAACCCGGGGAAACTCGGGCTAATACCGGATACGACCGACTCGGGCATCCGATGTTGGTGAAAAGTTTTTCGGCGAGGGATGGGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGATGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGCGACCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCGCAATGGGCGAAAGCCTGACGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGCAGGGACGAATTCAGAGTGACGGTACCTGCAGAAGAAGCACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTCTGTCGCGTCGGCTGTGAAAACTCGGGGCTCAGCCCCGAGCCTGCAGTCGATACGGGCAGACTAGAGTGCTGTAGGGGAGACTGGAATTCCTGGTGTAGCGGTGAGATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTGCTAGGTGTGAGCGGTATTCCGCGCCGTTCGTGCCGCAGCTAACGCATTAAGCACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCATGTGGCTTAATTCGACGCAACGCGAAGAACCTTACCAAGGCTTGACATACACCGAAAACTCGTAGAGATACGGGGTCCGCAAGGGCGGTGTACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCGTTCTATGTTGCCAGCACATCATGGTGGGGACTCATAGGAGACTGCCGGGGCCAACTCGGAGGAAGGTGGGGACGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTGCACACATGCTACAATGGCCGGTACAAAGGGCTGCTAAGCCGCGAGGTGGAGCGAATCCCAAAAAGCCGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTTGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCACGAAAGTCGGTAACACCCGAAGCCAGTGGCCCAACCGTTCGCGGAGGGAGCTGTCGAAGGTGGGAC\n'

diff -r 000000000000 -r c11972e98d44 test-data/pick_otus/seqs.aligned.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_otus/seqs.aligned.fna Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,306 @@\n+>PC.634_1 FLP3FBN01ELBSX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0 RC:1..217\n+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C--C-TA-G--C-C-CAT--GT-G------------------------------------------------------------------T-CC----GGG-AT-AA-CTG-------------------------C-T-G-----------------------GAA-A---CGG-TAG-CTAA-AA---CC-G--G-AT-A----------G----------------------G--T-A-T--A--C-----------------AG---AG-C-----------------------------------------------------------------------------------------------------------------------G-CA-T--------------------------------------------------------------------------------------------------------------------------------------G-C-T--C-A---------------G--T-A-T-A-T-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAA-GCGCCCATC-----A-----------------------------------------------------------------------------------------------------------------------------AGG--------------------------------------------------------------------------------------------------------------------------------CG--T---G-A--------------A----C-A---T-G--G---AT---G-G-----A-CCT-GCG--G-CGC--A------TT--A--G-CT-A----G---TTGG-T-G-AG-G-T----AAC-GG-C-C-C-ACCA--A-GG-C-G--A-TG-A------------TGC-G-T------AG-CC-G-G-CCT-G-AG----A--GG-GT--A-AA-C-GG-CCAC-A-TTGGG--A-C-TG-A-GA-C-AC-G-G-CCCAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------'..b'--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n'

diff -r 000000000000 -r c11972e98d44 test-data/pick_otus/seqs.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_otus/seqs.fna Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,306 @@\n+>PC.634_1 FLP3FBN01ELBSX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTTACCCTCTCAGGCCGGCTACGCATCATCGCCTTGGTGGGCCGTTACCTCACCAACTAGCTAATGCGCCGCAGGTCCATCCATGTTCACGCCTTGATGGGCGCTTTAATATACTGAGCATGCGCTCTGTATACCTATCCGGTTTTAGCTACCGTTTCCAGCAGTTATCCCGGACACATGGGCTAGG\n+>PC.634_2 FLP3FBN01EG8AX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGCCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACAACCTAATGGAACGCATCCCCATCGATGACCGAAGTTCTTTAATAGTTCTACCATGCGGAAGAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCA\n+>PC.354_3 FLP3FBN01EEWKD orig_bc=AGCACGAGCCTA new_bc=AGCACGAGCCTA bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTTAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCTTACCAACTAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGACATGCGTCTAGTGTTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCTTGGG\n+>PC.634_60 FLP3FBN01DVIVE orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACCAGCTAATGCGCCGCATGCCCATCCATAGCCGCCTCAACTTTCCTCCCCAAGGGATGCCCCTCAGGGAGTGCACGCGGATTTAGACCGGATTTCTCCGGATTATTCCCCTGACAAGGGTAGGTTGCATACGTGTTACTCACCCGTGCGCCGG\n+>PC.636_61 FLP3FBN01EQVOU orig_bc=ACGGTGAGTGTC new_bc=ACGGTGAGTGTC bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTTGGTGAGCCATTACCTCACCAACTAACTAATACGCCGCGGGATCATCTAAGAGCGACAGCAAAGCCGTCTTTCATTCATGAACCATGCGGTTCGCGAATCTATGCGGTATTAGCATCCGTTTCCGAATGTTATCCCCCACTCCTAGGCAGATTCCCC\n+>PC.355_291 FLP3FBN01D86I8 orig_bc=AACTCGTCGATG new_bc=AACTCGTCGATG bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCTGTTACCCCGCCAACCAGCTAATCAGACGCGGATCCATCGTATACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCACCTATTTCTAACTGTTATCCCCTGTATGAGGCAGGTTACCCACGCGTT\n+>PC.481_292 FLP3FBN01COOOS orig_bc=ACCAGCGACTAG new_bc=ACCAGCGACTAG bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGGTTAGGTGGGCCGTTACCCCGCCTACTGCCTAATGCGCCGCATGCCCATCCTCCACCGGTAATCCTTTCCTCCCCCAAGGATGCCCCCAAGGGATATACGCGGGATTAGCCTCCCTTTCGGAAGGTTGTCCCCCTGTGGAGGGCAGGTTGCATACGTGTTACTCACCCGTGCGCCAGTCGCCGGCAG\n+>PC.355_293 FLP3FBN01D8J4C orig_bc=AACTCGTCGATG new_bc=AACTCGTCGATG bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCCCGCCGACTAGCTAATGCGCCGCATGCCCATCCGCCACCGGTAATCCCTTTGGCACCAACAGGATGTCCCATAGGTGCATTATGCCGTATTAGACGGAATTTCTCCCGATTATCCGGCTGTGGCAGGCAGGTTGCATACGTGTTACT\n+>PC.636_294 FLP3FBN01BR61D orig_bc=ACGGTGAGTGTC new_bc=ACGGTGAGTGTC bc_diffs=0\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCCCGCCGACTAGCTAATGCGCCGCATGCCCATCCGCCACCGGTAATCCCTTTGGCGGCACCGGGATGCCCCGACGCCGCGTCACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGTGGCGGGCAGGTTGCATACGTGTTACTCACCCGTGCGCCGGTTTAATC\n+>PC.356_295 FLP3FBN01BF0UO orig_bc=ACAGACCACTCA new_bc=ACAGACCACTCA bc_diffs=0\n+CTGGACCGTGTCTCAGTTCCAGTGTGGGGGGCCTTCCTCTCAGAACCCCTACGCATCGTCGCCACGGTGGGCCGTTACCCCGCCGTCAAGCTAATGCGCCGCATGCCCAGCCGCCACCGGATTCCTCCTTTCGCCCGGTCCGGATGCCCGGTCCGGGCGGCATGGGGTATTAGGCCGGGTTTCCCCGGGTTATCCCCCTCGTGGCGGGCAGGTTCCATACGTGTTACTCACCCGTGCGCCGGTCGCCGGCAGGTG\n+>PC.354_296 FLP3FBN01DB7BE orig_bc=AGCACGAGCCTA new_bc=AGCACGAGCCTA bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTTGCCTTGGTGGGCCGTTACCCCTCCAACTAGCTAATCAGACGCGGGTCCATCTCATACCGTCTCGGCTTTTCACCCCGAACCATGCGGTTCTGTGTGCTTATGCGGTATTAGCAGTCATTTCTAACTGTTATCCCCCTGTATGAGGCAGGTTACCCACGCGTTACTCACCCGTCCG\n+>PC.607_297 FLP3FBN01AZSCT orig_bc=AACTGTGCGTAC new_bc=AACTGTGCGTAC bc_diffs=0\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTATGCATCATCGTCTTGGTGGGCCTTTACCCCGCCAACCAACTAATGCACCGCAGGTCCATCCGCGCCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTCCTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTTACTCACCCG\n+>PC.636_298 FLP3FBN01D3EWI orig_bc=ACGGTGAGTGTC new_bc=ACGGTGAGTGTC bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGGCTTGGTGGTCCGTTACACCGCCAACTACCTAATGCGACGCATGCCCATCCGCTACCGGATC'..b'A new_bc=ACAGACCACTCA bc_diffs=0\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGCCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTGCCCCGCCAACCAGCTAATCAGACGCGGGCCCATCCTGCACCGCCGGAGCTTCCCCCGCCGCCCCATGCGGGGCTGCGGGCATATGCGGTATTAGCAGCCGTTTCCGGCTGTTGTCCCCCAGTGCAGGGCAGGTTGCCCACGCGTTACT\n+>PC.607_457 FLP3FBN01A0QD0 orig_bc=AACTGTGCGTAC new_bc=AACTGTGCGTAC bc_diffs=0\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTATGCATCATCGTCTTGGTGGGCCTTTACCCCGCCAACCAACTAATGCACCGCAGGTCCATCCGCGCCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTCCTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTTACTCACCCG\n+>PC.354_458 FLP3FBN01B3PY0 orig_bc=AGCACGAGCCTA new_bc=AGCACGAGCCTA bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTGGGCCGCTACCCCGCCAACTGGCTAATCAGACGCGGATCCATCGTATACCACCGGAGTTTTTCACACTGTTCCATGCGGAATCGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTGCAAGGCAGGTTACCCACGCGTTACTCACCCG\n+>PC.355_459 FLP3FBN01B533J orig_bc=AACTCGTCGATG new_bc=AACTCGTCGATG bc_diffs=0\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGGCCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACAACCTAATGGAACGCATCCCCATCGATGACCGAAGTTCTTTAATAGTTCTACCATGCGGAAGAACTATGCCATCGGGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCG\n+>PC.355_460 FLP3FBN01EZQR8 orig_bc=AACTCGTCGATG new_bc=AACTCGTCGATG bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGGTGGAGGACCTTCCTCTCCAGAACCCCTAGACATCGTCGCCTTGGTCGGGCCGTTACCCCGCCAACTAGCTAATGTCACCGCATGCCCATCCGTCTCCGGAGTCGCCTCCTTTGGCCGAAGAAGATGCCTCCCCTCGGCCACATGCGGTATTAGGCCGGATTTCTCCGGGTTATCCCGCTGAAACGGGCAGATTGCATACGCGTTACTCACCCG\n+>PC.635_461 FLP3FBN01A2G7F orig_bc=ACCGCAGAGTCA new_bc=ACCGCAGAGTCA bc_diffs=0\n+CTGGGCCGTATCTCAGTCCCAATGTGGCCGGTCAACCTCTCAGTCCGGCTACTGATCGTCGCCTTGGTGAGCCTTTACCTCACCAACTAGCTAATCAGACGCGAGGCCATCTTTCAGCGATAAATCTTTGACATTCAAACCATGCGATTTAAATGTATCATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTCCTCACG\n+>PC.607_541 FLP3FBN01BYGK2 orig_bc=AACTGTGCGTAC new_bc=AACTGTGCGTAC bc_diffs=0\n+CTGGGCCGTGTCTCAGTCCCAGTGTGGCCGTTCACCCTCTCAGGTCGGCTATGTATCGTCGCCTAGGTGAGCCTTTACCTCACCTACTAGCTAATACAACGCAGGTCCATCTGGTAGTGATGCAGTTGCATCTTTCAAACTTCAATCATGCAATCAAAGATATTATGCGGTATTAGCTATCGTTTCCAATAGTTATCCCCCGCTACCAGGCAGG\n+>PC.356_542 FLP3FBN01D868W orig_bc=ACAGACCACTCA new_bc=ACAGACCACTCA bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCCCGCCAACCAGCTAATCAGACGCGGGTCCATCTTGCACCACCGGAGTTTTTCACACTGTCCCATGCAGGACCGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTGCAAGGCAGGTTACCCACGCGTTACTCACCCGTCCG\n+>PC.356_543 FLP3FBN01EAMCO orig_bc=ACAGACCACTCA new_bc=ACAGACCACTCA bc_diffs=0\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACTCTCTCAAGCCGGCTACTGATCGTTGCTTTGGTAGGCCATTACCCTGCCAACTGGCTAATCAGACGCGGGGCCATCGTATGCCGATAACTCTTTTCACACCATGCCATGCAGCATTGTGTGCTTATGCGGTATTAGCAGTCATTTCTGACTGTTGTCCCCCTGCA\n+>PC.355_544 FLP3FBN01B0H89 orig_bc=AACTCGTCGATG new_bc=AACTCGTCGATG bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTTGCTTTGGTAGGCCGTTACCCTGCCAACTGGCTAATCAGACGCGGGTCCATCTCATACCGATAAATCTTTTCCGTCCGTATCATGCGATACTAGCGGGTTATGCGGTATTAGCGGTCGTTTCCAACTGTTATCCCCCTGTATGAGGTAGGTTACCCACGCGTTACTCACCCGTCCGCC\n+>PC.355_545 FLP3FBN01CPQSL orig_bc=AACTCGTCGATG new_bc=AACTCGTCGATG bc_diffs=0\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTTGACTTGGTAGGCCATTACCCCACCAACTATCTAATCAGACGCAAGCCCATCTATTAGCGGATTTCTCCTTTCCCACTAGAACCATGTGGTTCCTATGGCATATGCGGTATTAGCAATGATTTCTCACTGTTATTCCCCTCTAATAGGCAGGTTGCTTACG\n+>PC.355_546 FLP3FBN01DZX6B orig_bc=AACTCGTCGATG new_bc=AACTCGTCGATG bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGTGGACTTGGTGAGCCGTTACCTCACCAACTATCTAATGGAACGCATGCCCATCTATCAGCGATAATTCTTTAACAAATATTTCCATGTGGAACCCCTGTTTTATGCGGTATTAGTCCGACTTTCGCCGGGTTATTCCCTCTGATAGGTAGGTTGCATACGCGTTACTTCACCCGTCGCG\n+>PC.593_547 FLP3FBN01ARBPM orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACTAGCTAATGCGCCGCATGGCCATCCGCAGCCGGTAAACCTTTAAACCACCGGAGATGCCTCCGACGGTTGTTACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTGCGGGCAGGTTCCATACGTGTTACTCACCCGTGCGCCGGTCGCCGG\n'

diff -r 000000000000 -r c11972e98d44 test-data/pick_rep_set/first_otu_fasta.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_rep_set/first_otu_fasta.fasta Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,834 @@\n+>0 PC.635_779\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGTTGACTTGGTGGGCCGTTACCCCGCCAACTATCTAATGGAACGCATCCCCATCGATAACCGAAATTCTTTAATAGTGAAACCATGCGGAAATACTATACTATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTTATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCATCAA\n+>1 PC.636_263\n+CTGGGCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGGCTTGGTGGTCCGTTACACCGCCAACTACCTAATGCGACGCATGCCCATCCGCTACCGGATCGCTCCTTTGGAATCCCGGGGATGTCCCCGGAACTCGTTATGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGTAGCGGGCAGGTTGCATACGTGTTACTCACCCGTCCGCCACTAGGGCG\n+>10 PC.355_740\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCCGGCTACTGATTGTCGCTTTGGTAGGCCGTTACCCCTGCCAACTGGCTAATCAGACGCGGGTCCATCCCATACCACCGGAGTTTTTCACACAGCAACATGCGTTGCCGTGCGCTTATGCGGTATTAGCAGTCATTTCTAACTGTTATCCCCCTGTATGGGGCAGGTTGCCCACGCGTTACT\n+>100 PC.356_1196\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCTGGCTACTGATCGTCGCCTTGGTAGGCCGTTACCCTGCCAACAAGCTAATCAGACGCGGGTCCATCTCGCACCACCGGAGTTTTCAGGGCGGGGGCATGCGCCCCCCTCCCGTTATGCGGTGTTAGCACCTATTTCTGGGTGTTATCCCCCTGTACAGGCCAGGTTGCCCACGCGTTACTCACCCGTCCG\n+>101 PC.634_99\n+CTGGGCCGTGTCTCAGTCCCAGTGTGGCCGGCCACCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTAGGCCGTTACCCCGCCAACCAGCTAATCAGACGCGGGTCCATCCCGTACCACCGGAGTTTTCAAGAAAGGAACATGCGTCCCCTTCTGTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCGGTACGGGGCAGGTTCCCCACGCGTTACTCACCCGTTCGCCACTCGGGCAC\n+>102 PC.634_91\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACCTATCATTGCCTTGGTGGGCCGTTACCCCCCAACTAGCTAATAGGACGCATGCCCATCTGATACCTCGAATGATTTAATTATTAAAAGATGCCTTCAAATAATATTATGGGGTGTTAATCCACGTTTCCATGGGCTATCCCCCTGTATCAGCCAGGTTGCATACGCGTTACTCACCCGTGCGCCGG\n+>103 PC.481_49\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTAGGCCGTTACCCTGCCAACTGGCTAATCAGACGCGGGTCCATCATATACCACCGGAGTTTTTCACACCGGGGCATGCGCCCCTGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCTGTATATGGCAGGTTACCCACGCGTTACTCACCCG\n+>104 PC.607_151\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGGTTAGGTGGGCCGTTACCCCGCCTACTGCCTAATGCGCCGCATGCCCATCCCTGTCCGGCCGAAGCCTTTCCTGCCTCCGGGATGCCCCGGTGGCATGTACGCGGGATTAGCCTCCCTTTCGGAAGGTTGTCCCCCTGTGGAGGGCAGGTTGCATACGTGTTACTCACCCGTGCGCCAGTCGCCGG\n+>105 PC.607_1176\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTTGCCCTCTCAGGCCGGCTACTGATCGTCGGTTTGGTGGGCCGTTACCCCGCCAACTGCCTAATCAGACGCGGGCCCATCCCATACCGCGAAAGCTTTCCATGCAGGGGCATGCGCCCCCGCATGTGCATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGGAAGGCAGGTTCCTCACGCGTTACTC\n+>106 PC.636_850\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGGCTTGGTGGTCCGTTACACCGCCAACTACCTAATGCGACGCATGCCCATCCGCTACCGGATCGCTCCTTTGGAATCCCGGGGATGTCCCCGGAACTCGTTATGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGTAGCGGGCAGGTTGTCCACGCGTTACTCACCCGTCCGCCGCTAAGCC\n+>107 PC.355_301\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCTGTTACCCCGCCAACCAGCTAATCAGACGCGGATCCATCGTATACCACCGGAGTTTTTACCTCAGAACCATGCGGTTCCGCGGTCTTATGCGGTATTAGCAGTCATTTCTAACTGTTATCCCCCTGTGTAAGGCAGGTTGCCCACGCGTTACTCACCCGTCCGCCG\n+>108 PC.355_1283\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTCGCTTTGGTGGGCCGTTACCCCGCCAACTGGCTAATCAGACGCGGGTCCATCTTACACCACTAATGTTTTTCACTCTGTCCCATGCGGGACTGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTATACGGCAGGTTCTCCACGCGTTACTCACCCGTCCG\n+>109 PC.593_1236\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAACCTCTCAGTTCGGCTACGCATCATTGCCTTGGTAAGCCTTTACCCCACCAACTAGCTAATGCGCCGCGGGCCCATCCAAAAGCGGTAGCATAGCCACCTTTTACATAGTTACCATGCGGTAACTATGGTTATGCGGTATTAGCACCTGTTTCCAAGTGTTATCCCCCTCTTTTGGGCAGGTTGCCCACGTGTTACT\n+>11 PC.354_1171\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCCCTCCAACCAGCTAATCAGACGCGGGTCCATCCTGTACCACCGGAGTTTTTCACACCGGACCATGCGGTCCTGTGCGCTTATGCGGTATTAGCAGTCATTTCTAACTGTTGTCCCCCTGTACAGGGCAGGTTACCCACGCGTTACTCACCCGTCCGCC\n+>110 PC.634_170\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGCTGCCCCGCCAACAAGCTAATCAGACGCGGGCCCCTCCCATACCGCCGGAGCTTTCCCCACAAAGGCATGCGCCTCCCTGGTTTATGCGGTATTAGCAGCCGTTTCCGGCTGTTATCCCCCTGTATGAGGCAGGTTGCCCACGCGTTACTCACCCGTCCGCCG\n+>111 PC.634_173\n+TTGGTCCGTGTCTCAGTACCAATGTGGGGGGTTAACCTCTCAGTCCCCCTATGTATCGTTGCCTTGGTGAGCCGTTACCTCACCAACTAGCTAATACAACGCATGCCCATCT'..b'TACGCGTTACTCACCCGTGCGCCGG\n+>85 PC.356_249\n+CTGGGCCGTGTCTCAGTCCCAGTGTGGCCGTCCACCCTCTCAGGCCGGCTGCTGATCGTCGCTTTGGTGGGCCGTTACCCCGCCAACTGGCTAATCGGACGCGGATCCATCGTATGCCGATAAATCTTTTCACACCAGACCATGCGATCCTGTGCGCTTATGCGGTTTTAGCACCTATTTCTAAGTGTTATCCCCCTGTATACGGCAGGTTACCCACGCGTTACT\n+>86 PC.481_1022\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACTCTCTCAAGCCGGCTACTGATCGTCGCTTTGGTAGGCCATTACCCTGCCAACTGGCTAATCAGACGCGGGCCCATCCTGTACCTATAAATATTTGATAGCAATATCATGCGGTATCGCTATGTTATGCGGTGTTAGCAGCCGTTTCCAGCTGTTATCCCCCTGTACAGGGCAGGTTACCCACG\n+>87 PC.481_1025\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGCTGCCCCGCCAACAAGCTAATCAGACGCGGGCCCATCGCATACCACCGGAGTTTTTCACACCAAGCCATGCGGCTCTGTGCGCTTATGCGGTATTAGCAGTCATTTCTAACTGTTATCCCCCTGTGTAAGGCAGGTTGCCCACG\n+>88 PC.481_738\n+CTGGGCCGTATCTCAGTCCCAATGTGGCCGATCGACCTCTCAGTCCGGCTACCCATCGCAGGCTCGGTGGGCCGTTACCCCGCCGACTACCTAATGGGCCGCGACCCCATCTCACACCGCGAGAGCTTTCATCCGGCTAACATGTGTTGGCCGGATAGTATCCGGTATTAGCTACCGTTTCCAGTAGTTATCCCGGTGTGTGAGGCAGGTTGGTCACGTGTTACTCACCCGTTCG\n+>89 PC.635_968\n+CTGGACCGTGTCTCAGTTCCAGTGTGGGGGACCTTCCTCTCAGAACCCCTAGACATCGTCGGCTTGGTGGGCCGTTGCCCCGCCAACTACCTAATGTCGCGCGTGCCCGTCCCGTACCACCGGAATTTTAAATCGAGAGCCATGCGGCTCTCGAGTATCATGGGATGTTAGTCCACGTTTCCGCGGGTTATCTCCCGGTACGGGGTTGGTTGCACACGTGTTACTCACCCGTGCGCCGGTCGCCGGCG\n+>9 PC.481_1193\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTTACCAACCAGCTAATCAGACGCGGGCCCATCCTGTACCACCGTGGTTTTCCCTGCTGTTCCATGCGGCACAGCAGGCTTATGCGGTATTAGCAGCCATTTCTGGCTGTTGTCCCCCGGTACAGGGCAGGTTGCCCACGCGTTACT\n+>90 PC.635_966\n+CTGGACCGTGTCTCAGTTCCAGTGTGGGGGACCTTCCTCTCAGAACCCCTAGACATCGTCGCCTCGGTGGGCCGTTACCCCGCCGACTAGCTAATGCGCCGCATGCCCATCCGTGGCCGGGATTGCTCCCTTTGGCGGCCCGGGGATGCCCCAAGGCCGCGTTACGCGGTATTAGACGGGGTTTCCCCCGCTTATCCCCCTGCCACGGGCAGGTTGCATACGTGTTACTCACCCGTGCGCCGGTCGCCGGCGG\n+>91 PC.635_364\n+CTGGGCCGTGTCTCAGTCCCAGTGTGGCCGTCCGCCCTCTCAGGCCGGCTACTGATCGTGGGCTTGGTGGGCCGTTACCCCGCCAACTACCTAATCAGACGCGGACCCATCGTGTACCGTACTAGATAAGATCTAGGCTTTCCGCCCTGTGCCATGCGGCACTGTGCGCATATGCGGTATTAGCAGCCGTTTCCGGCTGTTATCCCCCTGTACACGGCAGGTTG\n+>92 PC.356_233\n+CTGGGCCGTGTCTCAGTCCCAGTGTGGCCGTCCGCCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTAGGCCGTTACCCTGCCAACTGGCTAATCAGACGCGGGCCCATCCTGTACCACCGGAGTTTTCAGGGAAAAGCCATGCGGCTTCCCCCGTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCTGTACAGGCCAGGTTGCCCACGCGTTACTCACCCGTCCGCCACT\n+>93 PC.635_367\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGGCCAACCTCTCAGTCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTGCCCCGCCAACTAGCTAATCAGACGCGAGCTCATCTCAGAGCGATAAATCTTTGGCGTCCAGAGAGATGCCTCCCAGACGCATCATGCGGTATTAGCGGCTGTTTCCAACCGTTATTCCCCACTCCAAGG\n+>94 PC.593_932\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTACGCATCGTCGCCGTCGGTGGGCCGTTACCCCGCCGACTAGCTAATGCGCCGCATGGCCATCCGCAGCCGATAAATCTTTAAACATCGGGAGATGCCTCCCAACGTTGTTACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTGCGGGCAGGTTCCATACGTGTTACTCACCCG\n+>95 PC.356_238\n+TTGGACCGTATCTCAGTTCCAATGTGGCCGATCAGCCTCTCAGCTCGGCTATGCATCGTTGCCTTGGTAGGCCATTGCCCCACCAACTAGCTAATACACCGCAAGCTCATCCTAAGGTGAAGCAAACGCTTCTTTTAACATATCTAGTTATCTAGTTATGTATCATCCGGTATTAGCGTTCGTTTCCAAACGTTATCCCAGTCCCTAGGGTAGATTACCC\n+>96 PC.481_283\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGAGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTACACCACCGGAGTTTTTCACACCGAACCATGCGGTTCTGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTGCAAGGCAGGTTACCCACGCGTTACTCACCCGTCCG\n+>97 PC.354_773\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTGGGCCGTTACCCCGCCAACTGGCTAATCAGACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACACTACCATGCGGTACTGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTGCAAGGCAGGTTACCCACGCGTTACTCACCCGTCCG\n+>98 PC.636_592\n+CTGGTCCGTGTCTCAGTACCAGCGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGTGGACTTGGTGAGCCGTTACCTCACCAACTATCTAATGGAACGCATGCCCATCTATCAGCGATAATTCTTTAACAAATATTTCCATGTGGAACCCCTGTTTTATGCGGTATTAGTCCGACTTTCGCCGGGTTATTCCCTCTGATAGGTAGGTTGCATACGCGTTACTCACCCGTGCGCCGG\n+>99 PC.356_336\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGCCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTCTACCCCGCCAACAAGCTAATCAGACGCGGGTCCATCGTATACCACCGGAGTTTTTCACACCAGACCATGCGATCCTGTGCGCTTATGCGGTTTTAGCACCTATTTCTAAGTGTTATCCCCCTGTACAGGCCAGGTTGCCCACGCGTTACTCACCCG\n'

diff -r 000000000000 -r c11972e98d44 test-data/pick_rep_set/first_otu_fasta_ref.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_rep_set/first_otu_fasta_ref.fasta Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/pick_rep_set/first_seq_id_fasta.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_rep_set/first_seq_id_fasta.fasta Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,834 @@\n+>184 PC.481_4\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCAGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGGTATTCCGGCGATGCCGCCAAAATCATTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTGCTCACG\n+>374 PC.634_5\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTAGGCCGTTACCCTGCCAACTGGCTAATCAGACGCGGGTCCATCTCACACCGATTAATCTTTTTCCAACCAGAGCATGCGCCCCTGTTGGCTTATGCGGTATTAGCGGTCGTTTCCAACTGTTATCCCCCTGTGTGAGGCAGGTTACCCACGCGTTACTCACCCGTCCG\n+>84 PC.636_6\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCTTATACCGGTAAACCTTTAATCATGAGAAAATGCTCACTCATGATACCATCTTGTATTAATCTCCCTTTCAGAAGGCTATCCAAGAGTATAAGGCAGGTTGGATACGCGTTACTCACCCGTGCGCCGG\n+>377 PC.634_8\n+TTGGTCCGTGTCTCAGTACCAATGTGGGGGGTTAACCTCTCAGTCCCCCTATGTATCGTCGCCTTGGTAAGCCGTTACCTTACCAACCAGCTAATACAACGCATGCCCATCTGTAACCGCCGAAACTTTCAACCACAAGAGATGCCTCTCATAGTGTTATGCGGTATTAGTACCGATTTCTCAGTGTTATCCCCCTGTTACAGGTAGGTTGCATACGCGTTACGCACCCGTGCGCCGGTCG\n+>378 PC.634_9\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCCG\n+>162 PC.355_13\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTCAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCTTACCAACTAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGACATGCGTCTAGTGTTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCTTGGG\n+>25 PC.635_15\n+CTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTAGGCCGTTACCCCACCAACTATCTAATCAGACGCAAGCCCATCTATCAGCGGATTGCTCCTTTCCCATTTATATCATGTGATATTCATGGCATATGCGGTATTAGCAGTCATTTCTAACTGTTGTTCCCCTCTGATAGG\n+>362 PC.635_16\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGGCCTTCCTCTCAGAACCCCTACGCATCGTCGCCACGGTGGGCCGTTACCCCGCCGTCAAGCTAATGTCACGCGAGCCTATCCTCATCCGACGGATCTTTAGATGGAACCAGATGCCTGATTCCATCGCCATGGGGCATTAGACGCCGTTTCCAGCGATTATTCCCCTGATCGAGGGCAAGTTGCATACGCG\n+>309 PC.356_17\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCCCGCCAACCAGCTAATCAGACGCGGGTCCATCCTGCACCGCCGGAGCTTCCCCCGCCGCCCCATGCGGGGCTGCGGGCATATGCGGTATTAGCAGCCGTTTCCGGCTGTTGTCCCCCAGTGCAGGGCAGGTTGCCCACGCGTTACTCACCCGTCCG\n+>412 PC.634_19\n+CTGGACCGTGTCTCAGTTCCAGTGTGGGGGACCTTCCTCTCAGAACCCCTAGACATCGTCGCCACGGTGGGCCGTTACCCCGCCGTCAAGCTAATGTCACGCGAGCCTATCCTCATCCGACGGATCTTTAGATGGAACCAGATGCCTGATTCCATCGCCATGGGGCATTAGACGCCGTTTCCAGCGATTATTCCCCTGATGAGGGCAAGTTGCTCACGCG\n+>267 PC.634_25\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTAGGCCGTTACCCTGCCAACTAGCTAATCAGACGCGGGCCCATCTCATACCACCGGAGTTTTTGCCGCTGCACCATGCGGTGCTGTGGCCTTATGCGGTATTAGCAGCCATTTCTGGCTGTTATCCCCCTGTATGAGGCAGGTTGCCCACG\n+>387 PC.634_34\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTCGGCTTGGTGAGCCGTTACCTCACCAACTACCTAATCAGACGCGGGCCCATCTTACACCACCGGAGTTTTTACCTCAGAACCATGCGGTTCCGCGGTCTTATGCGGTATTAGCAGTCATTTCTAACTGTTATCCCCCTGTGTAAGGCAGGTTGCCCACGCGTTACTCACCCGTCCGCCG\n+>386 PC.634_36\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGCTGCCCCGCCAACAAGCTAATCAGACGCGGGCCCATCCTGTACCACCGGAGTTTTCAGGGAAAAGCCATGCGGCTTCCCCCGTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCTGTACAGGCCAGGTTGCCCACGCGTTACTCACCCGTCCGCC\n+>29 PC.634_41\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTCGGTTTGGTGGGCCGTTACCCCGCCAACTGCCTAATCAGACGCGGGGCCATCTCATACCACCGGAGTTTTTCACACCGTGTCATGCGACACTGTGCGCTTATGCGGCATTAGCAGTCATTTCTAACTGTTATTCCCCTGTATGAGGCAGGTTCCCCACGCGTTACT\n+>28 PC.634_44\n+CTGGGCCGTGTCTCAGTCCCAGTCTGGATGATCATCCTCTCAAACCATCTAACGATCGTCGACTTGGTGAGCCTTTACCTCACCAACTATCTAATCGTACGCAGGCCATTCCTAAAGCGCATAAATGCTTTAATCCGAAGATCATATGCGGTATTAGCCACTCTTTCGAGTAGTTATCCCTCACTTTAGGGTATGTTCCCACGCGTTACTCAGCCGTCCG\n+>27 PC.634_46\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTAGGCCGTTACCCTGCCAACTGGCTAATCAGACGCGGGTCCATCATATACCACCGGAGTTTTTCACACAGAAACATGCGTCCCCGTGCGCTTATGCGGTATTAGCAGTCATTTCTAACTGTTATCCCCCTGTATAAGGCAGATTACCCACGTGTTACTCACCCG\n+>103 PC.481_49\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTACTGATCG'..b'GTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCCCGCCGACTAGCTAATGCGCCGCATGGCCATCCGCAGCCGATAAATCTTTAAACATCGGGAGATGCCTCCCAACGTTCTTACGCGGTATTAGACGGAATTTCTCCCGATTATCCGGCTGTGGCAGGCAGGTTGCATACGTGTTACTC\n+>364 PC.356_1261\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGCCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTGCCCCGCCAACCAGCTAATCAGACGCGGGCCCATCCTGCACCGCCGGAGCTTCCCCCGCCGCCCCATGCGGGGCTGCGGGCATATGCGGTATTAGCAGCCGTTTCCGGCTGTTGTCCCCCGGTATACGGCAGGTTTTCCACGCGTTACTCACCCGTCCG\n+>172 PC.593_1268\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCCCGCCAACAACCTAATGGAACGCATCCCCATCGATGACCGAAGTTCTTTAATAGTTCTACCATGCGGAAGAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCG\n+>62 PC.593_1279\n+CTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGCCTTGGTAGGCCTTTACCCCACCAACTAGCTAATCAGACGCAAGCCCATCTGTAAGTGGATTGCTCCTTTCCTCACTCTAACATGTGTCAGTGTGAGCATATGCGGTATTAGCAATGATTTCTCACTGTTATTCCCCTCTTACAGG\n+>3 PC.481_1280\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTAGGCCGTTACCCTGCCAACTGGCTAATCAGACGCGGGTCCATCGTATGCCACCGGAGTTTTTCACACAGGAGCATGCGCTCCCGTGCGCTTATGCGGTGTTAGCACCTATTTCTAAGTGTTATCCCCCTGCATACGGCAGGTTACCCACGCGTTACT\n+>108 PC.355_1283\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTCGCTTTGGTGGGCCGTTACCCCGCCAACTGGCTAATCAGACGCGGGTCCATCTTACACCACTAATGTTTTTCACTCTGTCCCATGCGGGACTGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTATACGGCAGGTTCTCCACGCGTTACTCACCCGTCCG\n+>390 PC.356_1286\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCGCCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCCCGCCAACCAGCTAATCAGACGCGGGTCCATCCTGCACCACCGGAGTTTTCAAAGGATTACCATGCGGTATTCCCTATTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCGGTACAGGGCAGGTTGCCCACGCGTTACTCACCCGTGCGCCAGTCG\n+>52 PC.593_1290\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCGCCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCAGACGCGGGTCCATCTTGCACCACCGGAGTTTTTCACACTGAGCCATGCAGCTCCGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTGCAAGGCAGGTTACCCACG\n+>54 PC.593_1292\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACTGATCGTCGCCTTGGTGAGCCGTTACCTCACCAACCAGCTAATCAGACGCAGGTCCATCTTACACCGATAAAATCTTTTCCGTCCGGGCCATGCGGCCCTAGCGGGTTATGCGGTATTAGCAGTCATTTCTAACTGTTATCCCCCTGTGTAAGGCAGGTTACCCACGCGTTACTCACCCG\n+>400 PC.355_1294\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTTGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCGGGCCCATCTTACACCACCGGAGTTTTTCACACTGTCCCATGCAGGACCGTGCGCTTATGCGGTTTTAGCACCTATTTCTAAGTGTTATCCCCCTGTACAGGGCGAGGTTACCCACGCGTTACTCACCCGTCCGCCACTAAG\n+>173 PC.593_1305\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTGGGCCGTTACCCCGCCAACTAGCTAATCAGACGCGGGCCCATCTCATACCACCGGAGTTTTTCACACTGTTCCATGCGGAACCGTGCGCTTATGCGGTATTAGCACCTGTTTCCAAGTGTTATCCCCCTCTTTTGGGCAGGTTGCCCACGTGTTACTCACCCGTTCG\n+>288 PC.593_1312\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACCGATCGTCGACTTGGTGGGCCGTTACCTCACCAACTATCTAATCGGGTGCGAGCCCATCTCTAAGCGGATTTCTCCTTTGCCGGTTGTACAATGCTATACTGCCGGTTTATGTGGTATTACCACCCGTTTCCAGGTGCTATCCCTCTCTTAAAGGTAGGTTGCTCACATGTTACTCACCC\n+>285 PC.593_1314\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTCGGTTTGGTGGGCCGTTACCCCACCAACTAGCTAATCAGACGCAAGCCCATCTGTAAGTGGATTGCTCCTTTCCTCACTCTAACATGTGTCAGTGTGAGCATATGCGGTATTAGCACCCTATTTCTAACGTGTTATCCCCCAGTATACGGCAGGTTCTCCACG\n+>7 PC.593_1320\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAACCTCTCAGTTCGGCTACGCATCATTGCCTTGGTAAGCCCTTTACCCCACCAACTAGCTAATGCGCCGCGGGCCCATCCAAAAGCGGTAGCATAGCCACCTTTTACATAGTTACCATGCGGTAACTATGGTTATGCGGTATTAGCACCTGTTTCCAAGTGTTACTCCCCCTTCTTTTGGGCAGGGTTCGCCCCACGTTGTTACT\n+>26 PC.593_1326\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGGTTAGGTGGGCCTTTACCCCGCCAACAAACTAATGCACCGCAGGTCCATCCGCGCCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTCCTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTTACTCACCCGTTCGCC\n+>5 PC.593_1329\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTTGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCGGGTCCATCTTACACCACCGGAGTTTTCAAGTAAAAGACATGCGTCTCCTACTGTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTGCAAGGCAGGTTACCCACGCGTTACTCACCCGTCCGCC\n'

diff -r 000000000000 -r c11972e98d44 test-data/pick_rep_set/longest_otu_fasta.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_rep_set/longest_otu_fasta.fasta Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,834 @@\n+>0 PC.635_779\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGTTGACTTGGTGGGCCGTTACCCCGCCAACTATCTAATGGAACGCATCCCCATCGATAACCGAAATTCTTTAATAGTGAAACCATGCGGAAATACTATACTATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTTATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCATCAA\n+>1 PC.636_263\n+CTGGGCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGGCTTGGTGGTCCGTTACACCGCCAACTACCTAATGCGACGCATGCCCATCCGCTACCGGATCGCTCCTTTGGAATCCCGGGGATGTCCCCGGAACTCGTTATGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGTAGCGGGCAGGTTGCATACGTGTTACTCACCCGTCCGCCACTAGGGCG\n+>10 PC.354_832\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCCGGCTACTGATCGTCGTTTTGGTAGGCCGTTACCCTGCCAACTGGCTAATCAGACGCGGGTCCATCCCATACCACCGGAGTTTTTCACACAGCAACATGCGTTGCCGTGCGCTTATGCGGTATTAGCAGTCATTTCTAACTGTTATCCCCCTGTATGGGGCAGGTTGCCCACGCGTTACTCACCCG\n+>100 PC.356_1196\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCTGGCTACTGATCGTCGCCTTGGTAGGCCGTTACCCTGCCAACAAGCTAATCAGACGCGGGTCCATCTCGCACCACCGGAGTTTTCAGGGCGGGGGCATGCGCCCCCCTCCCGTTATGCGGTGTTAGCACCTATTTCTGGGTGTTATCCCCCTGTACAGGCCAGGTTGCCCACGCGTTACTCACCCGTCCG\n+>101 PC.634_99\n+CTGGGCCGTGTCTCAGTCCCAGTGTGGCCGGCCACCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTAGGCCGTTACCCCGCCAACCAGCTAATCAGACGCGGGTCCATCCCGTACCACCGGAGTTTTCAAGAAAGGAACATGCGTCCCCTTCTGTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCGGTACGGGGCAGGTTCCCCACGCGTTACTCACCCGTTCGCCACTCGGGCAC\n+>102 PC.481_808\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCGTTCCTCTCAGAACCCCTACCTATCATTGCCTTGGTGGGCCGTTACCCCCCAACCTAGCTAATAGGACGCATGCCCATCTGATACCTCGAACGATTTAATTATTATAAGATGCCTTACAATAATATTATGGGTGGTTAATCCACGTTTCCATGGGCTATCCCCCTCGTATCAGCCAGGTTGCATACGCGTTACTCACCCGTGCGCCGG\n+>103 PC.481_49\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTAGGCCGTTACCCTGCCAACTGGCTAATCAGACGCGGGTCCATCATATACCACCGGAGTTTTTCACACCGGGGCATGCGCCCCTGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCTGTATATGGCAGGTTACCCACGCGTTACTCACCCG\n+>104 PC.607_151\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGGTTAGGTGGGCCGTTACCCCGCCTACTGCCTAATGCGCCGCATGCCCATCCCTGTCCGGCCGAAGCCTTTCCTGCCTCCGGGATGCCCCGGTGGCATGTACGCGGGATTAGCCTCCCTTTCGGAAGGTTGTCCCCCTGTGGAGGGCAGGTTGCATACGTGTTACTCACCCGTGCGCCAGTCGCCGG\n+>105 PC.607_1176\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTTGCCCTCTCAGGCCGGCTACTGATCGTCGGTTTGGTGGGCCGTTACCCCGCCAACTGCCTAATCAGACGCGGGCCCATCCCATACCGCGAAAGCTTTCCATGCAGGGGCATGCGCCCCCGCATGTGCATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGGAAGGCAGGTTCCTCACGCGTTACTC\n+>106 PC.636_850\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGGCTTGGTGGTCCGTTACACCGCCAACTACCTAATGCGACGCATGCCCATCCGCTACCGGATCGCTCCTTTGGAATCCCGGGGATGTCCCCGGAACTCGTTATGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGTAGCGGGCAGGTTGTCCACGCGTTACTCACCCGTCCGCCGCTAAGCC\n+>107 PC.355_301\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCTGTTACCCCGCCAACCAGCTAATCAGACGCGGATCCATCGTATACCACCGGAGTTTTTACCTCAGAACCATGCGGTTCCGCGGTCTTATGCGGTATTAGCAGTCATTTCTAACTGTTATCCCCCTGTGTAAGGCAGGTTGCCCACGCGTTACTCACCCGTCCGCCG\n+>108 PC.355_1283\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTCGCTTTGGTGGGCCGTTACCCCGCCAACTGGCTAATCAGACGCGGGTCCATCTTACACCACTAATGTTTTTCACTCTGTCCCATGCGGGACTGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTATACGGCAGGTTCTCCACGCGTTACTCACCCGTCCG\n+>109 PC.481_676\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAACCTCTCAGTTCGGCTACGCATCATTGCCTTGGTAAGCCTTTACCCCACCAACTAGCTAATGCGTCGCGGGCCCATCCAAAAGCGGTAGCATAGCCACCTTTTACATAGTTACCATGCGGTAACTATGGTTATGCGGTATTAGCACCTGTTTCCAAGTGTTATCCCCCTCTTTTGGGCAGGTTGCCCACGTGTTACTCACCCG\n+>11 PC.355_26\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTCGGCTTGGTGGGCCGTTACCCCGCCAACTACCTAATCAGACGCGGGTCCATCCTGTACCACCGGAGTTTTTCACACCGGACCATGCGGTCCTGTGCGCTTATGCGGTATTAGCAGTCATTTCTAACTGTTGTCCCCCTGTACAGGGCAGGTTACCCACGCGTTACTCACCCGTCCGCCACT\n+>110 PC.634_170\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGCTGCCCCGCCAACAAGCTAATCAGACGCGGGCCCCTCCCATACCGCCGGAGCTTTCCCCACAAAGGCATGCGCCTCCCTGGTTTATGCGGTATTAGCAGCCGTTTCCGGCTGTTATCCCCCTGTATGAGGCAGGTTGCCCACGCGTTACTCACCCGTCCGCCG\n+>111 PC.634_173\n+TTGGTCCGTGTCTCAGTACCAATGTGGGGGGTTAACCTCTCAGTCCCCCTATGTATCGTTGCCTTGGTGAGCCGTTACCTCACCAACTAGCTAATAC'..b'CCCGTGCGCCGGTCG\n+>85 PC.356_249\n+CTGGGCCGTGTCTCAGTCCCAGTGTGGCCGTCCACCCTCTCAGGCCGGCTGCTGATCGTCGCTTTGGTGGGCCGTTACCCCGCCAACTGGCTAATCGGACGCGGATCCATCGTATGCCGATAAATCTTTTCACACCAGACCATGCGATCCTGTGCGCTTATGCGGTTTTAGCACCTATTTCTAAGTGTTATCCCCCTGTATACGGCAGGTTACCCACGCGTTACT\n+>86 PC.481_1022\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACTCTCTCAAGCCGGCTACTGATCGTCGCTTTGGTAGGCCATTACCCTGCCAACTGGCTAATCAGACGCGGGCCCATCCTGTACCTATAAATATTTGATAGCAATATCATGCGGTATCGCTATGTTATGCGGTGTTAGCAGCCGTTTCCAGCTGTTATCCCCCTGTACAGGGCAGGTTACCCACG\n+>87 PC.481_1025\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGCTGCCCCGCCAACAAGCTAATCAGACGCGGGCCCATCGCATACCACCGGAGTTTTTCACACCAAGCCATGCGGCTCTGTGCGCTTATGCGGTATTAGCAGTCATTTCTAACTGTTATCCCCCTGTGTAAGGCAGGTTGCCCACG\n+>88 PC.481_738\n+CTGGGCCGTATCTCAGTCCCAATGTGGCCGATCGACCTCTCAGTCCGGCTACCCATCGCAGGCTCGGTGGGCCGTTACCCCGCCGACTACCTAATGGGCCGCGACCCCATCTCACACCGCGAGAGCTTTCATCCGGCTAACATGTGTTGGCCGGATAGTATCCGGTATTAGCTACCGTTTCCAGTAGTTATCCCGGTGTGTGAGGCAGGTTGGTCACGTGTTACTCACCCGTTCG\n+>89 PC.635_576\n+CTGGACCGTGTCTCAGTTCCAGTGTGGGGGACCTTCCTCTCAGAACCCCTAGACATCGTCGGCTTGGTGGGCCGTTACCCCGCCAACTACCTAATGTCGCGCGTGCCCGTCCCGTACCACCGGAATTTTAAATCGAGAGCCATGCGGCTCTCGAGTATCATGGGATGTTAGTCCACGTTTCCGCGGGTTATCTCCCGGTACGGGGTTGGTTGCACACGTGTTACTCACCCGTACGCCGGTCGCCACCAGTG\n+>9 PC.481_1193\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTTACCAACCAGCTAATCAGACGCGGGCCCATCCTGTACCACCGTGGTTTTCCCTGCTGTTCCATGCGGCACAGCAGGCTTATGCGGTATTAGCAGCCATTTCTGGCTGTTGTCCCCCGGTACAGGGCAGGTTGCCCACGCGTTACT\n+>90 PC.635_966\n+CTGGACCGTGTCTCAGTTCCAGTGTGGGGGACCTTCCTCTCAGAACCCCTAGACATCGTCGCCTCGGTGGGCCGTTACCCCGCCGACTAGCTAATGCGCCGCATGCCCATCCGTGGCCGGGATTGCTCCCTTTGGCGGCCCGGGGATGCCCCAAGGCCGCGTTACGCGGTATTAGACGGGGTTTCCCCCGCTTATCCCCCTGCCACGGGCAGGTTGCATACGTGTTACTCACCCGTGCGCCGGTCGCCGGCGG\n+>91 PC.635_364\n+CTGGGCCGTGTCTCAGTCCCAGTGTGGCCGTCCGCCCTCTCAGGCCGGCTACTGATCGTGGGCTTGGTGGGCCGTTACCCCGCCAACTACCTAATCAGACGCGGACCCATCGTGTACCGTACTAGATAAGATCTAGGCTTTCCGCCCTGTGCCATGCGGCACTGTGCGCATATGCGGTATTAGCAGCCGTTTCCGGCTGTTATCCCCCTGTACACGGCAGGTTG\n+>92 PC.356_579\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTGCTGATCGTCGCTTTGGTGGGCCGTTACCCCGCCAACTGGCTAATCAGACGCGGGCCCATCCTGTACCACCGGAGTTTTCAGGGAAAAGCCATGCGGCTTCCCCCGTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCTGTACAGGCCAGGTTGCCCACGCGTTACTCACCCGTCCGCCACTAACAG\n+>93 PC.635_367\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGGCCAACCTCTCAGTCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTGCCCCGCCAACTAGCTAATCAGACGCGAGCTCATCTCAGAGCGATAAATCTTTGGCGTCCAGAGAGATGCCTCCCAGACGCATCATGCGGTATTAGCGGCTGTTTCCAACCGTTATTCCCCACTCCAAGG\n+>94 PC.593_932\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTACGCATCGTCGCCGTCGGTGGGCCGTTACCCCGCCGACTAGCTAATGCGCCGCATGGCCATCCGCAGCCGATAAATCTTTAAACATCGGGAGATGCCTCCCAACGTTGTTACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTGCGGGCAGGTTCCATACGTGTTACTCACCCG\n+>95 PC.356_238\n+TTGGACCGTATCTCAGTTCCAATGTGGCCGATCAGCCTCTCAGCTCGGCTATGCATCGTTGCCTTGGTAGGCCATTGCCCCACCAACTAGCTAATACACCGCAAGCTCATCCTAAGGTGAAGCAAACGCTTCTTTTAACATATCTAGTTATCTAGTTATGTATCATCCGGTATTAGCGTTCGTTTCCAAACGTTATCCCAGTCCCTAGGGTAGATTACCC\n+>96 PC.355_1298\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGAGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTACACCACCGGAGTTTTTCACACCGAACCATGCGGTTCTGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTGCAAGGCAGGTTACCCACGCGTTACTCACCCGTCCCG\n+>97 PC.354_773\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTGGGCCGTTACCCCGCCAACTGGCTAATCAGACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACACTACCATGCGGTACTGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTGCAAGGCAGGTTACCCACGCGTTACTCACCCGTCCG\n+>98 PC.636_592\n+CTGGTCCGTGTCTCAGTACCAGCGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGTGGACTTGGTGAGCCGTTACCTCACCAACTATCTAATGGAACGCATGCCCATCTATCAGCGATAATTCTTTAACAAATATTTCCATGTGGAACCCCTGTTTTATGCGGTATTAGTCCGACTTTCGCCGGGTTATTCCCTCTGATAGGTAGGTTGCATACGCGTTACTCACCCGTGCGCCGG\n+>99 PC.356_336\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGCCCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTCTACCCCGCCAACAAGCTAATCAGACGCGGGTCCATCGTATACCACCGGAGTTTTTCACACCAGACCATGCGATCCTGTGCGCTTATGCGGTTTTAGCACCTATTTCTAAGTGTTATCCCCCTGTACAGGCCAGGTTGCCCACGCGTTACTCACCCG\n'

diff -r 000000000000 -r c11972e98d44 test-data/pick_rep_set/most_abundant_otu_fasta.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_rep_set/most_abundant_otu_fasta.fasta Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/pick_rep_set/refseqs.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_rep_set/refseqs.fasta Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,50 @@\n+>378462\n+GATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGAACAGATAAGGAGCTTGCTCCTTTGACGTTAGCGGCGGACGGGTGAGTAACACGTGGGTAACCTACCTATAAGACTGGAATAACTCCGGGAAACCGGGGCTAATGCCGGATAACATGTTGAACCGCATGGTTCTACAGTGAAAGGCGGCTTTGCTGTCACTTATAGATGGACCCGCGCCGTATTAGCTAGTTGGTGAGGTGACGGCTCACCAAGGCAACGATACGTAGCCGACCTGAGAGGGTGATCGGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACAAATGCGTAAGTAACTGTGCGCGTCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGGAGGGTCATTGGAAACTGAAAAAACTTGAGTGCAGAGAGGGAAAGTGGAAATCCATGTGTAGCGGTGAAATGCGCAGAGATATGGGAGGAACTCCAGTGGCGAAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGGCCGCAAGGCTTAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAAATCTTGACATCCTTTGACCGCTCTAGAGATAGAGTCTTCCCCTTCGGGGGACAAAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTAAGCTTAGTTGCCATCATTCAGTTGGGCACTCTAAGTTGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGATTTGGGCTACACACGTGCTACAATGGACAATACAAAGGGCAGCGAAACCGCGAGGTCAAGCAAATCCCATAAAGTTGTTCTCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGTAGATCAGCATGCTACGGTGAATACGTTCCCGGGTCT\n+>186233\n+AGAGTTTGATCCTGGCTCAGGATGAACACTAGCTACAGGCTTAACACATGCAAGTCGAGGGGCATCAGTTTGGTTTGCTTGCAAACCAAAGCTGGCGACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCGACAACACTGGGATAGCCTTTCGAAAGAAAGATTAATACCGCATGAAGCAGGGATCCCGCATGGGAATATTTGCTAAAGATTCATCGCTGATAGATAGGCATGCGTTCCATTAGGCAGTTGGCGGGGTAACGGCCCACCAAACCGACGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGTACTGAGACACGGACCAAACTCCTACGGGAGGCAGCAGTGAGGAATATTGGTCAATGGCCGAGAGGCTGAACCAGCCAAGTCGCGTGAGGGATGAAGGTTCTATGGATCGTAAACCTCTTTTATAAGGGAATAAAGTGCGGGACGTGTCCCGTTTTGTATGTACCTTATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCCCTTAAGTCAGCGGTGAAAGTCTGTGGCTCAACCATAGAATTGCCGTTGAAACTGGGAGGCTTGAGTATGTTTGAGGCAGGTGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTGCCAAGCCATTACTGACGCTGATGCACGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCAGTAAACGATGATCACTAGCTGTCTGCGATACACTGTAAGCGGCACAGCGAAAGCGTTAAGTGATCCACCTGGGGAGTACGCCGGCAACGGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGAGGAACATGTGGTTTAATTCGATGATACGCGAGGAACCTTACCCGGGTTTGAACGCATTTCGACAGCTCTGGAAACAGAGTCTCTAGCGATAGCGATTTGCGAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTGCCACTAGTTACTAACAGGTAAAGCTGAGGACTCTGGTGGGACTGCCAGCGTAAGCTGCGAGGAAGGCGGGGATGACGTCAAATCAGCACGGCCCTTACATCCGGGGCGACACACGTGTTACAATGGCGTGGACAAAGGGAGGCCACCTGGTGACAGGGAGCGAATCCCCAAACCACGTCTCAGTTCGGATCGGAGTCTGCAACCCGACTCCGTGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCATGGCGCGGTGAATACGTTCCCGGGCCTTGCACACACAGCCCGTCAAG\n+>260529\n+AGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGAAGCATAAGGGAAGGAAGATTCGTCTGACGGAACTTATGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCCCATACCGGGGGATAACATTCAGAAATGAGTGCTAATACCGCATAAGACCACAGTGCCGCATGGCACAGGGGTCAAAACTCCGGTGGTATGGGATGGACCCGCGTCTGATTAGGTAGTTGGCGGGGTAACGGCCCACCAAGCCGACGATCAGTAGCCGACCTGAGAGGGTGACCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGTGAGGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAAATGACGGTACCTGACTAAGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTCCTGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTAAGGCTAGAGTGTCGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGACTACTAGGTGTCGGGTGGCAAAGCCATTCGGTGCCGCAGCCAACGCAATAAGTAGTCCACCTGGGGAGTACGTTCGCAAGAATGAAACTCAAGGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCTGGCCTTGACATCCCCCTGACGTAGGGGCAATGCCCTATTTCTTTCGGGACAGGGGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTTGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTATCTTCAGTAGCCAGCATTACGGATGGGAACTCTGGAGAGACTGCCAGGGACAACCTGGAGGAAGGTGGGG'..b'AGGAAGAAGGTTTTCGGATTGTAAACTATTGTCTGCAGGGAAGAAATAAGACTGTACCTGCAAAGAAAGCTCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGAGCAAGCGTTATCCGGATTTATTGGGTGTAAAGGGTGCGTAGACGGGAAATTAAGTTAGTTGTGAAATCCCTCGGCTTAACTGAGGAACTGCAACTAAAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGACTGTAACTGACGTTGAGGCACGAAAGTGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACACTGTAAACGATGGATACTAGGTGTAGGGGGTATTAAGCCTTCTGTGCCGTCGCTAACGCAGTAAGTATCCCACCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCAGTGGAGTATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGGCTTGACATATACAGGAATATATTAGAGATAGTATAGCTCTTCGGAGTCTGTATACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGTTTCTAGTTGCCAGCACGTTAAGGTGGGAACTCTAGAGAGACTGCCGTTGATAAAACGGAGGAAGGTGGGGACGACGTCAAATCATCATGCCCTTTATGTCCCTGGGCTACACACGTACTACAATGGCTATAACAAAGGGAAGCGAAACAGCGATGTGAAGCGAAACTCAAAAAAGTAGTCTCAGTTCGGATTGTAGGCTGAAATTCGCCTACATGAAGCCGGAATTGCTAGTAATGGCAGGTCAGCATACTGCCGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGAGAGTTGGGAATACCCGAAGCCTGTGAGCTAACATTTTATGAGGCAGCAGTCGAAGGTAGAATCAATGATTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTT\n+>571697\n+AGTGAACGCTGGCGGCGTGCTTAACACATGCACGTCGAACGGAAACAACAATCTTCGGATTGGGTGTCGAGTGGCGGACGGGTGAGTAATGTATAGTTAATTTGCCCCTTAGAGAGGAATAGGCACTGGAAACGGTGATTAATACCTCATACTCCTTCCTACTTAATGTGGGTTGGGAAATGTTTTTTCGCTAAGGGATAAGACTATATGGTATCAGGTAGTTGGTAGGGTAAGAGCCTACCAAGCCTATGACGCCTAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGAGGAAACTCTGATGCAGCAACGCCGCGTGGAGGATGACACATTTCGGTGCGTAAACTCCTTTTATATGGGAAGATAATGACGGTACCATATGAATAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTACTCGGAATCACTGGGCGTAAAGCGCGCGCAGGCGGTCTTTTAAGTTGGATGTGAAAGCCTACGGCTCAACCGTAGAACTGCATCCAAAACTATTAGACTAGAGTGTGGGAGAGGAAGATGGAATTAGTTGTGTAGGGGTAAAATCCGTAGAGATAACTAGGAATACCAAAAGCGAAGGGCAAATCTTTCTGGAACACTACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCACGCAGTAAACGATGAATGTTAGTCGTCGGAGGCCTAGTGTCTTCGGTGATGCAGCTAACGCATTAAACATTCCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATAGACGGGGACCCGCACAAGTGGTGGAGCATGTGGTTTAATTCGAAGATACGCGAAGAACCTTACCTAGCCTTGACATATTTTAGAATTCTTTAGAGATAGAGAAGTGCCTTCGGGAGCTAATTTACAGGTGCTGCACGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCGTCACTAGTTACTAACGGTTCGGCCGAGGACTCTAGTGAGACTGCCTTCGTAAGGAGGAGGAAGGTGAGGACGACGTCAAGTCATCATGGCCCTTACGGCTAGGGCAACACACGTGCTACAATGGTTGGGACAGTGAGACGCAATACCGCGAGGTGGAGCAAATCTATAAACCCAATCTCAGTTCGGATTGTTCTCTGCAACTCGAGAACATGAAGCTGGAATCACTAGTAATCGTAGATCAGCTATGCTACGGTGAATACGTTCCCGGGTCTTGTACTCACCGCCCGTCACACCATGGGAGTTGATTTCACCCGAAGCGGGGAAGCTAAATTGGCTACCCTCCACGGTGGAATTAGCGACTGGGGTGA\n+>571690\n+AGTCGAACGGTGACGGAGGAGCTTGCTTCTCTTGATCAGTGGCGAACGGGTGAGTAACACGTGAGTAACCTGCCCCAGACTCTGGGATAACCTCGGGAAACCGGGGCTAATACCGGATAAGCGGCTCCACCGCATGGTGAGGGTCGGGAAAGTTTTTCGGTCTGGGATGGACTCGCGGCCTATCAGCTTGTTGGTGAGGTAGTGGCTCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGCGACCGGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGGGGGATGAAGGCCTTCGGGTTGTAAACCCCTTTCAGCAGGGAAGAAGCGAAAGTGACGGTACCTGCAGAAGAAGCGCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGCGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTCTGTCGCGTCTGCTGTGAAAACCCGAGGCTCAACCTCGGGCCTGCAGTGGGTACGGGCAGACTAGAGTGTGGTAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTCTCTGGGCCACAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGCACTAGATGTGGGGCTCTTTCCATGAGTTCCGCGTCGCAGCTAACGCATTAAGTGCCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGCGGATTAATTCGATGCAACGCGAAGAACCTTACCAAGGCTTGACATATACCCTCTACCCCCAGAGATGGGGGGTGCTTCGGCGGGGTATACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCGTCCTATGTTGCCAGCACGTAATGGTGGGGACTCATAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTTCACGCATGCTACAATGGCCGGTACAAAGGGCTGCGATACCGTAAGGTGGAGCGAATCCCAAAAAGCCGGTCTCAGTTCGGATTGAGGTCTGCAACTCGACCTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCAAGTCACGAAAGTCGGTAACACCCGAAGCCAGTGGCCCAACCCTTGTGGGGGAGATCTGTCTAGTGTGAGAGTGGAGAGTGAGAATAACTCATAAAGGGGTA\n'

diff -r 000000000000 -r c11972e98d44 test-data/pick_rep_set/seqs.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_rep_set/seqs.fna Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,2666 @@\n+>PC.634_1 FLP3FBN01ELBSX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTTACCCTCTCAGGCCGGCTACGCATCATCGCCTTGGTGGGCCGTTACCTCACCAACTAGCTAATGCGCCGCAGGTCCATCCATGTTCACGCCTTGATGGGCGCTTTAATATACTGAGCATGCGCTCTGTATACCTATCCGGTTTTAGCTACCGTTTCCAGCAGTTATCCCGGACACATGGGCTAGG\n+>PC.634_2 FLP3FBN01EG8AX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGCCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACAACCTAATGGAACGCATCCCCATCGATGACCGAAGTTCTTTAATAGTTCTACCATGCGGAAGAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCA\n+>PC.354_3 FLP3FBN01EEWKD orig_bc=AGCACGAGCCTA new_bc=AGCACGAGCCTA bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTTAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCTTACCAACTAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGACATGCGTCTAGTGTTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCTTGGG\n+>PC.481_4 FLP3FBN01DEHK3 orig_bc=ACCAGCGACTAG new_bc=ACCAGCGACTAG bc_diffs=0\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCAGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGGTATTCCGGCGATGCCGCCAAAATCATTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTGCTCACG\n+>PC.634_5 FLP3FBN01DGFYQ orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTAGGCCGTTACCCTGCCAACTGGCTAATCAGACGCGGGTCCATCTCACACCGATTAATCTTTTTCCAACCAGAGCATGCGCCCCTGTTGGCTTATGCGGTATTAGCGGTCGTTTCCAACTGTTATCCCCCTGTGTGAGGCAGGTTACCCACGCGTTACTCACCCGTCCG\n+>PC.636_6 FLP3FBN01A55WZ orig_bc=ACGGTGAGTGTC new_bc=ACGGTGAGTGTC bc_diffs=0\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCTTATACCGGTAAACCTTTAATCATGAGAAAATGCTCACTCATGATACCATCTTGTATTAATCTCCCTTTCAGAAGGCTATCCAAGAGTATAAGGCAGGTTGGATACGCGTTACTCACCCGTGCGCCGG\n+>PC.634_7 FLP3FBN01D7O1S orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGATAACCGAAATTCTTTAATAGTGAAACCATGCGGAAATACTATACTATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTTATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCATC\n+>PC.634_8 FLP3FBN01CV5ZU orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+TTGGTCCGTGTCTCAGTACCAATGTGGGGGGTTAACCTCTCAGTCCCCCTATGTATCGTCGCCTTGGTAAGCCGTTACCTTACCAACCAGCTAATACAACGCATGCCCATCTGTAACCGCCGAAACTTTCAACCACAAGAGATGCCTCTCATAGTGTTATGCGGTATTAGTACCGATTTCTCAGTGTTATCCCCCTGTTACAGGTAGGTTGCATACGCGTTACGCACCCGTGCGCCGGTCG\n+>PC.634_9 FLP3FBN01DQ783 orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCCG\n+>PC.634_10 FLP3FBN01DDPFF orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+TTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTCCCTTTCAGAAGGCTATCCAAGAGTATAAGGCAGGTTGGGTACGCGTTACTC\n+>PC.634_11 FLP3FBN01CPD70 orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0\n+CTGGACCGTGTCTCAGTTCCAATGTGGGGGGCCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACAACCTAATGGAACGCATCCCCATCGATGACCGAAGTTCTTTAATAGTTCTACCATGCGGAAGAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCG\n+>PC.593_12 FLP3FBN01BBAE6 orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCCCGCCGACTAGCTAATGCGCCGCATGCCCATCCGCCACCGGTAATCCCTTTGGCGGCACCGGGATGCCCCGATGCCGCGTCACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGTGGCGGGCAGGTTGCATACGTGTTACTCACCCGTGCG\n+>PC.355_13 FLP3FBN01AWYZD orig_bc=AACTCGTCGATG new_bc=AACTCGTCGATG bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTCAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCTTACCAACTAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGACATG'..b'GTCCGCCCTCTCAGGCCGGCTATGCATCATCGTCTTGGTGGGCCTTTACCCCGCCAACCAACTAATGCACCGCAGGTCCATCCGCGCCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTCCTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTT\n+>PC.593_1322 FLP3FBN01DBF9Z orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGACCGTGTCTCAGTTCCAGTGTGTCCGATCACCCTCTCAGGCCGGATACCCGTCATAGCCTTGGTGAGCCATTACCTCACCAACAAGCTGATAGGACATAGGCTGATCCTTTAGCGAAAAACTTTCCCCCGTAGGGAGTATCCAGTATTAATCACCGTTTCCAGTGGCTATCCCAGACTAAAGGGCACATAACCTATGCATTACTCACCCGTGCGCC\n+>PC.593_1323 FLP3FBN01APHXO orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTATGCATCATCGTCTTGGTGGGCCTTTACCCCGCCAACCAACTAATGCACCGCAGGTCCATCCGCGCCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTCCTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTTACT\n+>PC.593_1324 FLP3FBN01C0GRI orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTGGGCCGTTACCCCGCCAACTGGCTAATCAGACGCGGATCCATCGTATACCACCGGAGTTTTTCACACTGTTCCATGCGGAACCGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCGGTATACGGCAGGTTATCCACGCGTTACTCACCCGTCCG\n+>PC.593_1325 FLP3FBN01CEZZE orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTATGCATCATCGTCTTGGTGGGCCTTTACCCCGCCAACAAACTAATGCACCGCAGGTCCATCCGCGCCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTCCTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTT\n+>PC.593_1326 FLP3FBN01AGO5G orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGGTTAGGTGGGCCTTTACCCCGCCAACAAACTAATGCACCGCAGGTCCATCCGCGCCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTCCTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTTACTCACCCGTTCGCC\n+>PC.593_1327 FLP3FBN01A9WKI orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCGCCCTCTCAGGCCGGCTATGCATCATCGTCTTGGTGGGCCTTTACCCCGCCAACAAACTAATGCACCGCAGGTCCATCCGCACCCCATCCCCTAAAGGATGTTTCACAGAAAGAAGATGCCTCCTTCCTGTACATCGGGATTTGTTCTCCGTTTCCAGAGCGTATTCCCGGTGCGCGGGCAGGTTCCCTACGTGTT\n+>PC.593_1328 FLP3FBN01AMKUE orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCCCGCCGACTAGCTAATGCGCCGCATGGCCATCCGCAGCCGATAAATCTTTAAACATCGGGAGATGCCTCCCAACGTTGTTACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTGCGGGCAGGTTCCATACGTGTTACTCACCCGTGCG\n+>PC.593_1329 FLP3FBN01CD50B orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTTGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCGGGTCCATCTTACACCACCGGAGTTTTCAAGTAAAAGACATGCGTCTCCTACTGTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTGCAAGGCAGGTTACCCACGCGTTACTCACCCGTCCGCC\n+>PC.593_1330 FLP3FBN01CXEQE orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCTTTACCCCGCCAACAAGCTAATCAGACGCGGATCCATCGTATACCACCAAAAGCTTTAGCTTTTTGTTTTCCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCAGTATACGGCAGGTT\n+>PC.593_1331 FLP3FBN01C6MIF orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGGCCGTGTCTCAGTCCCAGTGTGGCCGTCCGCCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTAGGCCGTTACCCTGCCAACTGGCTAATCAGACGCGGGCCCATCCTGTACCACCGGAGTTTTCAGGGAAAAGCCATGCGGCTTCCCCCGTTATGCGGTATTAGCACCTATTTCTAAGTGTTATCCCCCTGTACAGGCCAGGTTGCCCACGCGTTACTCACCCGTCCGCC\n+>PC.593_1332 FLP3FBN01CKQYM orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCCCGCCGACTAGCTAATGCGCCGCATGGCCATCCGCAGCCGATAAATCTTTAAACATCGGGAGATGCCTCCCAACGTTGTTACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTGCGGGCAGGTTCCATACGTGTTACTCACCCGTGCG\n+>PC.593_1333 FLP3FBN01A68AG orig_bc=AGCAGCACTTGT new_bc=AGCAGCACTTGT bc_diffs=0\n+CTGGTCCGTGTCTCAGTACCAGTGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTCGGTGGGCCGTTACCCCGCCGACTAGCTAATGCGCCGCATGGCCATCCGCAGCCGGTAAACCTTTAAACCACCGGAGATGCCTCCAACGGTTGTTACGCGGTATTAGACGGAATTTCTTCCGCTTATCCCCCTGCTGCGGGCAGGTTCCATACGTGTTACTCACCCGTGCGCCGGTCGCCGG\n'

diff -r 000000000000 -r c11972e98d44 test-data/pick_rep_set/seqs_otus.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pick_rep_set/seqs_otus.txt Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,417 @@\n+0\tPC.635_779\tPC.634_176\tPC.634_7\n+1\tPC.636_263\n+2\tPC.636_264\n+3\tPC.481_1280\n+4\tPC.354_610\n+5\tPC.593_1329\tPC.355_960\tPC.356_1142\n+6\tPC.481_1214\tPC.635_315\n+7\tPC.593_1320\n+8\tPC.354_665\tPC.635_514\tPC.636_366\tPC.356_543\n+9\tPC.481_1193\n+10\tPC.355_740\tPC.354_832\n+11\tPC.354_1171\tPC.354_1014\tPC.355_26\n+12\tPC.635_570\tPC.356_1092\n+13\tPC.635_574\n+14\tPC.607_541\n+15\tPC.356_1131\n+16\tPC.634_203\n+17\tPC.634_200\n+18\tPC.634_201\n+19\tPC.481_775\tPC.354_1209\n+20\tPC.607_530\n+21\tPC.355_361\n+22\tPC.607_267\tPC.607_1221\n+23\tPC.635_818\n+24\tPC.481_1072\tPC.635_822\n+25\tPC.635_15\n+26\tPC.593_1326\n+27\tPC.634_46\n+28\tPC.634_44\tPC.634_206\n+29\tPC.634_41\n+30\tPC.635_131\n+31\tPC.481_71\tPC.481_1070\tPC.481_981\n+32\tPC.607_1004\n+33\tPC.356_1009\n+34\tPC.635_645\n+35\tPC.607_1002\n+36\tPC.607_1003\tPC.607_1047\n+37\tPC.356_668\tPC.354_296\n+38\tPC.636_396\tPC.636_1029\tPC.355_384\tPC.481_1170\tPC.636_765\tPC.593_165\n+39\tPC.607_302\tPC.607_497\tPC.607_422\tPC.607_272\tPC.607_446\n+40\tPC.607_752\tPC.607_1057\tPC.481_69\n+41\tPC.607_631\n+42\tPC.607_1189\n+43\tPC.354_518\n+44\tPC.607_1186\tPC.607_759\n+45\tPC.593_1053\n+46\tPC.607_1133\n+47\tPC.354_334\tPC.354_358\tPC.354_811\tPC.354_833\tPC.354_865\tPC.593_890\tPC.354_1017\tPC.354_1152\tPC.593_1273\tPC.593_1315\tPC.593_1316\tPC.354_230\tPC.593_758\tPC.593_976\tPC.354_411\tPC.354_1040\tPC.593_420\tPC.593_1151\tPC.354_378\tPC.593_1324\tPC.354_539\tPC.593_538\tPC.354_370\tPC.354_308\tPC.593_946\tPC.354_880\tPC.354_256\tPC.593_109\n+48\tPC.354_729\tPC.356_845\tPC.356_980\tPC.354_1230\tPC.593_689\tPC.593_938\tPC.354_505\tPC.354_829\tPC.354_991\tPC.356_449\tPC.354_502\tPC.356_1098\n+49\tPC.636_402\tPC.636_494\tPC.607_582\tPC.607_736\tPC.636_837\tPC.634_39\tPC.634_183\tPC.634_220\tPC.635_319\tPC.635_404\tPC.636_477\tPC.634_108\tPC.607_656\tPC.634_236\tPC.636_493\tPC.636_791\n+50\tPC.481_481\n+51\tPC.481_994\n+52\tPC.593_1290\n+53\tPC.354_1210\n+54\tPC.593_1292\n+55\tPC.593_400\n+56\tPC.607_197\n+57\tPC.636_389\n+58\tPC.354_1037\n+59\tPC.636_222\tPC.636_250\tPC.636_298\tPC.636_376\tPC.636_415\tPC.636_430\tPC.636_492\tPC.636_506\tPC.636_507\tPC.636_532\tPC.636_586\tPC.636_587\tPC.636_618\tPC.636_685\tPC.636_719\tPC.636_786\tPC.636_821\tPC.636_825\tPC.636_854\tPC.636_858\tPC.636_912\tPC.636_914\tPC.636_959\tPC.636_970\tPC.634_51\tPC.635_102\tPC.635_235\tPC.634_237\tPC.635_246\tPC.636_512\tPC.635_760\tPC.635_776\tPC.635_814\tPC.635_977\tPC.636_746\tPC.636_778\tPC.635_731\tPC.634_27\tPC.635_561\tPC.636_310\tPC.636_1023\tPC.635_444\tPC.636_261\tPC.636_100\tPC.636_467\tPC.636_407\tPC.636_438\tPC.634_33\tPC.636_978\tPC.636_894\tPC.636_988\tPC.481_962\n+60\tPC.607_949\n+61\tPC.607_927\n+62\tPC.593_1279\n+63\tPC.636_148\tPC.636_339\tPC.607_348\tPC.636_709\tPC.607_1084\tPC.607_1095\tPC.593_1319\tPC.481_292\tPC.354_359\tPC.635_702\tPC.355_1117\tPC.636_156\tPC.607_588\tPC.607_883\tPC.607_97\tPC.634_21\tPC.607_478\tPC.607_589\tPC.355_771\tPC.635_517\tPC.635_306\tPC.635_638\tPC.607_1206\tPC.355_728\tPC.634_129\tPC.481_1165\tPC.356_1216\tPC.636_331\n+64\tPC.607_395\n+65\tPC.636_635\n+66\tPC.356_1256\n+67\tPC.355_293\n+68\tPC.607_891\n+69\tPC.607_1068\n+70\tPC.593_526\tPC.593_755\tPC.593_944\tPC.593_954\tPC.593_1211\tPC.593_1308\tPC.593_1311\tPC.593_1328\tPC.593_1332\tPC.356_650\tPC.356_664\tPC.635_799\tPC.354_868\tPC.356_1031\tPC.355_1184\tPC.593_369\tPC.593_463\tPC.593_585\tPC.593_726\tPC.593_1258\tPC.481_279\tPC.354_503\tPC.356_563\tPC.356_707\tPC.593_1296\tPC.593_1304\tPC.356_882\tPC.593_22\tPC.356_1262\tPC.481_557\tPC.593_1288\tPC.593_454\tPC.593_1108\tPC.593_1000\tPC.593_856\tPC.593_1077\tPC.636_846\tPC.356_180\tPC.356_743\tPC.593_1313\tPC.356_1182\n+71\tPC.481_860\n+72\tPC.607_573\n+73\tPC.607_673\tPC.635_886\tPC.636_708\tPC.634_73\tPC.607_1157\tPC.593_1212\tPC.635_398\tPC.635_271\tPC.635_572\tPC.593_1306\n+74\tPC.635_72\tPC.634_190\tPC.634_205\tPC.636_311\tPC.635_999\tPC.636_751\tPC.635_784\n+75\tPC.635_647\tPC.636_792\tPC.636_904\tPC.356_67\tPC.356_1080\n+76\tPC.355_1239\n+77\tPC.355_1238\n+78\tPC.635_742\tPC.636_273\tPC.635_622\tPC.636_340\n+79\tPC.354_1044\n+80\tPC.635_621\n+81\tPC.356_1168\n+82\tPC.356_1161\n+83\tPC.356_1166\n+84\tPC.636_6\tPC.636_195\tPC.636_268\tPC.636_309\tPC.636_373\tPC.636_409\tPC.636_448\tPC.636_748\tPC.636_895\tPC.636_950\tPC.636_318\tPC.636_354\tPC.636_421\tPC.636_575\tPC.634_30\tPC.635_783\tPC.481_326\tPC.635_7'..b'77\n+324\tPC.481_666\n+325\tPC.634_78\n+326\tPC.356_1030\n+327\tPC.636_874\tPC.355_1285\n+328\tPC.607_1153\n+329\tPC.607_1019\n+330\tPC.593_718\n+331\tPC.636_972\n+332\tPC.354_855\n+333\tPC.356_679\tPC.356_700\n+334\tPC.355_1147\n+335\tPC.607_724\n+336\tPC.355_281\tPC.355_898\tPC.356_363\n+337\tPC.355_324\n+338\tPC.636_479\n+339\tPC.356_930\n+340\tPC.607_1124\n+341\tPC.354_458\tPC.354_1220\tPC.354_1073\n+342\tPC.635_394\n+343\tPC.635_390\n+344\tPC.593_547\tPC.593_1333\n+345\tPC.636_252\n+346\tPC.634_187\n+347\tPC.636_392\tPC.636_953\tPC.634_123\tPC.634_132\tPC.593_43\tPC.593_975\tPC.354_670\tPC.636_535\n+348\tPC.607_956\n+349\tPC.634_189\tPC.635_688\tPC.634_60\n+350\tPC.593_74\tPC.593_633\tPC.593_1192\n+351\tPC.355_1096\n+352\tPC.481_851\n+353\tPC.481_853\n+354\tPC.607_889\n+355\tPC.356_1252\n+356\tPC.634_115\n+357\tPC.481_859\n+358\tPC.634_110\n+359\tPC.607_595\tPC.634_223\n+360\tPC.635_521\n+361\tPC.593_343\tPC.593_769\tPC.634_35\n+362\tPC.635_16\n+363\tPC.635_528\n+364\tPC.356_1261\n+365\tPC.634_232\n+366\tPC.607_501\n+367\tPC.355_1241\n+368\tPC.635_1016\tPC.636_795\n+369\tPC.635_826\n+370\tPC.481_1083\tPC.481_888\n+371\tPC.607_312\tPC.607_658\tPC.607_841\tPC.607_973\tPC.607_1125\tPC.635_556\tPC.481_675\tPC.481_681\tPC.481_715\tPC.355_1011\tPC.356_935\tPC.355_1277\tPC.635_613\tPC.635_632\tPC.635_1001\tPC.634_24\tPC.356_1275\tPC.481_418\tPC.635_1038\n+372\tPC.355_459\n+373\tPC.635_634\n+374\tPC.634_5\n+375\tPC.356_1078\tPC.356_1274\n+376\tPC.593_754\n+377\tPC.634_8\tPC.634_90\tPC.634_177\tPC.634_178\tPC.636_185\tPC.634_193\tPC.635_259\tPC.635_277\tPC.607_712\tPC.636_807\tPC.607_834\tPC.607_947\tPC.607_1149\tPC.607_1195\tPC.635_59\tPC.634_128\tPC.634_179\tPC.634_161\tPC.635_251\tPC.636_986\tPC.634_98\tPC.635_713\n+378\tPC.634_9\tPC.634_31\tPC.634_37\tPC.634_40\tPC.634_48\tPC.634_56\tPC.634_64\tPC.355_85\tPC.634_86\tPC.634_92\tPC.634_95\tPC.634_104\tPC.634_105\tPC.634_112\tPC.634_127\tPC.634_182\tPC.355_231\tPC.354_242\tPC.355_265\tPC.355_375\tPC.481_483\tPC.355_580\tPC.355_599\tPC.354_741\tPC.355_819\tPC.355_877\tPC.635_893\tPC.355_1110\tPC.355_1154\tPC.355_1169\tPC.355_1265\tPC.355_1269\tPC.636_116\tPC.636_275\tPC.636_471\tPC.636_591\tPC.634_55\tPC.355_1250\tPC.635_253\tPC.634_53\tPC.355_288\tPC.634_89\tPC.634_145\tPC.634_32\tPC.634_10\tPC.635_1021\tPC.355_1263\tPC.355_695\tPC.635_496\tPC.355_1295\n+379\tPC.481_630\n+380\tPC.607_75\tPC.355_1145\tPC.355_460\n+381\tPC.356_555\n+382\tPC.356_553\tPC.354_522\n+383\tPC.356_552\n+384\tPC.356_410\tPC.635_1043\n+385\tPC.356_1175\tPC.636_469\n+386\tPC.634_36\n+387\tPC.634_34\tPC.355_537\tPC.355_651\tPC.355_847\tPC.355_1215\tPC.355_433\tPC.355_843\tPC.355_1128\tPC.355_1248\tPC.355_440\tPC.355_789\tPC.356_484\tPC.593_1203\tPC.355_941\tPC.355_1247\tPC.355_896\tPC.355_1199\tPC.355_1243\tPC.593_612\tPC.355_1180\tPC.356_485\tPC.634_184\tPC.355_523\tPC.355_1163\tPC.355_1204\tPC.634_45\n+388\tPC.635_916\n+389\tPC.356_325\n+390\tPC.356_1286\n+391\tPC.481_682\n+392\tPC.356_639\n+393\tPC.354_817\tPC.356_862\tPC.355_933\n+394\tPC.593_393\tPC.593_536\tPC.593_1299\tPC.593_1318\tPC.636_531\tPC.607_866\tPC.593_767\tPC.635_482\tPC.636_136\tPC.634_199\tPC.356_1033\tPC.636_379\tPC.593_1013\tPC.593_642\tPC.593_225\tPC.593_907\tPC.355_260\tPC.356_655\n+395\tPC.634_88\tPC.634_79\n+396\tPC.634_83\tPC.481_1099\tPC.593_790\tPC.593_810\tPC.634_181\tPC.355_641\tPC.636_294\tPC.356_1270\tPC.636_928\tPC.356_1127\tPC.636_337\tPC.593_12\tPC.356_1074\tPC.634_227\tPC.593_1178\tPC.636_878\tPC.355_974\tPC.634_101\tPC.634_204\n+397\tPC.634_82\n+398\tPC.636_848\n+399\tPC.481_357\tPC.634_54\tPC.355_802\tPC.636_447\tPC.356_706\tPC.355_770\tPC.481_397\tPC.635_226\n+400\tPC.355_1294\n+401\tPC.481_455\n+402\tPC.355_1115\n+403\tPC.634_140\n+404\tPC.634_143\tPC.634_196\tPC.634_211\tPC.634_1\n+405\tPC.634_147\tPC.355_607\tPC.634_194\tPC.634_18\n+406\tPC.636_218\n+407\tPC.634_149\tPC.481_304\tPC.481_499\tPC.481_926\tPC.481_943\tPC.481_1138\tPC.481_443\tPC.481_1063\tPC.634_144\tPC.481_627\tPC.481_1254\tPC.634_141\n+408\tPC.593_678\n+409\tPC.636_282\n+410\tPC.354_568\n+411\tPC.356_1219\n+412\tPC.634_19\tPC.634_125\tPC.634_212\tPC.635_812\tPC.635_835\tPC.635_934\tPC.635_958\tPC.634_154\tPC.635_554\tPC.635_857\tPC.635_903\tPC.634_42\tPC.634_169\tPC.635_867\tPC.634_65\tPC.635_744\tPC.636_567\tPC.636_881\tPC.635_215\tPC.634_198\n+413\tPC.481_1100\tPC.481_1272\tPC.481_1129\tPC.356_191\n+414\tPC.355_1050\n+415\tPC.481_897\n+416\tPC.481_1106\n'

diff -r 000000000000 -r c11972e98d44 test-data/plot_taxa_summary/class.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plot_taxa_summary/class.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,9 @@
+Taxon PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+Root;k__Bacteria;Other 0.0202702702703 0.0469798657718 0.0266666666667 0.027397260274 0.0134228187919 0.0134228187919 0.0136054421769 0.0469798657718 0.02
+Root;k__Bacteria;p__Actinobacteria 0.00675675675676 0.00671140939597 0.0 0.00684931506849 0.0 0.0 0.0 0.0201342281879 0.02
+Root;k__Bacteria;p__Bacteroidetes 0.695945945946 0.523489932886 0.193333333333 0.143835616438 0.0738255033557 0.389261744966 0.285714285714 0.275167785235 0.653333333333
+Root;k__Bacteria;p__Deferribacteres 0.0472972972973 0.0134228187919 0.0 0.0 0.0 0.0 0.0 0.0201342281879 0.0333333333333
+Root;k__Bacteria;p__Firmicutes 0.209459459459 0.395973154362 0.773333333333 0.787671232877 0.89932885906 0.41610738255 0.700680272109 0.456375838926 0.22
+Root;k__Bacteria;p__Proteobacteria 0.00675675675676 0.00671140939597 0.0 0.0 0.0 0.0335570469799 0.0 0.0201342281879 0.0133333333333
+Root;k__Bacteria;p__TM7 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0133333333333
+Root;k__Bacteria;p__Tenericutes 0.0135135135135 0.00671140939597 0.00666666666667 0.0342465753425 0.0134228187919 0.147651006711 0.0 0.161073825503 0.0266666666667

diff -r 000000000000 -r c11972e98d44 test-data/plot_taxa_summary/class/pie_charts.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plot_taxa_summary/class/pie_charts.html Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,157 @@\n+\n+<html>\n+<head>\n+<link rel="stylesheet" href="./css/qiime_style.css" type="text/css">\n+<script type="text/javascript" src="./js/overlib.js"></script>\n+\n+<script type="text/javascript">\n+\n+</script>\n+<title>Taxa Summaries</title>\n+</head>\n+<body>\n+<div id="overDiv" style="position:absolute; visibility:hidden; z-index:1000;"></div>\n+<table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: Class</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/7Q3bZGMW47yn8sRQzyy6wWm0EPxFI6.svg\' target="_blank">View Figure (.svg)</a>  <a href=\'charts/PiR5FZazQpBZ2mMPmuU0sNb4G9NFns_legend.svg\' target="_blank">View Legend (.svg)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/PiR5FZazQpBZ2mMPmuU0sNb4G9NFns.png\' border=1 ismap usemap="#points" /> <img src=\'charts/PiR5FZazQpBZ2mMPmuU0sNb4G9NFns_legend.png\' border=1/><br></td>\n+</tr>\n+</table>\n+\n+\n+<table cellpadding=2 cellspacing=2 border=0><tr class=ntitle> <td valign=bottom class=header nowrap>Pct</td> <td valign=bottom class=header nowrap>Taxonomy</td></tr>\n+<tr class=normal><td nowrap>53.99%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Firmicutes\\\');>p__Firmicutes</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Firmicutes</a></td></tr><tr class=normal><td nowrap>35.93%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Bacteroidetes\\\');>p__Bacteroidetes</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Bacteroidetes</a></td></tr><tr class=normal><td nowrap>4.56%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Tenericutes\\\');>p__Tenericutes</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Tenericutes</a></td></tr><tr class=normal><td nowrap>2.54%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'Other\\\');>Other</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;Other</a></td></tr><tr class=normal><td nowrap>1.27%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Deferribacteres\\\');>p__Deferribacteres</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Deferribacteres</a></td></tr><tr class=normal><td nowrap>0.89%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Proteobacteria\\\');>p__Proteobacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Proteobacteria</a></td></tr><tr class=normal><td nowrap>0.67%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Actinobacteria\\\');>p__Actinobacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Actinobacteria</a></td></tr><tr class=normal><td nowrap>0.15%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__TM7\\\');>p__TM7</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__TM7</a></td></tr>\n+</table><table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: Class_PC.636</td></tr>\n+<tr><td class="ntitl'..b'a href=javascript:gg(\\\'p__Proteobacteria\\\');>p__Proteobacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Proteobacteria</a></td></tr><tr class=normal><td nowrap>2.01%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Deferribacteres\\\');>p__Deferribacteres</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Deferribacteres</a></td></tr><tr class=normal><td nowrap>2.01%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Actinobacteria\\\');>p__Actinobacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Actinobacteria</a></td></tr>\n+</table><table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: Class_PC.634</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/4m9zz5Q4iBYZGebRHMe27r9Oi04lMk.svg\' target="_blank">View Figure (.svg)</a>  <a href=\'charts/OQPbwZQzzSS95eE6HjOHNrw07UWGQB_legend.svg\' target="_blank">View Legend (.svg)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/OQPbwZQzzSS95eE6HjOHNrw07UWGQB.png\' border=1 ismap usemap="#points" /> <img src=\'charts/OQPbwZQzzSS95eE6HjOHNrw07UWGQB_legend.png\' border=1/><br></td>\n+</tr>\n+</table>\n+\n+\n+<table cellpadding=2 cellspacing=2 border=0><tr class=ntitle> <td valign=bottom class=header nowrap>Pct</td> <td valign=bottom class=header nowrap>Taxonomy</td></tr>\n+<tr class=normal><td nowrap>65.33%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Bacteroidetes\\\');>p__Bacteroidetes</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Bacteroidetes</a></td></tr><tr class=normal><td nowrap>22.00%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Firmicutes\\\');>p__Firmicutes</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Firmicutes</a></td></tr><tr class=normal><td nowrap>3.33%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Deferribacteres\\\');>p__Deferribacteres</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Deferribacteres</a></td></tr><tr class=normal><td nowrap>2.67%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Tenericutes\\\');>p__Tenericutes</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Tenericutes</a></td></tr><tr class=normal><td nowrap>2.00%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Actinobacteria\\\');>p__Actinobacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Actinobacteria</a></td></tr><tr class=normal><td nowrap>2.00%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'Other\\\');>Other</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;Other</a></td></tr><tr class=normal><td nowrap>1.33%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__TM7\\\');>p__TM7</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__TM7</a></td></tr><tr class=normal><td nowrap>1.33%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Proteobacteria\\\');>p__Proteobacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Proteobacteria</a></td></tr>\n+</table>\n+</body>\n+</html>\n'

diff -r 000000000000 -r c11972e98d44 test-data/plot_taxa_summary/class_colorby/area_charts.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r c11972e98d44 test-data/plot_taxa_summary/class_colorby/bar_charts.html
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+<table><tr class=ntitle><td><a href="raw_data/class.txt" target="_blank">View Table (.txt)</a></td></tr></table><table cellpadding=1 cellspacing=1 border=1 style="text-align:center;border-color:white;border-style:groove;"><tr class="ntitle"><td class="header" colspan="2"></td><td valign="bottom" class="header">Total</td><td valign=bottom class=header>PC.636</td><td valign=bottom class=header>PC.635</td></tr><tr class=ntitle><td valign="bottom" class="header">Legend</td><td valign="bottom" class="header">Taxonomy</td><td class="header">%</td><td class="header">%</td><td class="header">%</td></tr><tr><td class="normal" bgcolor="#ff0000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;<a href=javascript:gg('Other');>Other</a></td><td class="normal">  3.4%</td><td class="normal" style="border-color:#ff0000;">  2.0%</td><td class="normal" style="border-color:#ff0000;">  4.7%</td></tr><tr><td class="normal" bgcolor="#0000ff">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;<a href=javascript:gg('p__Actinobacteria');>p__Actinobacteria</a></td><td class="normal">  0.7%</td><td class="normal" style="border-color:#0000ff;">  0.7%</td><td class="normal" style="border-color:#0000ff;">  0.7%</td></tr><tr><td class="normal" bgcolor="#f27304">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;<a href=javascript:gg('p__Bacteroidetes');>p__Bacteroidetes</a></td><td class="normal"> 61.0%</td><td class="normal" style="border-color:#f27304;"> 69.6%</td><td class="normal" style="border-color:#f27304;"> 52.3%</td></tr><tr><td class="normal" bgcolor="#008000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;<a href=javascript:gg('p__Deferribacteres');>p__Deferribacteres</a></td><td class="normal">  3.0%</td><td class="normal" style="border-color:#008000;">  4.7%</td><td class="normal" style="border-color:#008000;">  1.3%</td></tr><tr><td class="normal" bgcolor="#91278d">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;<a href=javascript:gg('p__Firmicutes');>p__Firmicutes</a></td><td class="normal"> 30.3%</td><td class="normal" style="border-color:#91278d;"> 20.9%</td><td class="normal" style="border-color:#91278d;"> 39.6%</td></tr><tr><td class="normal" bgcolor="#ffff00">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;<a href=javascript:gg('p__Proteobacteria');>p__Proteobacteria</a></td><td class="normal">  0.7%</td><td class="normal" style="border-color:#ffff00;">  0.7%</td><td class="normal" style="border-color:#ffff00;">  0.7%</td></tr><tr><td class="normal" bgcolor="#7cecf4">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;<a href=javascript:gg('p__TM7');>p__TM7</a></td><td class="normal">  0.0%</td><td class="normal">  0.0%</td><td class="normal">  0.0%</td></tr><tr><td class="normal" bgcolor="#f49ac2">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;<a href=javascript:gg('p__Tenericutes');>p__Tenericutes</a></td><td class="normal">  1.0%</td><td class="normal" style="border-color:#f49ac2;">  1.4%</td><td class="normal" style="border-color:#f49ac2;">  0.7%</td></tr></table>
+</body>
+</html>

diff -r 000000000000 -r c11972e98d44 test-data/plot_taxa_summary/class_colorby/pie_charts.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plot_taxa_summary/class_colorby/pie_charts.html Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,66 @@\n+\n+<html>\n+<head>\n+<link rel="stylesheet" href="./css/qiime_style.css" type="text/css">\n+<script type="text/javascript" src="./js/overlib.js"></script>\n+\n+<script type="text/javascript">\n+\n+</script>\n+<title>Taxa Summaries</title>\n+</head>\n+<body>\n+<div id="overDiv" style="position:absolute; visibility:hidden; z-index:1000;"></div>\n+<table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: Class</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/Hs0Kz907GEjBp4Xo7zTbeNDAR0QTGi.pdf\' target="_blank">View Figure (.pdf)</a>  <a href=\'charts/1QmIkatDEfiQHtkRid0G5hwmbeyiDz_legend.pdf\' target="_blank">View Legend (.pdf)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/1QmIkatDEfiQHtkRid0G5hwmbeyiDz.png\' border=1 ismap usemap="#points" /><br></td>\n+</tr>\n+</table>\n+\n+\n+<table cellpadding=2 cellspacing=2 border=0><tr class=ntitle> <td valign=bottom class=header nowrap>Pct</td> <td valign=bottom class=header nowrap>Taxonomy</td></tr>\n+<tr class=normal><td nowrap>53.99%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Firmicutes\\\');>p__Firmicutes</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Firmicutes</a></td></tr><tr class=normal><td nowrap>35.93%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Bacteroidetes\\\');>p__Bacteroidetes</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Bacteroidetes</a></td></tr><tr class=normal><td nowrap>4.56%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Tenericutes\\\');>p__Tenericutes</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Tenericutes</a></td></tr><tr class=normal><td nowrap>2.54%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'Other\\\');>Other</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;Other</a></td></tr><tr class=normal><td nowrap>1.27%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Deferribacteres\\\');>p__Deferribacteres</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Deferribacteres</a></td></tr><tr class=normal><td nowrap>0.89%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Proteobacteria\\\');>p__Proteobacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Proteobacteria</a></td></tr><tr class=normal><td nowrap>0.67%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Actinobacteria\\\');>p__Actinobacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Actinobacteria</a></td></tr><tr class=normal><td nowrap>0.15%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__TM7\\\');>p__TM7</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__TM7</a></td></tr>\n+</table><table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: Class_PC.636</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/6zQ0pw19l3OcnYXPeCZLze7LAb0BIs.pdf\' target="_b'..b'lass="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'Other\\\');>Other</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;Other</a></td></tr><tr class=normal><td nowrap>1.35%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Tenericutes\\\');>p__Tenericutes</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Tenericutes</a></td></tr><tr class=normal><td nowrap>0.68%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Proteobacteria\\\');>p__Proteobacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Proteobacteria</a></td></tr><tr class=normal><td nowrap>0.68%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Actinobacteria\\\');>p__Actinobacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Actinobacteria</a></td></tr>\n+</table><table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: Class_PC.635</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/rzLqsayDE035A6YuZW0nMafXyUEjo6.pdf\' target="_blank">View Figure (.pdf)</a>  <a href=\'charts/LBlOGZSPUJtpdxl7nMRE29zUzg70TK_legend.pdf\' target="_blank">View Legend (.pdf)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/LBlOGZSPUJtpdxl7nMRE29zUzg70TK.png\' border=1 ismap usemap="#points" /><br></td>\n+</tr>\n+</table>\n+\n+\n+<table cellpadding=2 cellspacing=2 border=0><tr class=ntitle> <td valign=bottom class=header nowrap>Pct</td> <td valign=bottom class=header nowrap>Taxonomy</td></tr>\n+<tr class=normal><td nowrap>52.35%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Bacteroidetes\\\');>p__Bacteroidetes</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Bacteroidetes</a></td></tr><tr class=normal><td nowrap>39.60%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Firmicutes\\\');>p__Firmicutes</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Firmicutes</a></td></tr><tr class=normal><td nowrap>4.70%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'Other\\\');>Other</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;Other</a></td></tr><tr class=normal><td nowrap>1.34%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Deferribacteres\\\');>p__Deferribacteres</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Deferribacteres</a></td></tr><tr class=normal><td nowrap>0.67%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Tenericutes\\\');>p__Tenericutes</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Tenericutes</a></td></tr><tr class=normal><td nowrap>0.67%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Proteobacteria\\\');>p__Proteobacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Proteobacteria</a></td></tr><tr class=normal><td nowrap>0.67%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br><a href=javascript:gg(\\\'p__Actinobacteria\\\');>p__Actinobacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Actinobacteria</a></td></tr>\n+</table>\n+</body>\n+</html>\n'

diff -r 000000000000 -r c11972e98d44 test-data/plot_taxa_summary/family.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plot_taxa_summary/family.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,15 @@
+Taxon PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+Root;k__Bacteria;Other;Other;Other 0.0202702702703 0.0469798657718 0.0266666666667 0.027397260274 0.0134228187919 0.0134228187919 0.0136054421769 0.0469798657718 0.02
+Root;k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Coriobacteriales 0.00675675675676 0.00671140939597 0.0 0.00684931506849 0.0 0.0 0.0 0.0201342281879 0.02
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales 0.695945945946 0.523489932886 0.193333333333 0.143835616438 0.0738255033557 0.389261744966 0.285714285714 0.275167785235 0.653333333333
+Root;k__Bacteria;p__Deferribacteres;c__Deferribacteres;o__Deferribacterales 0.0472972972973 0.0134228187919 0.0 0.0 0.0 0.0 0.0 0.0201342281879 0.0333333333333
+Root;k__Bacteria;p__Firmicutes;Other;Other 0.0 0.0 0.0 0.0 0.00671140939597 0.0 0.0 0.0268456375839 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales 0.0202702702703 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales 0.0 0.0 0.0933333333333 0.027397260274 0.107382550336 0.0335570469799 0.0136054421769 0.00671140939597 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales 0.0 0.0 0.0 0.0616438356164 0.0 0.0 0.0 0.0 0.02
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales 0.189189189189 0.395973154362 0.68 0.698630136986 0.785234899329 0.38255033557 0.687074829932 0.422818791946 0.2
+Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales 0.00675675675676 0.00671140939597 0.0 0.0 0.0 0.0 0.0 0.00671140939597 0.0133333333333
+Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales 0.0 0.0 0.0 0.0 0.0 0.0335570469799 0.0 0.0134228187919 0.0
+Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0133333333333
+Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales 0.0135135135135 0.00671140939597 0.0 0.0342465753425 0.0134228187919 0.147651006711 0.0 0.154362416107 0.0266666666667
+Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39 0.0 0.0 0.00666666666667 0.0 0.0 0.0 0.0 0.00671140939597 0.0

diff -r 000000000000 -r c11972e98d44 test-data/plot_taxa_summary/genus.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plot_taxa_summary/genus.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,28 @@
+Taxon PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+Root;k__Bacteria;Other;Other;Other;Other 0.0202702702703 0.0469798657718 0.0266666666667 0.027397260274 0.0134228187919 0.0134228187919 0.0136054421769 0.0469798657718 0.02
+Root;k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Coriobacteriales;f__Coriobacteriaceae 0.00675675675676 0.00671140939597 0.0 0.00684931506849 0.0 0.0 0.0 0.0201342281879 0.02
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;Other 0.00675675675676 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__ 0.466216216216 0.308724832215 0.173333333333 0.0753424657534 0.0536912751678 0.362416107383 0.136054421769 0.201342281879 0.186666666667
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae 0.168918918919 0.0469798657718 0.0 0.013698630137 0.0134228187919 0.0268456375839 0.12925170068 0.0 0.273333333333
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae 0.0135135135135 0.0268456375839 0.0 0.00684931506849 0.0 0.0 0.00680272108844 0.0 0.08
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae 0.0 0.00671140939597 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae 0.0405405405405 0.134228187919 0.02 0.0479452054795 0.00671140939597 0.0 0.0136054421769 0.0738255033557 0.113333333333
+Root;k__Bacteria;p__Deferribacteres;c__Deferribacteres;o__Deferribacterales;f__Deferribacteraceae 0.0472972972973 0.0134228187919 0.0 0.0 0.0 0.0 0.0 0.0201342281879 0.0333333333333
+Root;k__Bacteria;p__Firmicutes;Other;Other;Other 0.0 0.0 0.0 0.0 0.00671140939597 0.0 0.0 0.0268456375839 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae 0.0202702702703 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae 0.0 0.0 0.0933333333333 0.027397260274 0.107382550336 0.0335570469799 0.0136054421769 0.0 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.00671140939597 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales;f__Turicibacteraceae 0.0 0.0 0.0 0.0616438356164 0.0 0.0 0.0 0.0 0.02
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;Other 0.0 0.0201342281879 0.02 0.00684931506849 0.00671140939597 0.00671140939597 0.0 0.0134228187919 0.00666666666667
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__ 0.0 0.00671140939597 0.00666666666667 0.0 0.00671140939597 0.00671140939597 0.0204081632653 0.00671140939597 0.0
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Catabacteriaceae 0.00675675675676 0.0 0.0 0.0 0.0 0.0 0.0 0.0268456375839 0.0
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae 0.0 0.0 0.0 0.0 0.00671140939597 0.0671140939597 0.00680272108844 0.0 0.02
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales Family XIII. Incertae Sedis 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.00671140939597 0.00666666666667
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae 0.114864864865 0.268456375839 0.58 0.650684931507 0.718120805369 0.275167785235 0.65306122449 0.268456375839 0.113333333333
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptococcaceae 0.0 0.00671140939597 0.0 0.0 0.00671140939597 0.00671140939597 0.0 0.00671140939597 0.0
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae 0.0675675675676 0.0939597315436 0.0733333333333 0.041095890411 0.0402684563758 0.0201342281879 0.00680272108844 0.0939597315436 0.0533333333333
+Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae 0.00675675675676 0.00671140939597 0.0 0.0 0.0 0.0 0.0 0.00671140939597 0.0133333333333
+Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae 0.0 0.0 0.0 0.0 0.0 0.0335570469799 0.0 0.0134228187919 0.0
+Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;f__F16 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0133333333333
+Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae 0.0135135135135 0.00671140939597 0.0 0.0342465753425 0.0134228187919 0.147651006711 0.0 0.154362416107 0.0266666666667
+Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;f__ 0.0 0.0 0.00666666666667 0.0 0.0 0.0 0.0 0.00671140939597 0.0

diff -r 000000000000 -r c11972e98d44 test-data/plot_taxa_summary/order.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plot_taxa_summary/order.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,13 @@
+Taxon PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+Root;k__Bacteria;Other;Other 0.0202702702703 0.0469798657718 0.0266666666667 0.027397260274 0.0134228187919 0.0134228187919 0.0136054421769 0.0469798657718 0.02
+Root;k__Bacteria;p__Actinobacteria;c__Actinobacteria 0.00675675675676 0.00671140939597 0.0 0.00684931506849 0.0 0.0 0.0 0.0201342281879 0.02
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia 0.695945945946 0.523489932886 0.193333333333 0.143835616438 0.0738255033557 0.389261744966 0.285714285714 0.275167785235 0.653333333333
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+Root;k__Bacteria;p__Firmicutes;Other 0.0 0.0 0.0 0.0 0.00671140939597 0.0 0.0 0.0268456375839 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli 0.0202702702703 0.0 0.0933333333333 0.0890410958904 0.107382550336 0.0335570469799 0.0136054421769 0.00671140939597 0.02
+Root;k__Bacteria;p__Firmicutes;c__Clostridia 0.189189189189 0.395973154362 0.68 0.698630136986 0.785234899329 0.38255033557 0.687074829932 0.422818791946 0.2
+Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria 0.00675675675676 0.00671140939597 0.0 0.0 0.0 0.0 0.0 0.00671140939597 0.0133333333333
+Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria 0.0 0.0 0.0 0.0 0.0 0.0335570469799 0.0 0.0134228187919 0.0
+Root;k__Bacteria;p__TM7;c__TM7-3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0133333333333
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+Root;k__Bacteria;p__Tenericutes;c__Mollicutes 0.0 0.0 0.00666666666667 0.0 0.0 0.0 0.0 0.00671140939597 0.0

diff -r 000000000000 -r c11972e98d44 test-data/plot_taxa_summary/phylum.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plot_taxa_summary/phylum.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,2 @@
+Taxon PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+Root;k__Bacteria 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0

diff -r 000000000000 -r c11972e98d44 test-data/plot_taxa_summary/phylum/area_charts.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plot_taxa_summary/phylum/area_charts.html Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,50 @@
+
+<html>
+<head>
+<link rel="stylesheet" href="./css/qiime_style.css" type="text/css">
+<script type="text/javascript" src="./js/overlib.js"></script>
+
+<script type="text/javascript">
+
+</script>
+<title>Taxa Summaries</title>
+</head>
+<body>
+<div id="overDiv" style="position:absolute; visibility:hidden; z-index:1000;"></div>
+<table cellpadding=2 cellspacing=2 border=0>
+<tr><td class="normal" colspan=2> </td></tr>
+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: phylum</td></tr>
+<tr><td class="ntitle">  <a href='charts/qaN0CXAQ2NmPWSC0oi0Z0kufbY0Mcz.png' target="_blank">View Figure (.png)</a>  <a href='charts/5YAc31nYQHo47Z6qSoMlHrfbaKZaus_legend.png' target="_blank">View Legend (.png)</a><br></td>
+<td class="ntitle"> </td>
+</tr>
+<tr><td class="ntitle"><img src='charts/5YAc31nYQHo47Z6qSoMlHrfbaKZaus.png' border=1 ismap usemap="#pointsrect1" /><br></td>
+</tr>
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+<AREA shape="rect" coords="118.1400%,864.0000%,121.8600%,96.0000%" href="#Root;k__Bacteria"  onmouseover="return overlib('PC.636:Root;k__Bacteria (100.00%)');" onmouseout="return nd();">
+<AREA shape="rect" coords="211.1400%,864.0000%,214.8600%,96.0000%" href="#Root;k__Bacteria"  onmouseover="return overlib('PC.635:Root;k__Bacteria (100.00%)');" onmouseout="return nd();">
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+
+</MAP>
+
+<table><tr class=ntitle><td><a href="raw_data/phylum.txt" target="_blank">View Table (.txt)</a></td></tr></table><table cellpadding=1 cellspacing=1 border=1 style="text-align:center;border-color:white;border-style:groove;"><tr class="ntitle"><td class="header" colspan="2"></td><td valign="bottom" class="header">Total</td><td valign=bottom class=header>PC.636</td><td valign=bottom class=header>PC.635</td><td valign=bottom class=header>PC.356</td><td valign=bottom class=header>PC.481</td><td valign=bottom class=header>PC.354</td><td valign=bottom class=header>PC.593</td><td valign=bottom class=header>PC.355</td><td valign=bottom class=header>PC.607</td><td valign=bottom class=header>PC.634</td></tr><tr class=ntitle><td valign="bottom" class="header">Legend</td><td valign="bottom" class="header">Taxonomy</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td></tr><tr><td class="normal" bgcolor="#ff0000">  </td><td style="text-align:left;" class="normal">Root;<a href=javascript:gg('k__Bacteria');>k__Bacteria</a></td><td class="normal">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td></tr></table>
+</body>
+</html>

diff -r 000000000000 -r c11972e98d44 test-data/plot_taxa_summary/phylum/bar_charts.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plot_taxa_summary/phylum/bar_charts.html Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,50 @@
+
+<html>
+<head>
+<link rel="stylesheet" href="./css/qiime_style.css" type="text/css">
+<script type="text/javascript" src="./js/overlib.js"></script>
+
+<script type="text/javascript">
+
+</script>
+<title>Taxa Summaries</title>
+</head>
+<body>
+<div id="overDiv" style="position:absolute; visibility:hidden; z-index:1000;"></div>
+<table cellpadding=2 cellspacing=2 border=0>
+<tr><td class="normal" colspan=2> </td></tr>
+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: phylum</td></tr>
+<tr><td class="ntitle">  <a href='charts/58r0P9wlFaQJIWsQSilirD3wwbcbD0.png' target="_blank">View Figure (.png)</a>  <a href='charts/RKpo8C2Wq8EzDCpl4isrAFqmB787RZ_legend.png' target="_blank">View Legend (.png)</a><br></td>
+<td class="ntitle"> </td>
+</tr>
+<tr><td class="ntitle"><img src='charts/RKpo8C2Wq8EzDCpl4isrAFqmB787RZ.png' border=1 ismap usemap="#pointsrect1" /><br></td>
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+<AREA shape="rect" coords="166.5000%,864.0000%,222.3000%,96.0000%" href="#Root;k__Bacteria"  onmouseover="return overlib('PC.636:Root;k__Bacteria (100.00%)');" onmouseout="return nd();">
+<AREA shape="rect" coords="240.9000%,864.0000%,296.7000%,96.0000%" href="#Root;k__Bacteria"  onmouseover="return overlib('PC.635:Root;k__Bacteria (100.00%)');" onmouseout="return nd();">
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+<AREA shape="rect" coords="464.1000%,864.0000%,519.9000%,96.0000%" href="#Root;k__Bacteria"  onmouseover="return overlib('PC.354:Root;k__Bacteria (100.00%)');" onmouseout="return nd();">
+<AREA shape="rect" coords="538.5000%,864.0000%,594.3000%,96.0000%" href="#Root;k__Bacteria"  onmouseover="return overlib('PC.593:Root;k__Bacteria (100.00%)');" onmouseout="return nd();">
+<AREA shape="rect" coords="612.9000%,864.0000%,668.7000%,96.0000%" href="#Root;k__Bacteria"  onmouseover="return overlib('PC.355:Root;k__Bacteria (100.00%)');" onmouseout="return nd();">
+<AREA shape="rect" coords="687.3000%,864.0000%,743.1000%,96.0000%" href="#Root;k__Bacteria"  onmouseover="return overlib('PC.607:Root;k__Bacteria (100.00%)');" onmouseout="return nd();">
+<AREA shape="rect" coords="761.7000%,864.0000%,817.5000%,96.0000%" href="#Root;k__Bacteria"  onmouseover="return overlib('PC.634:Root;k__Bacteria (100.00%)');" onmouseout="return nd();">
+
+</MAP>
+
+<table><tr class=ntitle><td><a href="raw_data/phylum.txt" target="_blank">View Table (.txt)</a></td></tr></table><table cellpadding=1 cellspacing=1 border=1 style="text-align:center;border-color:white;border-style:groove;"><tr class="ntitle"><td class="header" colspan="2"></td><td valign="bottom" class="header">Total</td><td valign=bottom class=header>PC.636</td><td valign=bottom class=header>PC.635</td><td valign=bottom class=header>PC.356</td><td valign=bottom class=header>PC.481</td><td valign=bottom class=header>PC.354</td><td valign=bottom class=header>PC.593</td><td valign=bottom class=header>PC.355</td><td valign=bottom class=header>PC.607</td><td valign=bottom class=header>PC.634</td></tr><tr class=ntitle><td valign="bottom" class="header">Legend</td><td valign="bottom" class="header">Taxonomy</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td></tr><tr><td class="normal" bgcolor="#ff0000">  </td><td style="text-align:left;" class="normal">Root;<a href=javascript:gg('k__Bacteria');>k__Bacteria</a></td><td class="normal">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td></tr></table>
+</body>
+</html>

diff -r 000000000000 -r c11972e98d44 test-data/plot_taxa_summary/phylum/pie_charts.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plot_taxa_summary/phylum/pie_charts.html Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,157 @@\n+\n+<html>\n+<head>\n+<link rel="stylesheet" href="./css/qiime_style.css" type="text/css">\n+<script type="text/javascript" src="./js/overlib.js"></script>\n+\n+<script type="text/javascript">\n+\n+</script>\n+<title>Taxa Summaries</title>\n+</head>\n+<body>\n+<div id="overDiv" style="position:absolute; visibility:hidden; z-index:1000;"></div>\n+<table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: phylum</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/Sep2T6QyXquZh6Hw9Y0BSAuOp4lP4b.png\' target="_blank">View Figure (.png)</a>  <a href=\'charts/spW1AZyK0fKk0zYdBO22Z2NgzeX30k_legend.png\' target="_blank">View Legend (.png)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/spW1AZyK0fKk0zYdBO22Z2NgzeX30k.png\' border=1 ismap usemap="#points" /><br></td>\n+</tr>\n+</table>\n+\n+\n+<table cellpadding=2 cellspacing=2 border=0><tr class=ntitle> <td valign=bottom class=header nowrap>Pct</td> <td valign=bottom class=header nowrap>Taxonomy</td></tr>\n+<tr class=normal><td nowrap>100.00%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br><a href=javascript:gg(\\\'k__Bacteria\\\');>k__Bacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria</a></td></tr>\n+</table><table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: phylum_PC.636</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/5b3CgEzjI8z0CpUZklWxaY1c0m10y4.png\' target="_blank">View Figure (.png)</a>  <a href=\'charts/aa66D0pyHei7b2C10HkqL2ha7kaB58_legend.png\' target="_blank">View Legend (.png)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/aa66D0pyHei7b2C10HkqL2ha7kaB58.png\' border=1 ismap usemap="#points" /><br></td>\n+</tr>\n+</table>\n+\n+\n+<table cellpadding=2 cellspacing=2 border=0><tr class=ntitle> <td valign=bottom class=header nowrap>Pct</td> <td valign=bottom class=header nowrap>Taxonomy</td></tr>\n+<tr class=normal><td nowrap>100.00%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br><a href=javascript:gg(\\\'k__Bacteria\\\');>k__Bacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria</a></td></tr>\n+</table><table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: phylum_PC.635</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/O0npuXflZpq2AA4DKZXqZnL947jIkA.png\' target="_blank">View Figure (.png)</a>  <a href=\'charts/JuiMb9mZ8k7WuPDsAKZLjPyx1LnNtR_legend.png\' target="_blank">View Legend (.png)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/JuiMb9mZ8k7WuPDsAKZLjPyx1LnNtR.png\' border=1 ismap usemap="#points" /><br></td>\n+</tr>\n+</table>\n+\n+\n+<table cellpadding=2 cellspacing=2 border=0><tr class=ntitle> <td valign=bottom class=header nowrap>Pct</td> <td valign=bottom class=header nowrap>Taxonomy</td></tr>\n+<tr class=normal><td nowrap>100.00%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br><a href=javascript:gg(\\\'k__Bacteria\\\');>k__Bacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria</a></td></tr>\n+</table><table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: phylum_PC.356</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/PP8lCZYp0g'..b'a href=\'charts/OrLGHxrD4I9gy02ByLosAfaEz5kZmT.png\' target="_blank">View Figure (.png)</a>  <a href=\'charts/tmEIGUfxxmO3U33Hr8gPd9WpDLzOYq_legend.png\' target="_blank">View Legend (.png)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/tmEIGUfxxmO3U33Hr8gPd9WpDLzOYq.png\' border=1 ismap usemap="#points" /><br></td>\n+</tr>\n+</table>\n+\n+\n+<table cellpadding=2 cellspacing=2 border=0><tr class=ntitle> <td valign=bottom class=header nowrap>Pct</td> <td valign=bottom class=header nowrap>Taxonomy</td></tr>\n+<tr class=normal><td nowrap>100.00%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br><a href=javascript:gg(\\\'k__Bacteria\\\');>k__Bacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria</a></td></tr>\n+</table><table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: phylum_PC.355</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/l5ByrNZSmzdCf1QrIbkp2084T07lGk.png\' target="_blank">View Figure (.png)</a>  <a href=\'charts/LXuzZoyGD7OS0ZwS50LSNKjW7ZTL44_legend.png\' target="_blank">View Legend (.png)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/LXuzZoyGD7OS0ZwS50LSNKjW7ZTL44.png\' border=1 ismap usemap="#points" /><br></td>\n+</tr>\n+</table>\n+\n+\n+<table cellpadding=2 cellspacing=2 border=0><tr class=ntitle> <td valign=bottom class=header nowrap>Pct</td> <td valign=bottom class=header nowrap>Taxonomy</td></tr>\n+<tr class=normal><td nowrap>100.00%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br><a href=javascript:gg(\\\'k__Bacteria\\\');>k__Bacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria</a></td></tr>\n+</table><table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: phylum_PC.607</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/0Xw4oHBqdraznUyhBljMFCE0DYfhEA.png\' target="_blank">View Figure (.png)</a>  <a href=\'charts/UZUwD6hqcNiKFAloxiqOnAxMIEMPtI_legend.png\' target="_blank">View Legend (.png)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/UZUwD6hqcNiKFAloxiqOnAxMIEMPtI.png\' border=1 ismap usemap="#points" /><br></td>\n+</tr>\n+</table>\n+\n+\n+<table cellpadding=2 cellspacing=2 border=0><tr class=ntitle> <td valign=bottom class=header nowrap>Pct</td> <td valign=bottom class=header nowrap>Taxonomy</td></tr>\n+<tr class=normal><td nowrap>100.00%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br><a href=javascript:gg(\\\'k__Bacteria\\\');>k__Bacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria</a></td></tr>\n+</table><table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: phylum_PC.634</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/DyuQ2xpbMr1zwZXUkSmdAEzLXtu6zE.png\' target="_blank">View Figure (.png)</a>  <a href=\'charts/u4h5QIk6q07Ha8ONf2ObOwN73Z5lst_legend.png\' target="_blank">View Legend (.png)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/u4h5QIk6q07Ha8ONf2ObOwN73Z5lst.png\' border=1 ismap usemap="#points" /><br></td>\n+</tr>\n+</table>\n+\n+\n+<table cellpadding=2 cellspacing=2 border=0><tr class=ntitle> <td valign=bottom class=header nowrap>Pct</td> <td valign=bottom class=header nowrap>Taxonomy</td></tr>\n+<tr class=normal><td nowrap>100.00%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br><a href=javascript:gg(\\\'k__Bacteria\\\');>k__Bacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria</a></td></tr>\n+</table>\n+</body>\n+</html>\n'

diff -r 000000000000 -r c11972e98d44 test-data/plot_taxa_summary/phylum_class_genus/area_charts.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plot_taxa_summary/phylum_class_genus/area_charts.html Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,247 @@\n+\n+<html>\n+<head>\n+<link rel="stylesheet" href="./css/qiime_style.css" type="text/css">\n+<script type="text/javascript" src="./js/overlib.js"></script>\n+\n+<script type="text/javascript">\n+\n+</script>\n+<title>Taxa Summaries</title>\n+</head>\n+<body>\n+<div id="overDiv" style="position:absolute; visibility:hidden; z-index:1000;"></div>\n+<table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: Phylum</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/t4cgszzZIThJaTrA2xTORP3378s0ZM.png\' target="_blank">View Figure (.png)</a>  <a href=\'charts/IaIkWkOrejBihXYEzFCFkZDe0PqtGf_legend.png\' target="_blank">View Legend (.png)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/IaIkWkOrejBihXYEzFCFkZDe0PqtGf.png\' border=1 ismap usemap="#pointsrect1" /><br></td>\n+</tr>\n+</table>\n+\n+<MAP name="pointsrect1">\n+<AREA shape="rect" coords="118.1400%,864.0000%,121.8600%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.636:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="211.1400%,864.0000%,214.8600%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.635:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="304.1400%,864.0000%,307.8600%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.356:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="397.1400%,864.0000%,400.8600%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.481:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="490.1400%,864.0000%,493.8600%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.354:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="583.1400%,864.0000%,586.8600%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.593:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="676.1400%,864.0000%,679.8600%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.355:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="769.1400%,864.0000%,772.8600%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.607:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="862.1400%,864.0000%,865.8600%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.634:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+\n+</MAP>\n+\n+<table><tr class=ntitle><td><a href="raw_data/phylum.txt" target="_blank">View Table (.txt)</a></td></tr></table><table cellpadding=1 cellspacing=1 border=1 style="text-align:center;border-color:white;border-style:groove;"><tr class="ntitle"><td class="header" colspan="2"></td><td valign="bottom" class="header">Total</td><td valign=bottom class=header>PC.636</td><td valign=bottom class=header>PC.635</td><td valign=bottom class=header>PC.356</td><td valign=bottom class=header>PC.481</td><td valign=bottom class=header>PC.354</td><td valign=bottom class=header>PC.593</td><td valign=bottom class=header>PC.355</td><td valign=bottom class=header>PC.607</td><td valign=bottom class=header>PC.634</td></tr><tr class=ntitle><td valign="bottom" class="header">Legend</td><td valign="bottom" class="header">Taxonomy</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header"'..b'mal"> 5.4%</td><td class="normal" style="border-color:#c49c6b;"> 6.8%</td><td class="normal" style="border-color:#c49c6b;"> 9.4%</td><td class="normal" style="border-color:#c49c6b;"> 7.3%</td><td class="normal" style="border-color:#c49c6b;"> 4.1%</td><td class="normal" style="border-color:#c49c6b;"> 4.0%</td><td class="normal" style="border-color:#c49c6b;"> 2.0%</td><td class="normal" style="border-color:#c49c6b;"> 0.7%</td><td class="normal" style="border-color:#c49c6b;"> 9.4%</td><td class="normal" style="border-color:#c49c6b;"> 5.3%</td></tr><tr><td class="normal" bgcolor="#808000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;<a href=javascript:gg(\'f__Desulfovibrionaceae\');>f__Desulfovibrionaceae</a></td><td class="normal"> 0.4%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal" style="border-color:#808000;"> 1.3%</td></tr><tr><td class="normal" bgcolor="#8c3fff">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;<a href=javascript:gg(\'f__Helicobacteraceae\');>f__Helicobacteraceae</a></td><td class="normal"> 0.5%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#8c3fff;"> 3.4%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#8c3fff;"> 1.3%</td><td class="normal"> 0.0%</td></tr><tr><td class="normal" bgcolor="#bc828d">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;<a href=javascript:gg(\'f__F16\');>f__F16</a></td><td class="normal"> 0.1%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#bc828d;"> 1.3%</td></tr><tr><td class="normal" bgcolor="#008080">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;<a href=javascript:gg(\'f__Erysipelotrichaceae\');>f__Erysipelotrichaceae</a></td><td class="normal"> 4.4%</td><td class="normal" style="border-color:#008080;"> 1.4%</td><td class="normal" style="border-color:#008080;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#008080;"> 3.4%</td><td class="normal" style="border-color:#008080;"> 1.3%</td><td class="normal" style="border-color:#008080;"> 14.8%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#008080;"> 15.4%</td><td class="normal" style="border-color:#008080;"> 2.7%</td></tr><tr><td class="normal" bgcolor="#800000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;<a href=javascript:gg(\'f__\');>f__</a></td><td class="normal"> 0.1%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#800000;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#800000;"> 0.7%</td><td class="normal"> 0.0%</td></tr></table>\n+</body>\n+</html>\n'

diff -r 000000000000 -r c11972e98d44 test-data/plot_taxa_summary/phylum_class_genus/bar_charts.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plot_taxa_summary/phylum_class_genus/bar_charts.html Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,247 @@\n+\n+<html>\n+<head>\n+<link rel="stylesheet" href="./css/qiime_style.css" type="text/css">\n+<script type="text/javascript" src="./js/overlib.js"></script>\n+\n+<script type="text/javascript">\n+\n+</script>\n+<title>Taxa Summaries</title>\n+</head>\n+<body>\n+<div id="overDiv" style="position:absolute; visibility:hidden; z-index:1000;"></div>\n+<table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: Phylum</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/HuMhmfslKaYJiRzHoHuXnjhmeKUaAS.png\' target="_blank">View Figure (.png)</a>  <a href=\'charts/KtTFt0sTJktLujcsRlXlmb3qbHs4KM_legend.png\' target="_blank">View Legend (.png)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/KtTFt0sTJktLujcsRlXlmb3qbHs4KM.png\' border=1 ismap usemap="#pointsrect1" /><br></td>\n+</tr>\n+</table>\n+\n+<MAP name="pointsrect1">\n+<AREA shape="rect" coords="166.5000%,864.0000%,222.3000%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.636:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="240.9000%,864.0000%,296.7000%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.635:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="315.3000%,864.0000%,371.1000%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.356:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="389.7000%,864.0000%,445.5000%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.481:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="464.1000%,864.0000%,519.9000%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.354:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="538.5000%,864.0000%,594.3000%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.593:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="612.9000%,864.0000%,668.7000%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.355:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="687.3000%,864.0000%,743.1000%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.607:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="761.7000%,864.0000%,817.5000%,96.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.634:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+\n+</MAP>\n+\n+<table><tr class=ntitle><td><a href="raw_data/phylum.txt" target="_blank">View Table (.txt)</a></td></tr></table><table cellpadding=1 cellspacing=1 border=1 style="text-align:center;border-color:white;border-style:groove;"><tr class="ntitle"><td class="header" colspan="2"></td><td valign="bottom" class="header">Total</td><td valign=bottom class=header>PC.636</td><td valign=bottom class=header>PC.635</td><td valign=bottom class=header>PC.356</td><td valign=bottom class=header>PC.481</td><td valign=bottom class=header>PC.354</td><td valign=bottom class=header>PC.593</td><td valign=bottom class=header>PC.355</td><td valign=bottom class=header>PC.607</td><td valign=bottom class=header>PC.634</td></tr><tr class=ntitle><td valign="bottom" class="header">Legend</td><td valign="bottom" class="header">Taxonomy</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header"'..b'mal"> 5.4%</td><td class="normal" style="border-color:#c49c6b;"> 6.8%</td><td class="normal" style="border-color:#c49c6b;"> 9.4%</td><td class="normal" style="border-color:#c49c6b;"> 7.3%</td><td class="normal" style="border-color:#c49c6b;"> 4.1%</td><td class="normal" style="border-color:#c49c6b;"> 4.0%</td><td class="normal" style="border-color:#c49c6b;"> 2.0%</td><td class="normal" style="border-color:#c49c6b;"> 0.7%</td><td class="normal" style="border-color:#c49c6b;"> 9.4%</td><td class="normal" style="border-color:#c49c6b;"> 5.3%</td></tr><tr><td class="normal" bgcolor="#808000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;<a href=javascript:gg(\'f__Desulfovibrionaceae\');>f__Desulfovibrionaceae</a></td><td class="normal"> 0.4%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal" style="border-color:#808000;"> 1.3%</td></tr><tr><td class="normal" bgcolor="#8c3fff">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;<a href=javascript:gg(\'f__Helicobacteraceae\');>f__Helicobacteraceae</a></td><td class="normal"> 0.5%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#8c3fff;"> 3.4%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#8c3fff;"> 1.3%</td><td class="normal"> 0.0%</td></tr><tr><td class="normal" bgcolor="#bc828d">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;<a href=javascript:gg(\'f__F16\');>f__F16</a></td><td class="normal"> 0.1%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#bc828d;"> 1.3%</td></tr><tr><td class="normal" bgcolor="#008080">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;<a href=javascript:gg(\'f__Erysipelotrichaceae\');>f__Erysipelotrichaceae</a></td><td class="normal"> 4.4%</td><td class="normal" style="border-color:#008080;"> 1.4%</td><td class="normal" style="border-color:#008080;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#008080;"> 3.4%</td><td class="normal" style="border-color:#008080;"> 1.3%</td><td class="normal" style="border-color:#008080;"> 14.8%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#008080;"> 15.4%</td><td class="normal" style="border-color:#008080;"> 2.7%</td></tr><tr><td class="normal" bgcolor="#800000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;<a href=javascript:gg(\'f__\');>f__</a></td><td class="normal"> 0.1%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#800000;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#800000;"> 0.7%</td><td class="normal"> 0.0%</td></tr></table>\n+</body>\n+</html>\n'

diff -r 000000000000 -r c11972e98d44 test-data/plot_taxa_summary/phylum_class_genus/pie_charts.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plot_taxa_summary/phylum_class_genus/pie_charts.html Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,417 @@\n+\n+<html>\n+<head>\n+<link rel="stylesheet" href="./css/qiime_style.css" type="text/css">\n+<script type="text/javascript" src="./js/overlib.js"></script>\n+\n+<script type="text/javascript">\n+\n+</script>\n+<title>Taxa Summaries</title>\n+</head>\n+<body>\n+<div id="overDiv" style="position:absolute; visibility:hidden; z-index:1000;"></div>\n+<table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: Phylum</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/tBXLhGZlYxtoNFctt3TTsHz4olz2r9.png\' target="_blank">View Figure (.png)</a>  <a href=\'charts/oPRcoNiZg3lorgiWTsGtogxc0FHnzh_legend.png\' target="_blank">View Legend (.png)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/oPRcoNiZg3lorgiWTsGtogxc0FHnzh.png\' border=1 ismap usemap="#points" /><br></td>\n+</tr>\n+</table>\n+\n+\n+<table cellpadding=2 cellspacing=2 border=0><tr class=ntitle> <td valign=bottom class=header nowrap>Pct</td> <td valign=bottom class=header nowrap>Taxonomy</td></tr>\n+<tr class=normal><td nowrap>100.00%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br><a href=javascript:gg(\\\'k__Bacteria\\\');>k__Bacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria</a></td></tr>\n+</table><table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: Phylum_PC.636</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/MXE7Z7eCExEwoIocSLPjxLRrTzYt8A.png\' target="_blank">View Figure (.png)</a>  <a href=\'charts/fmrdCwnCTaMpK36gsYFcRn1PUAedTW_legend.png\' target="_blank">View Legend (.png)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/fmrdCwnCTaMpK36gsYFcRn1PUAedTW.png\' border=1 ismap usemap="#points" /><br></td>\n+</tr>\n+</table>\n+\n+\n+<table cellpadding=2 cellspacing=2 border=0><tr class=ntitle> <td valign=bottom class=header nowrap>Pct</td> <td valign=bottom class=header nowrap>Taxonomy</td></tr>\n+<tr class=normal><td nowrap>100.00%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br><a href=javascript:gg(\\\'k__Bacteria\\\');>k__Bacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria</a></td></tr>\n+</table><table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: Phylum_PC.635</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/n4l7Wezk4mOits3PZLPCeUZ20weMhs.png\' target="_blank">View Figure (.png)</a>  <a href=\'charts/n99uUk3OyYaW2Kwb4Ph53HNMNWpbYq_legend.png\' target="_blank">View Legend (.png)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/n99uUk3OyYaW2Kwb4Ph53HNMNWpbYq.png\' border=1 ismap usemap="#points" /><br></td>\n+</tr>\n+</table>\n+\n+\n+<table cellpadding=2 cellspacing=2 border=0><tr class=ntitle> <td valign=bottom class=header nowrap>Pct</td> <td valign=bottom class=header nowrap>Taxonomy</td></tr>\n+<tr class=normal><td nowrap>100.00%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br><a href=javascript:gg(\\\'k__Bacteria\\\');>k__Bacteria</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria</a></td></tr>\n+</table><table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: Phylum_PC.356</td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/FPHRBkX46c'..b'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br>p__Deferribacteres<br>c__Deferribacteres<br>o__Deferribacterales<br><a href=javascript:gg(\\\'f__Deferribacteraceae\\\');>f__Deferribacteraceae</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Deferribacteres;c__Deferribacteres;o__Deferribacterales;f__Deferribacteraceae</a></td></tr><tr class=normal><td nowrap>2.67%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br>p__Tenericutes<br>c__Erysipelotrichi<br>o__Erysipelotrichales<br><a href=javascript:gg(\\\'f__Erysipelotrichaceae\\\');>f__Erysipelotrichaceae</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae</a></td></tr><tr class=normal><td nowrap>2.00%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br>p__Firmicutes<br>c__Clostridia<br>o__Clostridiales<br><a href=javascript:gg(\\\'f__Clostridiaceae\\\');>f__Clostridiaceae</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae</a></td></tr><tr class=normal><td nowrap>2.00%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br>p__Firmicutes<br>c__Bacilli<br>o__Turicibacterales<br><a href=javascript:gg(\\\'f__Turicibacteraceae\\\');>f__Turicibacteraceae</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales;f__Turicibacteraceae</a></td></tr><tr class=normal><td nowrap>2.00%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br>p__Actinobacteria<br>c__Actinobacteria<br>o__Coriobacteriales<br><a href=javascript:gg(\\\'f__Coriobacteriaceae\\\');>f__Coriobacteriaceae</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Coriobacteriales;f__Coriobacteriaceae</a></td></tr><tr class=normal><td nowrap>2.00%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br>Other<br>Other<br>Other<br><a href=javascript:gg(\\\'Other\\\');>Other</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;Other;Other;Other;Other</a></td></tr><tr class=normal><td nowrap>1.33%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br>p__TM7<br>c__TM7-3<br>o__CW040<br><a href=javascript:gg(\\\'f__F16\\\');>f__F16</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;f__F16</a></td></tr><tr class=normal><td nowrap>1.33%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br>p__Proteobacteria<br>c__Deltaproteobacteria<br>o__Desulfovibrionales<br><a href=javascript:gg(\\\'f__Desulfovibrionaceae\\\');>f__Desulfovibrionaceae</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae</a></td></tr><tr class=normal><td nowrap>0.67%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br>p__Firmicutes<br>c__Clostridia<br>o__Clostridiales<br><a href=javascript:gg(\\\'f__Clostridiales Family XIII. Incertae Sedis\\\');>f__Clostridiales Family XIII. Incertae Sedis</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales Family XIII. Incertae Sedis</a></td></tr><tr class=normal><td nowrap>0.67%</td><td class="normal" ><a onmouseover="return overlib(\'<b>Taxonomy:</b><br>Root<br>k__Bacteria<br>p__Firmicutes<br>c__Clostridia<br>o__Clostridiales<br><a href=javascript:gg(\\\'Other\\\');>Other</a> \',STICKY,MOUSEOFF,RIGHT);" onmouseout="return nd();">Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;Other</a></td></tr>\n+</table>\n+</body>\n+</html>\n'

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries/histograms.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries/histograms.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,9 @@
+# bins raw sequence lengths, length of sequences that pass quality filters before processing, and lengths of sequences that pass quality filters post processing.
+Length Raw Before After
+210 0 0 6
+220 0 0 0
+230 0 0 0
+240 2 2 2
+250 4 4 0
+260 0 0 0
+270 2 2 0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries/mapping_file.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries/mapping_file.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries/reads_1.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries/reads_1.fna Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,24 @@
+>FLP3FBN01ELBSX length=250 xy=1766_0111 region=1 run=R_2008_12_09_13_51_01_
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGG
+CCGTTTACCCTCTCAGGCCGGCTACGCATCATCGCCTTGGTGGGCCGTTACCTCACCAAC
+TAGCTAATGCGCCGCAGGTCCATCCATGTTCACGCCTTGATGGGCGCTTTAATATACTGA
+GCATGCGCTCTGTATACCTATCCGGTTTTAGCTACCGTTTCCAGCAGTTATCCCGGACAC
+ATGGGCTAGG
+>FLP3FBN01EG8AX length=276 xy=1719_1463 region=1 run=R_2008_12_09_13_51_01_
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGG
+GGGCCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACA
+ACCTAATGGAACGCATCCCCATCGATGACCGAAGTTCTTTAATAGTTCTACCATGCGGAA
+GAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGG
+TTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCA
+>FLP3FBN01EEWKD length=244 xy=1692_3531 region=1 run=R_2008_12_09_13_51_01_
+AGCACGAGCCTACATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGG
+CCGATCAGTCTCTTAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCTTACCAAC
+TAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGA
+CATGCGTCTAGTGTTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCT
+TGGG
+>FLP3FBN01DEHK3 length=252 xy=1278_0245 region=1 run=R_2008_12_09_13_51_01_
+ACCAGCGACTAGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGG
+CCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAAC
+TATCTAATCAGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGGTATTCCGGCGATGC
+CGCCAAAATCATTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGC
+AGGTTGCTCACG
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries/reads_1.qual
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries/reads_1.qual Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,24 @@
+>FLP3FBN01ELBSX length=250 xy=1766_0111 region=1 run=R_2008_12_09_13_51_01_
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 33 33 33 36 37 37 37 37 37 37 40 40 40 39 39 38 40 40 40 40 40 40 40 37 37 37 37 37 35 35 35 37 37 37 35 37 35 35
+35 31 31 23 23 23 31 21 21 21 35 35 37 37 37 36 36 36 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 28 28 28 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 35 32 32 32 32 35 37 37 37 37
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 32 32 32 36 37 35 32 32 32 32 32 32 32 32 36 37 37 37 37 36 36 31 31 32 32 36 36 36 36 36 36 36 36 36 36 36 28 27 27 27 26 26 26 30 29
+30 29 24 24 24 21 15 15 13 13
+>FLP3FBN01EG8AX length=276 xy=1719_1463 region=1 run=R_2008_12_09_13_51_01_
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 38 37 33 33 21 21 21 26 33 37 36 36 40 33 24 24 29 33 33 39 39 39 40 39 39 39 40 37 37 37 37 37 37 37 37 37 37 37 32 32 20 20
+20 20 20 35 35 37 37 37 37 37 37 37 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 36 36 36 36 37 37 37 37 37 36 36 36 36 37 37
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 33 28 28 28 28 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 33 33 33 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37
+37 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 28 28 28 37 28 28 28 37 37 37 37 37 36 36 36 36 36 28 26 26 26 26 28 36 36 36 36 36 36 36 37 38 38 38 38 38
+37 37 37 37 37 31 31 31 31 31 31 31 31 31 31 31 31 30 22 22 22 25 25 31 31 31 31 31 31 31 25 25 25 25 25 28
+>FLP3FBN01EEWKD length=244 xy=1692_3531 region=1 run=R_2008_12_09_13_51_01_
+36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 33 33 26 21 21 31 36 37 37 37 36 36 33 34 34 36 37 36 37 37 37 37 37 37 37 37 37 37 37 36 28 28 28 36 36 37 37 35 35 35
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 32 32 32 35 35 37 35 32 32 32 37 37 37 37 37 37 36 36 36 36 36
+36 36 36 37 37 37 37 37 37 37 35 35 35 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 35 35 35 37 37 37 37 37 37 37 37 37 37 36 36 36 37 36 35 35 35 37 28 28 28 32 35 37 37 37 36 36
+36 37 37 37 37 37 37 35 35 35 35 35 37 37 37 37 36 36 36 37 28 28 28 28 35 36 37 37 37 37 37 37 37 37 37 37 36 33 33 32 31 36 36 33 33 27 27 27 36 31 25 25 25 32 36 36 36 36 36 36
+36 36 36 36
+>FLP3FBN01DEHK3 length=252 xy=1278_0245 region=1 run=R_2008_12_09_13_51_01_
+36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 40 40 40 40 40 40 40 40 40 40 38 38 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 37 37 37 37 37 33 33 33 36 36 37 37 37 37 37
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 33 33 33 33 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 36 36 28 28 28 28 33 33 33 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 36 36 36 36 31 31 27 27 28 28 28 27 21 31 31 36 36 36 36 36 36
+36 36 36 36 36 31 31 31 31 31 31 31
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries/reads_2.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries/reads_2.fna Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,24 @@
+>FLP3FBN01ELBSX1 length=250 xy=1766_0111 region=1 run=R_2008_12_09_13_51_01_
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGG
+CCGTTTACCCTCTCAGGCCGGCTACGCATCATCGCCTTGGTGGGCCGTTACCTCACCAAC
+TAGCTAATGCGCCGCAGGTCCATCCATGTTCACGCCTTGATGGGCGCTTTAATATACTGA
+GCATGCGCTCTGTATACCTATCCGGTTTTAGCTACCGTTTCCAGCAGTTATCCCGGACAC
+ATGGGCTAGG
+>FLP3FBN01EG8AX2 length=276 xy=1719_1463 region=1 run=R_2008_12_09_13_51_01_
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGG
+GGGCCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACA
+ACCTAATGGAACGCATCCCCATCGATGACCGAAGTTCTTTAATAGTTCTACCATGCGGAA
+GAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGG
+TTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCA
+>FLP3FBN01EEWKD3 length=244 xy=1692_3531 region=1 run=R_2008_12_09_13_51_01_
+AGCACGAGCCTACATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGG
+CCGATCAGTCTCTTAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCTTACCAAC
+TAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGA
+CATGCGTCTAGTGTTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCT
+TGGG
+>FLP3FBN01DEHK34 length=252 xy=1278_0245 region=1 run=R_2008_12_09_13_51_01_
+ACCAGCGACTAGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGG
+CCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAAC
+TATCTAATCAGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGGTATTCCGGCGATGC
+CGCCAAAATCATTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGC
+AGGTTGCTCACG
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries/reads_2.qual
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries/reads_2.qual Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,24 @@
+>FLP3FBN01ELBSX1 length=250 xy=1766_0111 region=1 run=R_2008_12_09_13_51_01_
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 33 33 33 36 37 37 37 37 37 37 40 40 40 39 39 38 40 40 40 40 40 40 40 37 37 37 37 37 35 35 35 37 37 37 35 37 35 35
+35 31 31 23 23 23 31 21 21 21 35 35 37 37 37 36 36 36 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 28 28 28 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 35 32 32 32 32 35 37 37 37 37
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 32 32 32 36 37 35 32 32 32 32 32 32 32 32 36 37 37 37 37 36 36 31 31 32 32 36 36 36 36 36 36 36 36 36 36 36 28 27 27 27 26 26 26 30 29
+30 29 24 24 24 21 15 15 13 13
+>FLP3FBN01EG8AX2 length=276 xy=1719_1463 region=1 run=R_2008_12_09_13_51_01_
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 38 37 33 33 21 21 21 26 33 37 36 36 40 33 24 24 29 33 33 39 39 39 40 39 39 39 40 37 37 37 37 37 37 37 37 37 37 37 32 32 20 20
+20 20 20 35 35 37 37 37 37 37 37 37 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 36 36 36 36 37 37 37 37 37 36 36 36 36 37 37
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 33 28 28 28 28 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 33 33 33 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37
+37 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 28 28 28 37 28 28 28 37 37 37 37 37 36 36 36 36 36 28 26 26 26 26 28 36 36 36 36 36 36 36 37 38 38 38 38 38
+37 37 37 37 37 31 31 31 31 31 31 31 31 31 31 31 31 30 22 22 22 25 25 31 31 31 31 31 31 31 25 25 25 25 25 28
+>FLP3FBN01EEWKD3 length=244 xy=1692_3531 region=1 run=R_2008_12_09_13_51_01_
+36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 33 33 26 21 21 31 36 37 37 37 36 36 33 34 34 36 37 36 37 37 37 37 37 37 37 37 37 37 37 36 28 28 28 36 36 37 37 35 35 35
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 32 32 32 35 35 37 35 32 32 32 37 37 37 37 37 37 36 36 36 36 36
+36 36 36 37 37 37 37 37 37 37 35 35 35 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 35 35 35 37 37 37 37 37 37 37 37 37 37 36 36 36 37 36 35 35 35 37 28 28 28 32 35 37 37 37 36 36
+36 37 37 37 37 37 37 35 35 35 35 35 37 37 37 37 36 36 36 37 28 28 28 28 35 36 37 37 37 37 37 37 37 37 37 37 36 33 33 32 31 36 36 33 33 27 27 27 36 31 25 25 25 32 36 36 36 36 36 36
+36 36 36 36
+>FLP3FBN01DEHK34 length=252 xy=1278_0245 region=1 run=R_2008_12_09_13_51_01_
+36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 40 40 40 40 40 40 40 40 40 40 38 38 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 37 37 37 37 37 33 33 33 36 36 37 37 37 37 37
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 33 33 33 33 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 36 36 28 28 28 28 33 33 33 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 36 36 36 36 31 31 27 27 28 28 28 27 21 31 31 36 36 36 36 36 36
+36 36 36 36 36 31 31 31 31 31 31 31
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries/seqs.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries/seqs.fna Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,16 @@
+>PC.634_1 FLP3FBN01ELBSX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTTACCCTCTCAGGCCGGCTACGCATCATCGCCTTGGTGGGCCGTTACCTCACCAACTAGCTAATGCGCCGCAGGTCCATCCATGTTCACGCCTTGATGGGCGCTTTAATATACTGAGCATGCGCTCTGTATACCTATCCGGTTTTAGCTACCGTTTCCAGCAGTTATCCCGGACACATGGGCTAGG
+>PC.634_2 FLP3FBN01EG8AX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
+TTGGACCGTGTCTCAGTTCCAATGTGGGGGCCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACAACCTAATGGAACGCATCCCCATCGATGACCGAAGTTCTTTAATAGTTCTACCATGCGGAAGAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCA
+>PC.354_3 FLP3FBN01EEWKD orig_bc=AGCACGAGCCTA new_bc=AGCACGAGCCTA bc_diffs=0
+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTTAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCTTACCAACTAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGACATGCGTCTAGTGTTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCTTGGG
+>PC.481_4 FLP3FBN01DEHK3 orig_bc=ACCAGCGACTAG new_bc=ACCAGCGACTAG bc_diffs=0
+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCAGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGGTATTCCGGCGATGCCGCCAAAATCATTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTGCTCACG
+>PC.634_5 FLP3FBN01ELBSX1 orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTTACCCTCTCAGGCCGGCTACGCATCATCGCCTTGGTGGGCCGTTACCTCACCAACTAGCTAATGCGCCGCAGGTCCATCCATGTTCACGCCTTGATGGGCGCTTTAATATACTGAGCATGCGCTCTGTATACCTATCCGGTTTTAGCTACCGTTTCCAGCAGTTATCCCGGACACATGGGCTAGG
+>PC.634_6 FLP3FBN01EG8AX2 orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
+TTGGACCGTGTCTCAGTTCCAATGTGGGGGCCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACAACCTAATGGAACGCATCCCCATCGATGACCGAAGTTCTTTAATAGTTCTACCATGCGGAAGAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCA
+>PC.354_7 FLP3FBN01EEWKD3 orig_bc=AGCACGAGCCTA new_bc=AGCACGAGCCTA bc_diffs=0
+TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTTAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCTTACCAACTAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGACATGCGTCTAGTGTTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCTTGGG
+>PC.481_8 FLP3FBN01DEHK34 orig_bc=ACCAGCGACTAG new_bc=ACCAGCGACTAG bc_diffs=0
+CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCAGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGGTATTCCGGCGATGCCGCCAAAATCATTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTGCTCACG

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries/seqs_filtered.qual
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries/seqs_filtered.qual Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,42 @@
+>PC.634_1 FLP3FBN01ELBSX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
+40 40 39 39 38 40 40 40 40 40 40 40 37 37 37 37 37 35 35 35 37 37 37 35 37 35 35 35 31 31 23 23 23 31 21 21 21 35 35 37 37 37 36 36 36 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 37 37 37 37 37 28 28 28 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 36 36
+36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 35 32 32 32 32 35 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 32 32 32 36 37 35 32 32 32 32 32 32 32 32 36 37 37 37
+37 36 36 31 31 32 32 36 36 36 36 36 36 36 36 36 36 36 28 27 27 27 26 26 26 30 29 30 29 24 24 24 21 15 15 13 13
+>PC.634_2 FLP3FBN01EG8AX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
+24 29 33 33 39 39 39 40 39 39 39 40 37 37 37 37 37 37 37 37 37 37 37 32 32 20 20 20 20 20 35 35 37 37 37 37 37 37 37 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 37 37 37 37 37 37 37 36 36 36 36 36 36 37 37 37 37 37 36 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 33 28 28 28 28 36 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 36 33 33 33 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 28 28 28 37 28 28 28 37 37
+37 37 37 36 36 36 36 36 28 26 26 26 26 28 36 36 36 36 36 36 36 37 38 38 38 38 38 37 37 37 37 37 31 31 31 31 31 31 31 31 31 31 31 31 30 22 22 22 25 25 31 31 31 31 31 31 31 25 25 25
+25 25 28
+>PC.354_3 FLP3FBN01EEWKD orig_bc=AGCACGAGCCTA new_bc=AGCACGAGCCTA bc_diffs=0
+34 34 36 37 36 37 37 37 37 37 37 37 37 37 37 37 36 28 28 28 36 36 37 37 35 35 35 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 37 37 37 32 32 32 35 35 37 35 32 32 32 37 37 37 37 37 37 36 36 36 36 36 36 36 36 37 37 37 37 37 37 37 35 35 35 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 35 35 35 37 37
+37 37 37 37 37 37 37 37 36 36 36 37 36 35 35 35 37 28 28 28 32 35 37 37 37 36 36 36 37 37 37 37 37 37 35 35 35 35 35 37 37 37 37 36 36 36 37 28 28 28 28 35 36 37 37 37 37 37 37 37
+37 37 37 36 33 33 32 31 36 36 33 33 27 27 27 36 31 25 25 25 32 36 36 36 36 36 36 36 36 36 36
+>PC.481_4 FLP3FBN01DEHK3 orig_bc=ACCAGCGACTAG new_bc=ACCAGCGACTAG bc_diffs=0
+40 40 40 40 40 40 40 40 40 40 40 40 37 37 37 37 37 33 33 33 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 37 37 37 37 37 37 37 37 33 33 33 33 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 28 28 28 28 33 33 33 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 37 36 36 36 36 36 36 31 31 27 27 28 28 28 27 21 31 31 36 36 36 36 36 36 36 36 36 36 36 31 31 31 31 31 31 31
+>PC.634_5 FLP3FBN01ELBSX1 orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
+40 40 39 39 38 40 40 40 40 40 40 40 37 37 37 37 37 35 35 35 37 37 37 35 37 35 35 35 31 31 23 23 23 31 21 21 21 35 35 37 37 37 36 36 36 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 37 37 37 37 37 28 28 28 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 36 36
+36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 35 32 32 32 32 35 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 32 32 32 36 37 35 32 32 32 32 32 32 32 32 36 37 37 37
+37 36 36 31 31 32 32 36 36 36 36 36 36 36 36 36 36 36 28 27 27 27 26 26 26 30 29 30 29 24 24 24 21 15 15 13 13
+>PC.634_6 FLP3FBN01EG8AX2 orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
+24 29 33 33 39 39 39 40 39 39 39 40 37 37 37 37 37 37 37 37 37 37 37 32 32 20 20 20 20 20 35 35 37 37 37 37 37 37 37 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 37 37 37 37 37 37 37 36 36 36 36 36 36 37 37 37 37 37 36 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 33 28 28 28 28 36 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 36 33 33 33 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 28 28 28 37 28 28 28 37 37
+37 37 37 36 36 36 36 36 28 26 26 26 26 28 36 36 36 36 36 36 36 37 38 38 38 38 38 37 37 37 37 37 31 31 31 31 31 31 31 31 31 31 31 31 30 22 22 22 25 25 31 31 31 31 31 31 31 25 25 25
+25 25 28
+>PC.354_7 FLP3FBN01EEWKD3 orig_bc=AGCACGAGCCTA new_bc=AGCACGAGCCTA bc_diffs=0
+34 34 36 37 36 37 37 37 37 37 37 37 37 37 37 37 36 28 28 28 36 36 37 37 35 35 35 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 37 37 37 32 32 32 35 35 37 35 32 32 32 37 37 37 37 37 37 36 36 36 36 36 36 36 36 37 37 37 37 37 37 37 35 35 35 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 35 35 35 37 37
+37 37 37 37 37 37 37 37 36 36 36 37 36 35 35 35 37 28 28 28 32 35 37 37 37 36 36 36 37 37 37 37 37 37 35 35 35 35 35 37 37 37 37 36 36 36 37 28 28 28 28 35 36 37 37 37 37 37 37 37
+37 37 37 36 33 33 32 31 36 36 33 33 27 27 27 36 31 25 25 25 32 36 36 36 36 36 36 36 36 36 36
+>PC.481_8 FLP3FBN01DEHK34 orig_bc=ACCAGCGACTAG new_bc=ACCAGCGACTAG bc_diffs=0
+40 40 40 40 40 40 40 40 40 40 40 40 37 37 37 37 37 33 33 33 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 37 37 37 37 37 37 37 37 33 33 33 33 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 28 28 28 28 33 33 33 36 36 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37
+37 37 37 37 36 36 36 36 36 36 31 31 27 27 28 28 28 27 21 31 31 36 36 36 36 36 36 36 36 36 36 36 31 31 31 31 31 31 31

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries/split_library_log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries/split_library_log Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,36 @@
+Number raw input seqs 8
+
+Length outside bounds of 200 and 1000 0
+Num ambiguous bases exceeds limit of 6 0
+Missing Qual Score 0
+Mean qual score below minimum of 25 0
+Max homopolymer run exceeds limit of 6 0
+Num mismatches in primer exceeds limit of 0: 0
+
+Sequence length details for all sequences passing quality filters:
+Raw len min/max/avg 244.0/276.0/255.5
+Wrote len min/max/avg 211.0/243.0/222.5
+
+Barcodes corrected/not 0/0
+Uncorrected barcodes will not be written to the output fasta file.
+Corrected barcodes will be written with the appropriate barcode category.
+Corrected but unassigned sequences will not be written unless --retain_unassigned_reads is enabled.
+
+Total valid barcodes that are not in mapping file 0
+Sequences associated with valid barcodes that are not in the mapping file will not be written.
+
+Barcodes in mapping file
+Num Samples 3
+Sample ct min/max/mean: 2 / 4 / 2.67
+Sample Sequence Count Barcode
+PC.634 4 ACAGAGTCGGCT
+PC.354 2 AGCACGAGCCTA
+PC.481 2 ACCAGCGACTAG
+PC.593 0 AGCAGCACTTGT
+PC.636 0 ACGGTGAGTGTC
+PC.635 0 ACCGCAGAGTCA
+PC.356 0 ACAGACCACTCA
+PC.607 0 AACTGTGCGTAC
+PC.355 0 AACTCGTCGATG
+
+Total number seqs written 8
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries_fastq/barcodes.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries_fastq/barcodes.fastq Thu May 18 09:38:55 2017 -0400

[

b'@@ -0,0 +1,1000 @@\n+@HWI-EAS440_0386:1:23:17547:1423#0/1\n+ATGCAGCTCAGT\n++\n+hhhhhhhhhhhg\n+@HWI-EAS440_0386:1:23:14818:1533#0/1\n+CCCCTCAGCGGC\n++\n+ccc_c^_a[[JN\n+@HWI-EAS440_0386:1:23:14401:1629#0/1\n+GACGAGTCAGTC\n++\n+ffdfcfffffcf\n+@HWI-EAS440_0386:1:23:15259:1649#0/1\n+AGCAGTCGCGAT\n++\n+hhhhhhhhhhhh\n+@HWI-EAS440_0386:1:23:13748:2482#0/1\n+AGCACACCTACA\n++\n+ffffaffddffc\n+@HWI-EAS440_0386:1:23:6532:3028#0/1\n+GAGAGAATGATC\n++\n+ghhhhhhhhhhh\n+@HWI-EAS440_0386:1:23:8677:3027#0/1\n+CACAGTGGACGT\n++\n+eggggggggggg\n+@HWI-EAS440_0386:1:23:5678:3052#0/1\n+ATAGCTCCATAC\n++\n+hhhhhhhhhhhh\n+@HWI-EAS440_0386:1:23:11889:3171#0/1\n+ACGTTAGCACAC\n++\n+hhhhhhfhhhhh\n+@HWI-EAS440_0386:1:23:2112:3374#0/1\n+GAGAGAATGATC\n++\n+eddaabddddcf\n+@HWI-EAS440_0386:1:23:5900:3393#0/1\n+AGGTGTGATCGC\n++\n+fffefhhhhggh\n+@HWI-EAS440_0386:1:23:15468:3455#0/1\n+GAGAATACGTGA\n++\n+ehghghfhhggg\n+@HWI-EAS440_0386:1:23:4405:3490#0/1\n+ACGCGCAGATAC\n++\n+fffffaffffaf\n+@HWI-EAS440_0386:1:23:4674:3593#0/1\n+ACATTCAGCGCA\n++\n+fggggggggggg\n+@HWI-EAS440_0386:1:23:15912:3842#0/1\n+ATCAGGCGTGTG\n++\n+ccggggcgggff\n+@HWI-EAS440_0386:1:23:15732:4249#0/1\n+CTCATGTACAGT\n++\n+hhhhhhhhhhhh\n+@HWI-EAS440_0386:1:23:17444:4527#0/1\n+AACGCACGCTAG\n++\n+hhhhghhhhhhh\n+@HWI-EAS440_0386:1:23:10725:4873#0/1\n+AACGCACGCTAG\n++\n+gggggggggggg\n+@HWI-EAS440_0386:1:23:11691:4945#0/1\n+ATCTTAGACTGC\n++\n+hhhhhhhhhhhh\n+@HWI-EAS440_0386:1:23:4723:5217#0/1\n+CTCGCACATATA\n++\n+\\acaYW^^aYYV\n+@HWI-EAS440_0386:1:23:13608:5705#0/1\n+GATCGTCCAGAT\n++\n+chhhdhhhgheh\n+@HWI-EAS440_0386:1:23:5195:5979#0/1\n+CAGCAGCACATA\n++\n+ggggggggggg_\n+@HWI-EAS440_0386:1:23:1372:6057#0/1\n+AGCTCTCAGAGG\n++\n+\\aab`_ccc^ff\n+@HWI-EAS440_0386:1:23:2305:6385#0/1\n+CGTATCTGCGAA\n++\n+hhhhhhhhhghh\n+@HWI-EAS440_0386:1:23:17333:6563#0/1\n+CCAGTGTATGCA\n++\n+ggffgggggegg\n+@HWI-EAS440_0386:1:23:1091:6583#0/1\n+CGATGCACCAGA\n++\n+c^ca_\\\\_]``a\n+@HWI-EAS440_0386:1:23:16169:6630#0/1\n+CAACTATCAGCT\n++\n+hhhhhfhhhhhh\n+@HWI-EAS440_0386:1:23:14554:7030#0/1\n+AGTTAGTGCGTC\n++\n+hhhhhghhhhhh\n+@HWI-EAS440_0386:1:23:14518:7351#0/1\n+CTCGCACATATA\n++\n+gfgggggggggg\n+@HWI-EAS440_0386:1:23:17440:7360#0/1\n+GCTGCTGCAATA\n++\n+ggggfggggggf\n+@HWI-EAS440_0386:1:23:11290:7687#0/1\n+ATCGTACAACTC\n++\n+hhhfhhhhhhhh\n+@HWI-EAS440_0386:1:23:1465:8235#0/1\n+CACATCTAACAC\n++\n+cc^ccccccccc\n+@HWI-EAS440_0386:1:23:3176:8324#0/1\n+ACTGATCCTAGT\n++\n+add^dcda^ddd\n+@HWI-EAS440_0386:1:23:12535:8807#0/1\n+GAAGCTACTGTC\n++\n+hhfhhhhhhhhh\n+@HWI-EAS440_0386:1:23:14562:8883#0/1\n+CGAGTTGTAGCG\n++\n+fhhhhhhhhhhh\n+@HWI-EAS440_0386:1:23:5451:9226#0/1\n+AGATACACGCGC\n++\n+hhhhghhhhhhh\n+@HWI-EAS440_0386:1:23:19204:9448#0/1\n+GATCGCAGGTGT\n++\n+cccccc_ccTWU\n+@HWI-EAS440_0386:1:23:13161:10184#0/1\n+CTACATCTAAGC\n++\n+hhhhhhhhhhhh\n+@HWI-EAS440_0386:1:23:19192:10519#0/1\n+CATCGTATCAAC\n++\n+hhhhhhhhhhhh\n+@HWI-EAS440_0386:1:23:17370:10963#0/1\n+GCTCAGTGCAGA\n++\n+gffggggfgggg\n+@HWI-EAS440_0386:1:23:8386:11532#0/1\n+CAGCTAGAACGC\n++\n+hhhhhhhhhhhh\n+@HWI-EAS440_0386:1:23:10215:11663#0/1\n+AGATCGGCTCGA\n++\n+ffffffffffcW\n+@HWI-EAS440_0386:1:23:15454:11726#0/1\n+ACGTACTCAGTG\n++\n+ggggggggggff\n+@HWI-EAS440_0386:1:23:6589:11781#0/1\n+AGTACGCTCGAG\n++\n+gggggggggggg\n+@HWI-EAS440_0386:1:23:3256:12101#0/1\n+ATGCCTGAGCAG\n++\n+gggggggggggg\n+@HWI-EAS440_0386:1:23:5860:12157#0/1\n+ACATGTCACGTG\n++\n+hhhghhhhhhhh\n+@HWI-EAS440_0386:1:23:8148:12187#0/1\n+AACTGTGCGTAC\n++\n+hhghhhhhhhhh\n+@HWI-EAS440_0386:1:23:14399:12333#0/1\n+ACATGATCGTTC\n++\n+ZTPQFILLJJKK\n+@HWI-EAS440_0386:1:23:6966:12378#0/1\n+CATACCAGTAGC\n++\n+\\aa_aaa^aa\\^\n+@HWI-EAS440_0386:1:23:5056:12637#0/1\n+CGCATGAGGATC\n++\n+gggggggggggg\n+@HWI-EAS440_0386:1:23:2628:12653#0/1\n+ACGCTCATGGAT\n++\n+cccccccccccc\n+@HWI-EAS440_0386:1:23:3303:12826#0/1\n+AGGTGTGATCGC\n++\n+hffhhhhhhhhh\n+@HWI-EAS440_0386:1:23:11685:12866#0/1\n+CTCCACATGAGA\n++\n+hhhhghhhhchh\n+@HWI-EAS440_0386:1:23:3932:12883#0/1\n+CTACTGATATCG\n++\n+aZ]]]\\Sa^a]_\n+@HWI-EAS440_0386:1:23:3535:13218#0/1\n+ACGACGTCTTAG\n++\n+hhhhghhhhhhh\n+@HWI-EAS440_0386:1:23:6909:13409#0/1\n+AGTTCAGACGCT\n++\n+gggggfgggggg\n+@HWI-EAS440_0386:1:23:6191:13528#0/1\n+GCTCAGTGCAGA\n++\n+ggggggeggggg\n+@HWI-EAS440_0386:1:23:17158:13561#0/1\n+AATCGTGACTCG\n++'..b'/1\n+ACTACGTGTGGT\n++\n+hhhhhhhhhghg\n+@HWI-EAS440_0386:1:25:2027:2951#0/1\n+AGCTGACTAGTC\n++\n+gcggggeggfdf\n+@HWI-EAS440_0386:1:25:13175:2941#0/1\n+GCTGCTGCAATA\n++\n+hhhhhhhhhhhh\n+@HWI-EAS440_0386:1:25:13489:2951#0/1\n+AGCTGACTAGTC\n++\n+hhhhfhhhhhhh\n+@HWI-EAS440_0386:1:25:6132:2959#0/1\n+ACTACGTGTGGT\n++\n+a`aY]ada^e\\L\n+@HWI-EAS440_0386:1:25:2692:2971#0/1\n+ACACACTATGGC\n++\n+hhghhhhhhfhh\n+@HWI-EAS440_0386:1:25:1831:2983#0/1\n+ACACACTATGGC\n++\n+ggggcggacg^[\n+@HWI-EAS440_0386:1:25:6335:2989#0/1\n+CCTCTCGTGATC\n++\n+afdeff\\ffaca\n+@HWI-EAS440_0386:1:25:10162:3028#0/1\n+ATGGCAGCTCTA\n++\n+fffffdfRc]^[\n+@HWI-EAS440_0386:1:25:4348:3042#0/1\n+ATGGCAGCTCTA\n++\n+ffa_fffa_d\\J\n+@HWI-EAS440_0386:1:25:5972:3048#0/1\n+CTGAGATACGCG\n++\n+hhhhhfhhhghh\n+@HWI-EAS440_0386:1:25:9861:3050#0/1\n+ATGGCAGCTCTA\n++\n+gggggggcfcea\n+@HWI-EAS440_0386:1:25:10090:3050#0/1\n+CTGAGATACGCG\n++\n+ghhhghhhghhh\n+@HWI-EAS440_0386:1:25:3139:3077#0/1\n+AGCTGACTAGTC\n++\n+gggggggggggg\n+@HWI-EAS440_0386:1:25:9110:3081#0/1\n+AGTGCGATGCGT\n++\n+hhhhhhghhhhh\n+@HWI-EAS440_0386:1:25:17734:3100#0/1\n+ACTACGTGTGGT\n++\n+ggggggggggfc\n+@HWI-EAS440_0386:1:25:8423:3141#0/1\n+ACACACTATGGC\n++\n+hhhhhhhhhghh\n+@HWI-EAS440_0386:1:25:14009:3149#0/1\n+AGCTGACTAGTC\n++\n+hhhhhhhhhhhh\n+@HWI-EAS440_0386:1:25:3100:3158#0/1\n+CCGACTGAGATG\n++\n+hhhhhhhhhhhh\n+@HWI-EAS440_0386:1:25:4738:3152#0/1\n+AGTGCGATGCGT\n++\n+ggggggggggfg\n+@HWI-EAS440_0386:1:25:4197:3165#0/1\n+CGAGAGTTACGC\n++\n+hhhhehhhhhhh\n+@HWI-EAS440_0386:1:25:9072:3171#0/1\n+CCGACTGAGATG\n++\n+gggg_ffdffgg\n+@HWI-EAS440_0386:1:25:15751:3166#0/1\n+AGTGCGATGCGT\n++\n+fcccffdfffgg\n+@HWI-EAS440_0386:1:25:3473:3225#0/1\n+CTGAGATACGCG\n++\n+gfgfggfggggf\n+@HWI-EAS440_0386:1:25:4755:3229#0/1\n+CTGAGATACGCG\n++\n+hhhhghhhhghh\n+@HWI-EAS440_0386:1:25:3032:3237#0/1\n+CCTCTCGTGATC\n++\n+hhhhhhhhhhhh\n+@HWI-EAS440_0386:1:25:1630:3249#0/1\n+CTGAGATACGCG\n++\n+hhhhhghhhhhh\n+@HWI-EAS440_0386:1:25:4476:3251#0/1\n+AGCTGACTAGTC\n++\n+hghhhhhhhhhh\n+@HWI-EAS440_0386:1:25:3312:3259#0/1\n+ACTACGTGTGGT\n++\n+hhhhhhhhghhe\n+@HWI-EAS440_0386:1:25:3550:3291#0/1\n+ACACACTATGGC\n++\n+hhhhhhhhghhg\n+@HWI-EAS440_0386:1:25:5478:3298#0/1\n+CCGACTGAGATG\n++\n+hhhhhhhhhfhh\n+@HWI-EAS440_0386:1:25:15346:3296#0/1\n+CCTCTCGTGATC\n++\n+hhhhhhhhhhhh\n+@HWI-EAS440_0386:1:25:3468:3322#0/1\n+ACTACGTGTGGT\n++\n+fhdfhhhhgdfe\n+@HWI-EAS440_0386:1:25:4199:3321#0/1\n+CCTCTCGTGATC\n++\n+hhhhhhghhhhh\n+@HWI-EAS440_0386:1:25:8568:3330#0/1\n+ATGGCAGCTCTA\n++\n+gggggggf_fdd\n+@HWI-EAS440_0386:1:25:12050:3335#0/1\n+ACACACTATGGC\n++\n+gggggggggggg\n+@HWI-EAS440_0386:1:25:19075:3342#0/1\n+CAGTACGATCTT\n++\n+hfhfehgghhhh\n+@HWI-EAS440_0386:1:25:4994:3354#0/1\n+ATGGCAGCTCTA\n++\n+gggggggffef[\n+@HWI-EAS440_0386:1:25:12091:3381#0/1\n+ATGGCAGCTCTA\n++\n+ffffffffcaa_\n+@HWI-EAS440_0386:1:25:8594:3395#0/1\n+AGTGCGATGCGT\n++\n+hhhhhhhhhhhf\n+@HWI-EAS440_0386:1:25:2052:3400#0/1\n+CCTCTCGTGATC\n++\n+ggggggggfgfg\n+@HWI-EAS440_0386:1:25:11776:3405#0/1\n+ACTACGTGTGGT\n++\n+hhhhfhhfhe[f\n+@HWI-EAS440_0386:1:25:4155:3413#0/1\n+AGTGCGATGCGT\n++\n+fffffggggggg\n+@HWI-EAS440_0386:1:25:11052:3431#0/1\n+ACTACGTGTGGT\n++\n+hhhhhhghhhhe\n+@HWI-EAS440_0386:1:25:4122:3435#0/1\n+ATGGCAGCTCTA\n++\n+c_cYc`WKZP\\Y\n+@HWI-EAS440_0386:1:25:9796:3444#0/1\n+AGTGCGATGCGT\n++\n+hhhchhhhhhhh\n+@HWI-EAS440_0386:1:25:2235:3462#0/1\n+AGCTGACTAGTC\n++\n+fcaffffcfcgg\n+@HWI-EAS440_0386:1:25:14529:3458#0/1\n+CCGACTGAGATG\n++\n+hhhhhhhhhhhh\n+@HWI-EAS440_0386:1:25:6708:3509#0/1\n+ACACACTATGGC\n++\n+ffffdfffffcf\n+@HWI-EAS440_0386:1:25:13919:3507#0/1\n+CCTCTCGTGATC\n++\n+hhhhhhhhhhhh\n+@HWI-EAS440_0386:1:25:10705:3535#0/1\n+ACACACTATGGC\n++\n+hhhfhhghgfgh\n+@HWI-EAS440_0386:1:25:7788:3570#0/1\n+CTGAGATACGCG\n++\n+hhaghghhhdhh\n+@HWI-EAS440_0386:1:25:2273:3577#0/1\n+ACTACGTGTGGT\n++\n+ffffffdfffe_\n+@HWI-EAS440_0386:1:25:14850:3657#0/1\n+CCGACTGAGATG\n++\n+aaYc^aaYZZYT\n+@HWI-EAS440_0386:1:25:11581:3662#0/1\n+ACTACGTGTGGT\n++\n+hhhhhhhhhhhg\n+@HWI-EAS440_0386:1:25:16965:3660#0/1\n+ACTACGTGTGGT\n++\n+hhhhhhhhhhhg\n+@HWI-EAS440_0386:1:25:8197:3691#0/1\n+CTGAGATACGCG\n++\n+hhhhhhhhhhhh\n+@HWI-EAS440_0386:1:25:11617:3701#0/1\n+AGCTGACTAGTC\n++\n+`\\__\\W\\\\\\Y\\^\n+@HWI-EAS440_0386:1:25:15484:3705#0/1\n+CCGACTGAGATG\n++\n+hhhhhhhhhhhh\n'

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries_fastq/demultiplexed_sequences.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries_fastq/demultiplexed_sequences.fastq Thu May 18 09:38:55 2017 -0400

b"@@ -0,0 +1,344 @@\n+@L1S140_0 HWI-EAS440_0386:1:25:1851:1463#0/1 orig_bc=ATGGCAGCTCTA new_bc=ATGGCAGCTCTA bc_diffs=0\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGACATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATA\n++\n+ACCCGGGG@G?GGGGGGGGDGGGGGGGGGGGGGGGGDGGBGGGBGGGGGGGDGEGGDDG@GGGGEEEGGGGGG388GD>DDGGEE@DDDDB>FDGD>@-:74=;A*74====?BBD@\n+@L1S105_1 HWI-EAS440_0386:1:25:4646:1592#0/1 orig_bc=AGTGCGATGCGT new_bc=AGTGCGATGCGT bc_diffs=0\n+AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTG\n++\n+GGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFHBHHECCHBDHFEHAE@@BDB=B@@A2D(5553DAAAAE@EEA>;)9;==A>7B@=@78;:82?C<><9?<>>>98=@\n+@L1S281_2 HWI-EAS440_0386:1:25:4380:1628#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTA\n++\n+IIIGIIIIGIIIIIGIIHIDIHIHHF@IIFIIIIIGIIIHIHGHBIIIGHHGIFEEEFHHHDEEDG>DBEFBDB@BB=EEBBBEGEDDBA>D@@@@BCBB;BD@@>:@@>B@?=1@@@3<9767=6>;;?\n+@L1S208_3 HWI-EAS440_0386:1:25:1510:1668#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAG\n++\n+IIIIIGIIIIIIIGIIIIIIIIIIIFIIGEGGDIIIIIFFHIIGDGEGD>GDGIIEIGIIFH>GBDDGFGGEGBB2DBDDGBDEBEBB8?<B>B>A@D=38=AC>?>@@?DD@>=?=478;+;BE8>B\n+@L1S8_4 HWI-EAS440_0386:1:25:3929:1715#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTG\n++\n+IIIIIHIIIIIIHEEIIEIIIIIIGGHIHEIIHDFCIGHHHCEDBIEIEEHBBEBBEIHGGGGGDHGGEEGDG?<2A5DBBBBEBEBBB@BEDEBBBE;@@@B@@8:@B@@@@AE@@A0@>=<9:;9=7>:;==<?\n+@L1S257_5 HWI-EAS440_0386:1:25:2639:1894#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTAGAGGCAG\n++\n+HHHGGEGEGGGGGHHHHHHHGHHGGCGGHFHHHHHHHHEDBGGHFHHHHFHHHHHFHHHHHEBFCEEDFFFDE=;@C=CCCAABBD@@:=;?=BB@>DBD=@DBBB=D6'=;;A=?=99=9.9.2,/2===79@@6@\n+@L1S8_6 HWI-EAS440_0386:1:25:6139:2018#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGTACTAGAGTGT\n++\n+IIIIIIIIGIIIDGIIIFIIHIIIIIIIIIIIIIIEIFGFGGGHIIGIIIHBHIHGIGIHI@EG@EGFFIFEDFBC<FEC@B+@BBBB82==?BB@<BB@BB)AA@8=@?@@5?<>=;;2?-?=A?\n+@L1S208_7 HWI-EAS440_0386:1:25:3109:2059#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n+TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATTTCGGGGCTCAACCCTGAACGTGCCTCTAATACTGTTGAGCTAGAGAGTAGTTGCGGTAGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIBIIIGIIIIIIIIIIFIIIIIIIIIIIHGIIIIIIIEDGFGEDDGDBG:@@ECGEFEBHBHFHBB@@GGBBBDBECBBGECBECBFEBDEBEBB@@2B4?<=?;A??A@A+>?\n+@L1S281_8 HWI-EAS440_0386:1:25:7669:2080#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n+TACGGAGGATCCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATTTCGGGGCTCGACCCTGAACGTGCCTCTAATACTGTTGAGCTAGAGAGTAG\n++\n+IIIIIIIIIIIIHGGIIHIIIIIIIHIIIHIIIIIGIHHIIIIHDIIIHHHDIIIHIIHDHGEHEHGDGHEDGDHEEFEHG,EDCDCF@EBBECB@@B6>@A@ECBBCBBEEA>BBB@@DBAB=@8@@\n+@L1S140_9 HWI-EAS440_0386:1:25:3922:2110#0/1 orig_bc=ATGGCAGCTCTA new_bc=ATGGCAGCTCTA bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACAGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTT\n++\n+GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHGHHHHGBHHHHHHHHHFHHHHEHHHHEFEHFGGFGAA>C=GGDBDEDEEBCBBEEBB>BD@BB@DBBBB=C>BCCB>EBB8?\n+@L1S105_10 HWI-EAS440_0386:1:25:3806:2202#0/1 orig_bc=AGTGCGATGCGT new_bc=AGTGCGATGCGT bc_diffs=0\n+AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGTGTAAAGGGAGCGCAGGCGGGAGAACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAG\n++\n+HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGBGGGEGGGG@GGDGHHFGHHHHHHGGFEGBGGG3CE>EAABGDBFFEDFE>E>DCB@EFFBC>EDBDD+CAA>>9?=99DCC?A"..b'GCGTTATCCGGATTTACTGGGTGTAAAGGGAGTGTAGGTGGCCATGCAAGTCAGAAGTGAAAATCCGGGGCTCAACCCCGGAACTGCTTTTGAAACTGTGAGGCTAGAGTGCAGGAGGGGTGAGTGGAATTCCTAGTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIDIIIIIIIHIHIIGIIGIIHIIIIIIHHIBIIIIIIIGIEIHGIIIEHII@IGIHFDHIGDIHHFEEIGBB<DDFFFFEFDEBBDGGBFCEECDDD@D@FBBDD;BBAA@D9D::?3=<65855;:<\n+@L1S8_76 HWI-EAS440_0386:1:25:2235:3462#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n+AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAGTCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCA\n++\n+HHHGEGGGFGBGGHHHHHHFCHHHHHHHHHHHHHHDHEFFFG@EEEF<HFHHHHDHF8DHBHHHAGHGFFDADDDFCBEEDDACEBEBEB7>E>>)>@EDCC@B<>:5:6:>68>0A;9>;:@?<>??@B\n+@L1S57_77 HWI-EAS440_0386:1:25:6708:3509#0/1 orig_bc=ACACACTATGGC new_bc=ACACACTATGGC bc_diffs=0\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAAGGCAAGTCTGATGTGAAAACCCAGGGCTTAACCCTGGGACTGCATTGGAAACTGTCTGGCTCGAG\n++\n+GGGHHHHHHHGHHHHHHHHGHHHHHGHHHHHHHHHHHHHHHHGHHHHHHHHHHHGBHHHHHBHHHHHHHFHGHBHHFGEGEEBEHHHDDDB@GB=?=?EEE>EBD3=@AABDDD>BBCA<A=A\n+@L1S281_78 HWI-EAS440_0386:1:25:13919:3507#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGG\n++\n+IIIIIHIIFIIIGGHIIHIDIHIIGBIIIEIIIHHEIIHEGHHHEHGIDBEGBIFEFFEEHEBHEFCHGGHEHE@BHBFDFEEGEDDEBBBHE@DBBDBEBBEDEEDBE>AECDCDB@BB@:C@BB@B=0=0>?=>@\n+@L1S208_79 HWI-EAS440_0386:1:25:7788:3570#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGTCTGAAGTGAAATGCGGGGGCTCAACCCCTGAACTGCTTTGGAAACTGTCATGCTAGAGTGCAGGAGGGGTGAGCGGAATTCCTAGTG\n++\n+IIIIIIIHIIIIHIIIIIIIIIIIIIIIIIIIIHIIIIIIHIFIIIIIHHIFIIIHGHHIHIIIHHIIFFICIB8BDGD@DBACFEDGCEEBFFFCBBBEBEBAA;8?>?AAABBCC@BB>>C@DB@B@7@@@83;8@89<7+=8=(=5?9?\n+@L1S257_80 HWI-EAS440_0386:1:25:14850:3657#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTGGTAATTTAAGTCAGCGGTGAAAGTTTGTGGCTCAACCATAAAATTGCCGTTGAAACTGGGTTACTTGAGTG\n++\n+<@@GGGGGGGBGGGGGGGGGGGGGGGGGGGGDEGGGGGGGGGGGBGGGGGGDGGGB<BGGGGGGGGGG><GGGDGDGGGEGDGGGGGEGFE<DGDDDDGGGBGDDGD:BBDDD??:<?GGDBB;B\n+@L1S76_81 HWI-EAS440_0386:1:25:11581:3662#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGTACTAGAGTGTCGGAGGG\n++\n+IIIGIIIIGHIIGGIIIIIHIIIIHIHIIIHIIIIEIEIFFGGGIFIHIIHFIHIHDFIIIGEHEHHIHIGGFEGG<HEGBD>@>ADAEEE@D?A=<=@B@@@B@B>BBBBCA@@)>@<4>1>@@>;>A4:@A\n+@L1S76_82 HWI-EAS440_0386:1:25:16965:3660#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAGTTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAG\n++\n+IIIIIIIIIIIIIIIIIIIHIIIIIDIIIIIIIIIHIIHIIIIIHIIIHDIFIIIIIIIIIIHIGIGIHHIEIFFEIEIHIFIGGHGHDHHHGHGB<EEDHEFGGHBGEDHHHBCBEBEED@B8@@@A@B@@@8?3?\n+@L1S208_83 HWI-EAS440_0386:1:25:8197:3691#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGGACTAGAGTGTCG\n++\n+IIIIIIIIIIIIHIIIIIIIIIIIHGIIIHIIIIIIIIIHHIIIIIGFIIIIIIIIIIIIIHGIFFGIFIIFIGHBIHGIHIGHGGEDDBDBFD>B@@BBB=BBDB?@B:BBBEEECB??A4@4?==?\n+@L1S8_84 HWI-EAS440_0386:1:25:11617:3701#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACAGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCTGTCTTGAG\n++\n+=B@GDGGGEGEGGGGGGGGEGGGGGDGGGGEEEGGGBGGGGGGGDGGGGGGG@EEBBE???DBGGGEGBGGDGGGGBC?0?<BFGF>BDGDDGCBDDDDDDDDEGGFDDDAG+(2:39DBAAA\n+@L1S257_85 HWI-EAS440_0386:1:25:15484:3705#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n+TACGGAGGATCCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTAGTAAGTCAGCGGTGAAATTTTGGTGCTTAACACCAAACGTGCCGTTGATACTGCTGGGCTAGAGAGTAGTTGCGG\n++\n+IIIIIIIIHIIIIIIIIIIGIIIIFFIIIFIIIIIHIIIHEIIIHIIIHHIFIIIIHIIIHHHIGHHFHIHEIDBBFGHFHFEHEIIEBDBEEDCDEF=DBDDCBD=D@BDEBDFCC>B@B4B=@=>@=BB>8?\n'

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries_fastq/forward_reads.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries_fastq/forward_reads.fastq Thu May 18 09:38:55 2017 -0400

[

b'@@ -0,0 +1,1000 @@\n+@HWI-EAS440_0386:1:23:17547:1423#0/1\n+TACGNAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGGGGGGATTGGTGTG\n++\n+hhhdHddddddddfehhfhhhghggfhhhfhhgggfhhgfgdfcfhehfdgfhggfggfggffgddfgdffdgdaagaaddcbdccc]a^ad__a]_____ba_`a`__^__\\]^OWZR\\Z\\\\WYTZ_U^BBBBBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:23:14818:1533#0/1\n+CCCCNCAGCGGCAAAAATTAAAATTTTTACCGCTTCGGCGTTATAGCCTCACACTCAATCTTTTATCACGAAGTCATGATTGAATCGCGAGTGGTCGGCAGATTGCGATAAACGGGCACATTAAATTTAAACTGATGATTCCACTGCAACAA\n++\n+US[QCQSZPHNYIa[^aaccaac[]accBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:23:14401:1629#0/1\n+TACGNAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTAGAGGCAGGGGGGGGGTTGGGGG\n++\n+fffbF`bbWZZ]Zggggfgcgggggddggdgggggdbgdddgbgeggg`ffdggeabba`aaad]]]d\\]`]`[]]aWaYa\\aa`a`_````_^]^^^]]]X]_``____``BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:23:15259:1649#0/1\n+TACGNAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTAGAGGCAGGGGGGAGTTTGGGGG\n++\n+hhhdHcdd^bbbahhhhhhfhhhhhghhhhhhhhhghhhgehchfhhhgghghfhhhgehgaffaecfdggdh\\bafadddddgddfdbc^]a_\\^_a``\\X`^_`]`aaabcaYbY_^^X]^ZY^Z^a`_^aBBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:23:13748:2482#0/1\n+TACGNAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGGATTCGTGGTG\n++\n+fffbF^bbS[T[Uggggggg__gffddfggeggggaagfeefbfaaff_cfacfeceddgggegdgdgaggddcddd`a_aad`ddadd`daaWY]]Yddda_]_]]a_Y___X\\_]YaY]\\]WYNV]\\]_BBBBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:23:6532:3028#0/1\n+TACGNAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTAGAGGCAGGGGGGAGTCTTGGGG\n++\n+hhhfHdffacdcchhhhghfhhhhfehhhchhhehghhgghhgehghhffghhhgghghddgggfhfgdhhdea`Wf^dddddbgagcdedgcfddbcddaddcefb_addddd_daaaaaaa`ca`aX^Z\\X_^^^^BBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:23:8677:3027#0/1\n+TACANAGGTCTCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGCCGGCACATGATACTGTGAGACTAGCGTAACGGAGGGGGAACCGGAATTCTTGGTG\n++\n+ggg`Fbbbdeeeegggggggggggfgggggggggggggggggfgggggggggfgggggggf]gfccfcfbfbdged]ddda_dedaa]aZc__BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:23:5678:3052#0/1\n+TACGNAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGAAGAGCAAGTCTGATGTGAAAGGCTGGGGCTTAACCCCAGGACTGCATTGGAAACTGTTTTTCTTGAGTGCCGGAGAGGTAAGCGGAATTCCTGGGG\n++\n+hhheHeeeaaabbhghhhhhhhhhghhhhghhhhhfhghhghhghhhhdhehhfghhaehhgghddhhhhhadffffdb]Z__Z^_`^daadda`c`Z\\T[\\\\]\\RJ]YS[\\X_a]]P_XM\\T\\^\\^^BBBBBBBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:23:11889:3171#0/1\n+TACGNAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTTTTGCAAGTCTGAAGTGAAAGCCCGGGGCTTAACCCCGGGACTGCTTTGGAAACTGTATGACTAGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTG\n++\n+hhheHddeeeeddhghhhhhhhhhhchhhhhhhhhfhfdddffhgghhghgehhegghhhhffhffhhg_edaecdcc[dabaadddaadaaeY\\WQX^]]^^``RZZ___a__aa_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:23:2112:3374#0/1\n+TACGNAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGGGGGATTCGTGTGG\n++\n+fffdGcddZZ___ggggggggggggggggfggggggfgdggggeggggeggggggeggdggeggggggdggdgcaaf\\^_b_b_gdedd_eedR^Z^^`dcRb_P__R^\\[]^c`cbadaaab^da^aBBBBBBBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:23:5900:3393#0/1\n+TACGNATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGAAGGCTAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGGTCATCTAGAGTGTCGGAGGGGTAAGTGGAATTCCTAGTG\n++\n+hhheHeeea\\aaaghhhhhhhhhhhhhhhhghhhhfhgggghhhhhhfcghhhhgfhdgahddfbddfcfca]daed]cfcdcb]bbb^]_^bUZRYW___^_abaV_^SYYW````]^_[O_^```Z\\RS^BBBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:23:15468:3455#0/1\n+TACGNAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACAGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGA'..b'TCGGTG\n++\n+hhhhhhhhghhhghhhhhhegfhhfhfhahghhhchhdhhhhahhhhhggchffgggghhggfhbefbfbd_dddcdaR`_`a_NU^^^^__^`^`G^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:25:6708:3509#0/1\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAAGGCAAGTCTGATGTGAAAACCCAGGGCTTAACCCTGGGACTGCATTGGAAACTGTCTGGCTCGAGTGCCGGAGAGGTAAGCGGAATTCCTAGTG\n++\n+fffgggggggfggggggggfgggggfggggggggggggggggfgggggggggggfagggggagggggggegfgaggefdfddadgggccca_fa\\^\\^ddd]dacR\\_``accc]aab`[`\\`BBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:25:13919:3507#0/1\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGGATTCGTGGGG\n++\n+hhhhhghhehhhffghhghchghhfahhhdhhhggdhhgdfgggdgfhcadfahedeeddgdagdebgffgdgd_agaeceddfdccdaaagd_caacadaadcddcad]`dbcbca_aa_Yb_aa_a\\O\\O]^\\]_BBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:25:10705:3535#0/1\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAACTGGCCGGCTAGGGTGTCCGGGGGGGACAGGGGATTTCCTGTGT\n++\n+hhhhhhhhdhhhhhhhhhhhhhhhhehhhhhhhffdfeffffchhhhhhghhhhhhhhfhhhfhdhchhfheagghhcahgeg_ddbadeedh`][^`Z_ZZ```RK^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:25:7788:3570#0/1\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGTCTGAAGTGAAATGCGGGGGCTCAACCCCTGAACTGCTTTGGAAACTGTCATGCTAGAGTGCAGGAGGGGTGAGCGGAATTCCTAGTG\n++\n+hhhhhhhghhhhghhhhhhhhhhhhhhhhhhhhghhhhhhghehhhhhgghehhhgfgghghhhgghheehbhaWacfc_ca`bedcfbddaeeebaaadada``ZW^]^```aabb_aa]]b_ca_a_V___WRZW_WX[VJ\\W\\G\\T^X^\n+@HWI-EAS440_0386:1:25:2273:3577#0/1\n+AACGTAGGTCACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGACTTCCCGGTG\n++\n+cfffeffeggaggffffdggdgggggaggggggee]fb`]```fcfgdgaffgffbbd[ca_W]Z``ZY^]U]YS[^`_`_`\\`add```aa]a_[[a`a_a```a`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:25:14850:3657#0/1\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTGGTAATTTAAGTCAGCGGTGAAAGTTTGTGGCTCAACCATAAAATTGCCGTTGAAACTGGGTTACTTGAGTGTGGTTGAGGTAGGCGGAATGCGTGGTG\n++\n+[__fffffffaffffffffffffffffffffcdfffffffffffaffffffcfffa[affffffffff][fffcfcfffdfcfffffdfed[cfccccfffafccfcYaaccc^^Y[^ffcaaZaBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:25:11581:3662#0/1\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGTACTAGAGTGTCGGAGGGGTAAGCGGAATTCCTAGGG\n++\n+hhhfhhhhfghhffhhhhhghhhhghghhhghhhhdhdheefffhehghhgehghgcehhhfdgdgghghffedff[gdfac]_]`c`ddd_c^`\\[\\_a___a_a]aaaab`__H]_[S]P]__]Z]`SY_`BBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:25:16965:3660#0/1\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAGTTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGGGGGATTTGTGGGG\n++\n+hhhhhhhhhhhhhhhhhhhghhhhhchhhhhhhhhghhghhhhhghhhgchehhhhhhhhhhghfhfhgghdheedhdhghehffgfgcgggfgfa[ddcgdeffgafdcgggabadaddc_aW___`_a___W^R^BBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:25:8197:3691#0/1\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGGACTAGAGTGTCGGAGGGGTAAGTGGAATTCCTAGCG\n++\n+hhhhhhhhhhhhghhhhhhhhhhhgfhhhghhhhhhhhhgghhhhhfehhhhhhhhhhhhhgfheefhehhehfgahgfhghfgffdccacaec]a__aaa\\aaca^_aYaaadddba^^`S_S^\\\\^BBBBBBBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:25:11617:3701#0/1\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACAGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCTGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTG\n++\n+\\a_fcfffdfdffffffffdfffffcffffdddfffafffffffcfffffff_ddaad^^^cafffdfaffcffffab^O^[aefe]acfccfbaccccccccdffeccc`fJGQYRXca```BBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@HWI-EAS440_0386:1:25:15484:3705#0/1\n+TACGGAGGATCCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTAGTAAGTCAGCGGTGAAATTTTGGTGCTTAACACCAAACGTGCCGTTGATACTGCTGGGCTAGAGAGTAGTTGCGGTAGGCGGAATGGATGGTG\n++\n+hhhhhhhhghhhhhhhhhhfhhhheehhhehhhhhghhhgdhhhghhhgghehhhhghhhggghfggeghgdhcaaefgegedgdhhdacaddcbcde\\caccbac\\c_acdacebb]a_aSa\\_\\]_\\aa]W^BBBBBBBBBBBBBBBBBB\n'

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries_fastq/histograms.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries_fastq/histograms.tabular Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,8 @@
+Length Count
+116.0 20
+126.0 31
+136.0 33
+146.0 2
+156.0 0
+--
+

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries_fastq/histograms.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries_fastq/histograms.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,8 @@
+Length Count
+116.0 20
+126.0 31
+136.0 33
+146.0 2
+156.0 0
+--
+

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries_fastq/map.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries_fastq/map.tsv Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries_fastq/seqs.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries_fastq/seqs.fastq Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries_fastq/seqs.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries_fastq/seqs.fna Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries_fastq/seqs.qual
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries_fastq/seqs.qual Thu May 18 09:38:55 2017 -0400

[

b'@@ -0,0 +1,584 @@\n+>L1S140_0 HWI-EAS440_0386:1:25:1851:1463#0/1 orig_bc=ATGGCAGCTCTA new_bc=ATGGCAGCTCTA bc_diffs=0\n+[32 34 34 34 38 38 38 38 31 38 30 38 38 38 38 38 38 38 38 35 38 38 38 38 38\n+ 38 38 38 38 38 38 38 38 38 38 38 35 38 38 33 38 38 38 33 38 38 38 38 38 38\n+ 38 35 38 36 38 38 35 35 38 31 38 38 38 38 36 36 36 38 38 38 38 38 38 18 23\n+ 23 38 35 29 35 35 38 38 36 36 31 35 35 35 35 33 29 37 35 38 35 29 31 12 25\n+ 22 19 28 26 32 9 22 19 28 28 28 28 30 33 33 35 31]\n+>L1S105_1 HWI-EAS440_0386:1:25:4646:1592#0/1 orig_bc=AGTGCGATGCGT new_bc=AGTGCGATGCGT bc_diffs=0\n+[38 38 38 38 38 38 38 38 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39\n+ 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 37\n+ 39 33 39 39 36 34 34 39 33 35 39 37 36 39 32 36 31 31 33 35 33 28 33 31 31\n+ 32 17 35 7 20 20 20 18 35 32 32 32 32 36 31 36 36 32 29 26 8 24 26 28 28\n+ 32 29 22 33 31 28 31 22 23 26 25 23 17 30 34 27 29 27 24 30 27 29 29 29 24\n+ 23 28 31]\n+>L1S281_2 HWI-EAS440_0386:1:25:4380:1628#0/1 orig_bc=CCTCTCGTGATC new_bc=CCTCTCGTGATC bc_diffs=0\n+[40 40 40 38 40 40 40 40 38 40 40 40 40 40 38 40 40 39 40 35 40 39 40 39 39\n+ 37 31 40 40 37 40 40 40 40 40 38 40 40 40 39 40 39 38 39 33 40 40 40 38 39\n+ 39 38 40 37 36 36 36 37 39 39 39 35 36 36 35 38 29 35 33 36 37 33 35 33 31\n+ 33 33 28 36 36 33 33 33 36 38 36 35 35 33 32 29 35 31 31 31 31 33 34 33 33\n+ 26 33 35 31 31 29 25 31 31 29 33 31 30 28 16 31 31 31 18 27 24 22 21 22 28\n+ 21 29 26 26 30]\n+>L1S208_3 HWI-EAS440_0386:1:25:1510:1668#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n+[40 40 40 40 40 38 40 40 40 40 40 40 40 38 40 40 40 40 40 40 40 40 40 40 40\n+ 37 40 40 38 36 38 38 35 40 40 40 40 40 37 37 39 40 40 38 35 38 36 38 35 29\n+ 38 35 38 40 40 36 40 38 40 40 37 39 29 38 33 35 35 38 37 38 38 36 38 33 33\n+ 17 35 33 35 35 38 33 35 36 33 36 33 33 23 30 27 33 29 33 29 32 31 35 28 18\n+ 23 28 32 34 29 30 29 31 31 30 35 35 31 29 28 30 28 19 22 23 26 10 26 33 36\n+ 23 29 33]\n+>L1S8_4 HWI-EAS440_0386:1:25:3929:1715#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n+[40 40 40 40 40 39 40 40 40 40 40 40 39 36 36 40 40 36 40 40 40 40 40 40 38\n+ 38 39 40 39 36 40 40 39 35 37 34 40 38 39 39 39 34 36 35 33 40 36 40 36 36\n+ 39 33 33 36 33 33 36 40 39 38 38 38 38 38 35 39 38 38 36 36 38 35 38 30 27\n+ 17 32 20 35 33 33 33 33 36 33 36 33 33 33 31 33 36 35 36 33 33 33 36 26 31\n+ 31 31 33 31 31 23 25 31 33 31 31 31 31 32 36 31 31 32 15 31 29 28 27 24 25\n+ 26 24 28 22 29 25 26 28 28 27 30]\n+>L1S257_5 HWI-EAS440_0386:1:25:2639:1894#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n+[39 39 39 38 38 36 38 36 38 38 38 38 38 39 39 39 39 39 39 39 38 39 39 38 38\n+ 34 38 38 39 37 39 39 39 39 39 39 39 39 36 35 33 38 38 39 37 39 39 39 39 37\n+ 39 39 39 39 39 37 39 39 39 39 39 36 33 37 34 36 36 35 37 37 37 35 36 28 26\n+ 31 34 28 34 34 34 32 32 33 33 35 31 31 25 28 26 30 28 33 33 31 29 35 33 35\n+ 28 31 35 33 33 33 28 35 21 6 28 26 26 32 28 30 28 24 24 28 24 13 24 13 17\n+ 11 14 17 28 28 28 22 24 31 31 21 31]\n+>L1S8_6 HWI-EAS440_0386:1:25:6139:2018#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n+[40 40 40 40 40 40 40 40 38 40 40 40 35 38 40 40 40 37 40 40 39 40 40 40 40\n+ 40 40 40 40 40 40 40 40 40 40 36 40 37 38 37 38 38 38 39 40 40 38 40 40 40\n+ 39 33 39 40 39 38 40 38 40 39 40 31 36 38 31 36 38 37 37 40 37 36 35 37 33\n+ 34 27 37 36 34 31 33 10 31 33 33 33 33 23 17 28 28 30 33 33 31 27 33 33 31\n+ 33 33 8 32 32 31 23 28 31 30 31 31 20 30 27 29 28 26 26 17 30 12 30 28 32\n+ 30]\n+>L1S208_7 HWI-EAS440_0386:1:25:3109:2059#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n+[40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40\n+ 33 40 40 40 38 40 40 40 40 40 40 40 40 40 40 37 40 40 40 40 40 40 40 40 40\n+ 40 40 39 38 40 40 40 40 40 40 40 36 35 38 37 38 36 35 35 38 35 33 38 25 31\n+ 31 36 34 38 36 37 36 33 39 33 39 37 39 33 33 31 31 38 38 33 33 33 35 33 36\n+ 34 33 33 38 36 34 33 36 34 33 37 36 33 35 36 33 36 33 33 31 31 17 33 19 30\n+ 27 28 30 26 32 30 3'..b' 40 40 40 40 39 40 40 37 40 40 40 38 38 39 40 40 39 40 35 40 39 40 40 38\n+ 33 40 40 40 36 40 40 40 39 39 36 40 40 39 36 38 39 39 39 36 39 38 40 35 33\n+ 36 38 33 40 37 36 37 37 36 36 39 36 33 39 36 37 34 39 38 38 39 36 39 36 31\n+ 33 39 33 37 35 37 36 36 38 36 35 35 36 33 33 33 39 36 31 35 33 33 35 33 36\n+ 33 33 36 35 36 36 35 33 36 29 32 36 34 35 34 35 33 31 33 33 31 25 34 31 33\n+ 33 31 33 28 15 28 15 29 30 28 29 31]\n+>L1S208_79 HWI-EAS440_0386:1:25:7788:3570#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n+[40 40 40 40 40 40 40 39 40 40 40 40 39 40 40 40 40 40 40 40 40 40 40 40 40\n+ 40 40 40 40 40 40 40 40 39 40 40 40 40 40 40 39 40 37 40 40 40 40 40 39 39\n+ 40 37 40 40 40 39 38 39 39 40 39 40 40 40 39 39 40 40 37 37 40 34 40 33 23\n+ 33 35 38 35 31 35 33 32 34 37 36 35 38 34 36 36 33 37 37 37 34 33 33 33 36\n+ 33 36 33 32 32 26 23 30 29 30 32 32 32 33 33 34 34 31 33 33 29 29 34 31 35\n+ 33 31 33 31 22 31 31 31 23 18 26 23 31 23 24 27 22 10 28 23 28 7 28 20 30\n+ 24 30]\n+>L1S257_80 HWI-EAS440_0386:1:25:14850:3657#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n+[27 31 31 38 38 38 38 38 38 38 33 38 38 38 38 38 38 38 38 38 38 38 38 38 38\n+ 38 38 38 38 38 38 35 36 38 38 38 38 38 38 38 38 38 38 38 33 38 38 38 38 38\n+ 38 35 38 38 38 33 27 33 38 38 38 38 38 38 38 38 38 38 29 27 38 38 38 35 38\n+ 35 38 38 38 36 38 35 38 38 38 38 38 36 38 37 36 27 35 38 35 35 35 35 38 38\n+ 38 33 38 35 35 38 35 25 33 33 35 35 35 30 30 25 27 30 38 38 35 33 33 26 33]\n+>L1S76_81 HWI-EAS440_0386:1:25:11581:3662#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n+[40 40 40 38 40 40 40 40 38 39 40 40 38 38 40 40 40 40 40 39 40 40 40 40 39\n+ 40 39 40 40 40 39 40 40 40 40 36 40 36 40 37 37 38 38 38 40 37 40 39 40 40\n+ 39 37 40 39 40 39 35 37 40 40 40 38 36 39 36 39 39 40 39 40 38 38 37 36 38\n+ 38 27 39 36 38 33 35 29 31 29 32 35 32 36 36 36 31 35 30 32 28 27 28 31 33\n+ 31 31 31 33 31 33 29 33 33 33 33 34 32 31 31 8 29 31 27 19 29 16 29 31 31\n+ 29 26 29 32 19 25 31 32]\n+>L1S76_82 HWI-EAS440_0386:1:25:16965:3660#0/1 orig_bc=ACTACGTGTGGT new_bc=ACTACGTGTGGT bc_diffs=0\n+[40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 40 40 40 40 40\n+ 35 40 40 40 40 40 40 40 40 40 39 40 40 39 40 40 40 40 40 39 40 40 40 39 35\n+ 40 37 40 40 40 40 40 40 40 40 40 40 39 40 38 40 38 40 39 39 40 36 40 37 37\n+ 36 40 36 40 39 40 37 40 38 38 39 38 39 35 39 39 39 38 39 38 33 27 36 36 35\n+ 39 36 37 38 38 39 33 38 36 35 39 39 39 33 34 33 36 33 36 36 35 31 33 23 31\n+ 31 31 32 31 33 31 31 31 23 30 18 30]\n+>L1S208_83 HWI-EAS440_0386:1:25:8197:3691#0/1 orig_bc=CTGAGATACGCG new_bc=CTGAGATACGCG bc_diffs=0\n+[40 40 40 40 40 40 40 40 40 40 40 40 39 40 40 40 40 40 40 40 40 40 40 40 39\n+ 38 40 40 40 39 40 40 40 40 40 40 40 40 40 39 39 40 40 40 40 40 38 37 40 40\n+ 40 40 40 40 40 40 40 40 40 40 40 39 38 40 37 37 38 40 37 40 40 37 40 38 39\n+ 33 40 39 38 40 39 40 38 39 38 38 36 35 35 33 35 33 37 35 29 33 31 31 33 33\n+ 33 28 33 33 35 33 30 31 33 25 33 33 33 36 36 36 34 33 30 30 32 19 31 19 30\n+ 28 28 30]\n+>L1S8_84 HWI-EAS440_0386:1:25:11617:3701#0/1 orig_bc=AGCTGACTAGTC new_bc=AGCTGACTAGTC bc_diffs=0\n+[28 33 31 38 35 38 38 38 36 38 36 38 38 38 38 38 38 38 38 36 38 38 38 38 38\n+ 35 38 38 38 38 36 36 36 38 38 38 33 38 38 38 38 38 38 38 35 38 38 38 38 38\n+ 38 38 31 36 36 33 33 36 30 30 30 35 33 38 38 38 36 38 33 38 38 35 38 38 38\n+ 38 33 34 30 15 30 27 33 37 38 37 29 33 35 38 35 35 38 34 33 35 35 35 35 35\n+ 35 35 35 36 38 38 37 35 35 35 32 38 10 7 17 25 18 24 35 33 32 32 32]\n+>L1S257_85 HWI-EAS440_0386:1:25:15484:3705#0/1 orig_bc=CCGACTGAGATG new_bc=CCGACTGAGATG bc_diffs=0\n+[40 40 40 40 40 40 40 40 39 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 37\n+ 37 40 40 40 37 40 40 40 40 40 39 40 40 40 39 36 40 40 40 39 40 40 40 39 39\n+ 40 37 40 40 40 40 39 40 40 40 39 39 39 40 38 39 39 37 39 40 39 36 40 35 33\n+ 33 37 38 39 37 39 37 36 39 36 40 40 36 33 35 33 36 36 35 34 35 36 37 28 35\n+ 33 35 35 34 33 35 28 35 31 33 35 36 33 35 37 34 34 29 33 31 33 19 33 28 31\n+ 28 29 31 28 33 33 29 23 30]\n'

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries_fastq/sequence_qualities.qual
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries_fastq/sequence_qualities.qual Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/split_libraries_fastq/sequences.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_libraries_fastq/sequences.fasta Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa/1_L2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa/1_L2.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,10 @@
+#SampleID BarcodeSequence LinkerPrimerSequence SampleType year month day subject days_since_epoch Description Unclassified;Other k__Bacteria;Other k__Bacteria;p__Proteobacteria
+f1 ACACTGTTCATG GTGCCAGCMGCCGCGGTAA feces 2008 10 22 1 14174 fecal1 0.0 1.0 0.0
+f2 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 14175 fecal2 0.0454545454545 0.954545454545 0.0
+f3 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 14175 identical sequences to fecal2 0.0 1.0 0.0
+f4 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 14175 all sequences identical, map to GG 295053 at 97 percent id 0.0 1.0 0.0
+p1 AACGCACGCTAG GTGCCAGCMGCCGCGGTAA L_palm 2008 10 21 1 14173 palm1, contains one randomly generated sequence 0.130434782609 0.869565217391 0.0
+p2 ACACTGTTCATG GTGCCAGCMGCCGCGGTAA L_palm 2008 10 22 1 14174 palm2 0.272727272727 0.681818181818 0.0454545454545
+t1 AGTGAGAGAAGC GTGCCAGCMGCCGCGGTAA Tongue 2008 10 21 1 14173 tongue1, contains one randomly generated sequence 0.869565217391 0.130434782609 0.0
+t2 ATACTATTGCGC GTGCCAGCMGCCGCGGTAA Tongue 2008 10 22 1 14174 tongue2 0.681818181818 0.318181818182 0.0
+not16S.1 ATACTATTGCGC GTGCCAGCMGCCGCGGTAA Other 2008 10 22 1 14174 randomly generated sequence plus some variants, these should not map to 16S 0.909090909091 0.0909090909091 0.0

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa/1_L3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa/1_L3.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa/1_L4.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa/1_L4.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,10 @@
+#SampleID BarcodeSequence LinkerPrimerSequence SampleType year month day subject days_since_epoch Description Unclassified;Other k__Bacteria;Other k__Bacteria;p__Proteobacteria Unclassified;Other;Other k__Bacteria;Other;Other k__Bacteria;p__Proteobacteria;Other Unclassified;Other;Other;Other k__Bacteria;Other;Other;Other k__Bacteria;p__Proteobacteria;Other;Other
+f1 ACACTGTTCATG GTGCCAGCMGCCGCGGTAA feces 2008 10 22 1 14174 fecal1 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0
+f2 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 14175 fecal2 0.0454545454545 0.954545454545 0.0 0.0454545454545 0.954545454545 0.0 0.0454545454545 0.954545454545 0.0
+f3 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 14175 identical sequences to fecal2 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0
+f4 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 14175 all sequences identical, map to GG 295053 at 97 percent id 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0
+p1 AACGCACGCTAG GTGCCAGCMGCCGCGGTAA L_palm 2008 10 21 1 14173 palm1, contains one randomly generated sequence 0.130434782609 0.869565217391 0.0 0.130434782609 0.869565217391 0.0 0.130434782609 0.869565217391 0.0
+p2 ACACTGTTCATG GTGCCAGCMGCCGCGGTAA L_palm 2008 10 22 1 14174 palm2 0.272727272727 0.681818181818 0.0454545454545 0.272727272727 0.681818181818 0.0454545454545 0.272727272727 0.681818181818 0.0454545454545
+t1 AGTGAGAGAAGC GTGCCAGCMGCCGCGGTAA Tongue 2008 10 21 1 14173 tongue1, contains one randomly generated sequence 0.869565217391 0.130434782609 0.0 0.869565217391 0.130434782609 0.0 0.869565217391 0.130434782609 0.0
+t2 ATACTATTGCGC GTGCCAGCMGCCGCGGTAA Tongue 2008 10 22 1 14174 tongue2 0.681818181818 0.318181818182 0.0 0.681818181818 0.318181818182 0.0 0.681818181818 0.318181818182 0.0
+not16S.1 ATACTATTGCGC GTGCCAGCMGCCGCGGTAA Other 2008 10 22 1 14174 randomly generated sequence plus some variants, these should not map to 16S 0.909090909091 0.0909090909091 0.0 0.909090909091 0.0909090909091 0.0 0.909090909091 0.0909090909091 0.0

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa/1_L5.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa/1_L5.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,10 @@
+#SampleID BarcodeSequence LinkerPrimerSequence SampleType year month day subject days_since_epoch Description Unclassified;Other k__Bacteria;Other k__Bacteria;p__Proteobacteria Unclassified;Other;Other k__Bacteria;Other;Other k__Bacteria;p__Proteobacteria;Other Unclassified;Other;Other;Other k__Bacteria;Other;Other;Other k__Bacteria;p__Proteobacteria;Other;Other Unclassified;Other;Other;Other;Other k__Bacteria;Other;Other;Other;Other k__Bacteria;p__Proteobacteria;Other;Other;Other
+f1 ACACTGTTCATG GTGCCAGCMGCCGCGGTAA feces 2008 10 22 1 14174 fecal1 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0
+f2 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 14175 fecal2 0.0454545454545 0.954545454545 0.0 0.0454545454545 0.954545454545 0.0 0.0454545454545 0.954545454545 0.0 0.0454545454545 0.954545454545 0.0
+f3 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 14175 identical sequences to fecal2 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0
+f4 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 14175 all sequences identical, map to GG 295053 at 97 percent id 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0
+p1 AACGCACGCTAG GTGCCAGCMGCCGCGGTAA L_palm 2008 10 21 1 14173 palm1, contains one randomly generated sequence 0.130434782609 0.869565217391 0.0 0.130434782609 0.869565217391 0.0 0.130434782609 0.869565217391 0.0 0.130434782609 0.869565217391 0.0
+p2 ACACTGTTCATG GTGCCAGCMGCCGCGGTAA L_palm 2008 10 22 1 14174 palm2 0.272727272727 0.681818181818 0.0454545454545 0.272727272727 0.681818181818 0.0454545454545 0.272727272727 0.681818181818 0.0454545454545 0.272727272727 0.681818181818 0.0454545454545
+t1 AGTGAGAGAAGC GTGCCAGCMGCCGCGGTAA Tongue 2008 10 21 1 14173 tongue1, contains one randomly generated sequence 0.869565217391 0.130434782609 0.0 0.869565217391 0.130434782609 0.0 0.869565217391 0.130434782609 0.0 0.869565217391 0.130434782609 0.0
+t2 ATACTATTGCGC GTGCCAGCMGCCGCGGTAA Tongue 2008 10 22 1 14174 tongue2 0.681818181818 0.318181818182 0.0 0.681818181818 0.318181818182 0.0 0.681818181818 0.318181818182 0.0 0.681818181818 0.318181818182 0.0
+not16S.1 ATACTATTGCGC GTGCCAGCMGCCGCGGTAA Other 2008 10 22 1 14174 randomly generated sequence plus some variants, these should not map to 16S 0.909090909091 0.0909090909091 0.0 0.909090909091 0.0909090909091 0.0 0.909090909091 0.0909090909091 0.0 0.909090909091 0.0909090909091 0.0

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa/1_L6.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa/1_L6.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,10 @@
+#SampleID BarcodeSequence LinkerPrimerSequence SampleType year month day subject days_since_epoch Description Unclassified;Other k__Bacteria;Other k__Bacteria;p__Proteobacteria Unclassified;Other;Other k__Bacteria;Other;Other k__Bacteria;p__Proteobacteria;Other Unclassified;Other;Other;Other k__Bacteria;Other;Other;Other k__Bacteria;p__Proteobacteria;Other;Other Unclassified;Other;Other;Other;Other k__Bacteria;Other;Other;Other;Other k__Bacteria;p__Proteobacteria;Other;Other;Other Unclassified;Other;Other;Other;Other;Other k__Bacteria;Other;Other;Other;Other;Other k__Bacteria;p__Proteobacteria;Other;Other;Other;Other
+f1 ACACTGTTCATG GTGCCAGCMGCCGCGGTAA feces 2008 10 22 1 14174 fecal1 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0
+f2 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 14175 fecal2 0.0454545454545 0.954545454545 0.0 0.0454545454545 0.954545454545 0.0 0.0454545454545 0.954545454545 0.0 0.0454545454545 0.954545454545 0.0 0.0454545454545 0.954545454545 0.0
+f3 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 14175 identical sequences to fecal2 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0
+f4 ACCAGACGATGC GTGCCAGCMGCCGCGGTAA feces 2008 10 23 1 14175 all sequences identical, map to GG 295053 at 97 percent id 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0
+p1 AACGCACGCTAG GTGCCAGCMGCCGCGGTAA L_palm 2008 10 21 1 14173 palm1, contains one randomly generated sequence 0.130434782609 0.869565217391 0.0 0.130434782609 0.869565217391 0.0 0.130434782609 0.869565217391 0.0 0.130434782609 0.869565217391 0.0 0.130434782609 0.869565217391 0.0
+p2 ACACTGTTCATG GTGCCAGCMGCCGCGGTAA L_palm 2008 10 22 1 14174 palm2 0.272727272727 0.681818181818 0.0454545454545 0.272727272727 0.681818181818 0.0454545454545 0.272727272727 0.681818181818 0.0454545454545 0.272727272727 0.681818181818 0.0454545454545 0.272727272727 0.681818181818 0.0454545454545
+t1 AGTGAGAGAAGC GTGCCAGCMGCCGCGGTAA Tongue 2008 10 21 1 14173 tongue1, contains one randomly generated sequence 0.869565217391 0.130434782609 0.0 0.869565217391 0.130434782609 0.0 0.869565217391 0.130434782609 0.0 0.869565217391 0.130434782609 0.0 0.869565217391 0.130434782609 0.0
+t2 ATACTATTGCGC GTGCCAGCMGCCGCGGTAA Tongue 2008 10 22 1 14174 tongue2 0.681818181818 0.318181818182 0.0 0.681818181818 0.318181818182 0.0 0.681818181818 0.318181818182 0.0 0.681818181818 0.318181818182 0.0 0.681818181818 0.318181818182 0.0
+not16S.1 ATACTATTGCGC GTGCCAGCMGCCGCGGTAA Other 2008 10 22 1 14174 randomly generated sequence plus some variants, these should not map to 16S 0.909090909091 0.0909090909091 0.0 0.909090909091 0.0909090909091 0.0 0.909090909091 0.0909090909091 0.0 0.909090909091 0.0909090909091 0.0 0.909090909091 0.0909090909091 0.0

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa/2_L3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa/2_L3.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,5 @@
+# Constructed from biom file
+#OTU ID f2 f1 f3 f4 p2 p1 t1 not16S.1 t2
+Unclassified;Other;Other 0.0454545454545 0.0 0.0 0.0 0.272727272727 0.130434782609 0.869565217391 0.909090909091 0.681818181818
+k__Bacteria;Other;Other 0.954545454545 1.0 1.0 1.0 0.681818181818 0.869565217391 0.130434782609 0.0909090909091 0.318181818182
+k__Bacteria;p__Proteobacteria;Other 0.0 0.0 0.0 0.0 0.0454545454545 0.0 0.0 0.0 0.0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa/2_L6.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa/2_L6.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,5 @@
+# Constructed from biom file
+#OTU ID f2 f1 f3 f4 p2 p1 t1 not16S.1 t2
+Unclassified;Other;Other;Other;Other;Other 0.0454545454545 0.0 0.0 0.0 0.272727272727 0.130434782609 0.869565217391 0.909090909091 0.681818181818
+k__Bacteria;Other;Other;Other;Other;Other 0.954545454545 1.0 1.0 1.0 0.681818181818 0.869565217391 0.130434782609 0.0909090909091 0.318181818182
+k__Bacteria;p__Proteobacteria;Other;Other;Other;Other 0.0 0.0 0.0 0.0 0.0454545454545 0.0 0.0 0.0 0.0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa/map.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa/map.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa/otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa/otu_table.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/Fasting_Map.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/Fasting_Map.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping/area_charts.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping/area_charts.html Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,400 @@\n+\n+<html>\n+<head>\n+<link rel="stylesheet" href="./css/qiime_style.css" type="text/css">\n+<script type="text/javascript" src="./js/overlib.js"></script>\n+\n+<script type="text/javascript">\n+\n+</script>\n+<title>Taxa Summaries</title>\n+</head>\n+<body>\n+<div id="overDiv" style="position:absolute; visibility:hidden; z-index:1000;"></div>\n+<table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: </td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/0HwDtsTy0zx010mJJG5Tr60YYJeiTX.pdf\' target="_blank">View Figure (.pdf)</a>  <a href=\'charts/d2Z1yJqW4fWA4Zqgfdw2859OTzOHXg_legend.pdf\' target="_blank">View Legend (.pdf)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/d2Z1yJqW4fWA4Zqgfdw2859OTzOHXg.png\' border=1 ismap usemap="#pointsrect1" /><br></td>\n+</tr>\n+</table>\n+\n+<MAP name="pointsrect1">\n+<AREA shape="rect" coords="118.1400%,432.0000%,121.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.636:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="211.1400%,432.0000%,214.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.635:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="304.1400%,432.0000%,307.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.356:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="397.1400%,432.0000%,400.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.481:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="490.1400%,432.0000%,493.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.354:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="583.1400%,432.0000%,586.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.593:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="676.1400%,432.0000%,679.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.355:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="769.1400%,432.0000%,772.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.607:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="862.1400%,432.0000%,865.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.634:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+\n+</MAP>\n+\n+<table><tr class=ntitle><td><a href="raw_data/otu_table_L2.txt" target="_blank">View Table (.txt)</a></td></tr></table><table cellpadding=1 cellspacing=1 border=1 style="text-align:center;border-color:white;border-style:groove;"><tr class="ntitle"><td class="header" colspan="2"></td><td valign="bottom" class="header">Total</td><td valign=bottom class=header>PC.636</td><td valign=bottom class=header>PC.635</td><td valign=bottom class=header>PC.356</td><td valign=bottom class=header>PC.481</td><td valign=bottom class=header>PC.354</td><td valign=bottom class=header>PC.593</td><td valign=bottom class=header>PC.355</td><td valign=bottom class=header>PC.607</td><td valign=bottom class=header>PC.634</td></tr><tr class=ntitle><td valign="bottom" class="header">Legend</td><td valign="bottom" class="header">Taxonomy</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header"'..b'mal"> 5.4%</td><td class="normal" style="border-color:#c49c6b;"> 6.8%</td><td class="normal" style="border-color:#c49c6b;"> 9.4%</td><td class="normal" style="border-color:#c49c6b;"> 7.3%</td><td class="normal" style="border-color:#c49c6b;"> 4.1%</td><td class="normal" style="border-color:#c49c6b;"> 4.0%</td><td class="normal" style="border-color:#c49c6b;"> 2.0%</td><td class="normal" style="border-color:#c49c6b;"> 0.7%</td><td class="normal" style="border-color:#c49c6b;"> 9.4%</td><td class="normal" style="border-color:#c49c6b;"> 5.3%</td></tr><tr><td class="normal" bgcolor="#808000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;<a href=javascript:gg(\'f__Desulfovibrionaceae\');>f__Desulfovibrionaceae</a></td><td class="normal"> 0.4%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal" style="border-color:#808000;"> 1.3%</td></tr><tr><td class="normal" bgcolor="#8c3fff">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;<a href=javascript:gg(\'f__Helicobacteraceae\');>f__Helicobacteraceae</a></td><td class="normal"> 0.5%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#8c3fff;"> 3.4%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#8c3fff;"> 1.3%</td><td class="normal"> 0.0%</td></tr><tr><td class="normal" bgcolor="#bc828d">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;<a href=javascript:gg(\'f__F16\');>f__F16</a></td><td class="normal"> 0.1%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#bc828d;"> 1.3%</td></tr><tr><td class="normal" bgcolor="#008080">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;<a href=javascript:gg(\'f__Erysipelotrichaceae\');>f__Erysipelotrichaceae</a></td><td class="normal"> 4.4%</td><td class="normal" style="border-color:#008080;"> 1.4%</td><td class="normal" style="border-color:#008080;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#008080;"> 3.4%</td><td class="normal" style="border-color:#008080;"> 1.3%</td><td class="normal" style="border-color:#008080;"> 14.8%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#008080;"> 15.4%</td><td class="normal" style="border-color:#008080;"> 2.7%</td></tr><tr><td class="normal" bgcolor="#800000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;<a href=javascript:gg(\'f__\');>f__</a></td><td class="normal"> 0.1%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#800000;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#800000;"> 0.7%</td><td class="normal"> 0.0%</td></tr></table>\n+</body>\n+</html>\n'

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping/bar_charts.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping/bar_charts.html Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,400 @@\n+\n+<html>\n+<head>\n+<link rel="stylesheet" href="./css/qiime_style.css" type="text/css">\n+<script type="text/javascript" src="./js/overlib.js"></script>\n+\n+<script type="text/javascript">\n+\n+</script>\n+<title>Taxa Summaries</title>\n+</head>\n+<body>\n+<div id="overDiv" style="position:absolute; visibility:hidden; z-index:1000;"></div>\n+<table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: </td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/Poa8pIcXi3dWWDz9uzJcbyeQDMf1mH.pdf\' target="_blank">View Figure (.pdf)</a>  <a href=\'charts/4EF9Ee2W1Ld0H0KCUxEmeoYbAek3T8_legend.pdf\' target="_blank">View Legend (.pdf)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/4EF9Ee2W1Ld0H0KCUxEmeoYbAek3T8.png\' border=1 ismap usemap="#pointsrect1" /><br></td>\n+</tr>\n+</table>\n+\n+<MAP name="pointsrect1">\n+<AREA shape="rect" coords="166.5000%,432.0000%,222.3000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.636:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="240.9000%,432.0000%,296.7000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.635:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="315.3000%,432.0000%,371.1000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.356:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="389.7000%,432.0000%,445.5000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.481:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="464.1000%,432.0000%,519.9000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.354:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="538.5000%,432.0000%,594.3000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.593:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="612.9000%,432.0000%,668.7000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.355:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="687.3000%,432.0000%,743.1000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.607:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="761.7000%,432.0000%,817.5000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.634:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+\n+</MAP>\n+\n+<table><tr class=ntitle><td><a href="raw_data/otu_table_L2.txt" target="_blank">View Table (.txt)</a></td></tr></table><table cellpadding=1 cellspacing=1 border=1 style="text-align:center;border-color:white;border-style:groove;"><tr class="ntitle"><td class="header" colspan="2"></td><td valign="bottom" class="header">Total</td><td valign=bottom class=header>PC.636</td><td valign=bottom class=header>PC.635</td><td valign=bottom class=header>PC.356</td><td valign=bottom class=header>PC.481</td><td valign=bottom class=header>PC.354</td><td valign=bottom class=header>PC.593</td><td valign=bottom class=header>PC.355</td><td valign=bottom class=header>PC.607</td><td valign=bottom class=header>PC.634</td></tr><tr class=ntitle><td valign="bottom" class="header">Legend</td><td valign="bottom" class="header">Taxonomy</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header"'..b'mal"> 5.4%</td><td class="normal" style="border-color:#c49c6b;"> 6.8%</td><td class="normal" style="border-color:#c49c6b;"> 9.4%</td><td class="normal" style="border-color:#c49c6b;"> 7.3%</td><td class="normal" style="border-color:#c49c6b;"> 4.1%</td><td class="normal" style="border-color:#c49c6b;"> 4.0%</td><td class="normal" style="border-color:#c49c6b;"> 2.0%</td><td class="normal" style="border-color:#c49c6b;"> 0.7%</td><td class="normal" style="border-color:#c49c6b;"> 9.4%</td><td class="normal" style="border-color:#c49c6b;"> 5.3%</td></tr><tr><td class="normal" bgcolor="#808000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;<a href=javascript:gg(\'f__Desulfovibrionaceae\');>f__Desulfovibrionaceae</a></td><td class="normal"> 0.4%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal" style="border-color:#808000;"> 1.3%</td></tr><tr><td class="normal" bgcolor="#8c3fff">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;<a href=javascript:gg(\'f__Helicobacteraceae\');>f__Helicobacteraceae</a></td><td class="normal"> 0.5%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#8c3fff;"> 3.4%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#8c3fff;"> 1.3%</td><td class="normal"> 0.0%</td></tr><tr><td class="normal" bgcolor="#bc828d">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;<a href=javascript:gg(\'f__F16\');>f__F16</a></td><td class="normal"> 0.1%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#bc828d;"> 1.3%</td></tr><tr><td class="normal" bgcolor="#008080">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;<a href=javascript:gg(\'f__Erysipelotrichaceae\');>f__Erysipelotrichaceae</a></td><td class="normal"> 4.4%</td><td class="normal" style="border-color:#008080;"> 1.4%</td><td class="normal" style="border-color:#008080;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#008080;"> 3.4%</td><td class="normal" style="border-color:#008080;"> 1.3%</td><td class="normal" style="border-color:#008080;"> 14.8%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#008080;"> 15.4%</td><td class="normal" style="border-color:#008080;"> 2.7%</td></tr><tr><td class="normal" bgcolor="#800000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;<a href=javascript:gg(\'f__\');>f__</a></td><td class="normal"> 0.1%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#800000;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#800000;"> 0.7%</td><td class="normal"> 0.0%</td></tr></table>\n+</body>\n+</html>\n'

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping/log_20170501130931.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping/log_20170501130931.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,43 @@
+Logging started at 13:09:31 on 01 May 2017
+QIIME version: 1.9.1
+
+qiime_config values:
+pick_otus_reference_seqs_fp /Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
+sc_queue all.q
+pynast_template_alignment_fp /Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta
+cluster_jobs_fp start_parallel_jobs.py
+assign_taxonomy_reference_seqs_fp /Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
+torque_queue friendlyq
+jobs_to_start 1
+denoiser_min_per_core 50
+assign_taxonomy_id_to_taxonomy_fp /Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
+temp_dir /var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/
+blastall_fp blastall
+seconds_to_sleep 1
+
+parameter file values:
+
+Input file md5 sums:
+test-data/summarize_taxa_through_plots/otu_table.biom: dda91090fbdc0f69056852247bcd924f
+test-data/summarize_taxa_through_plots/Fasting_Map.txt: e16159d7122035797076d66b1a287962
+
+Executing commands.
+
+# Summarize Taxonomy command
+summarize_taxa.py -i test-data/summarize_taxa_through_plots/otu_table.biom -o summarize_taxa_through_plots_mapping
+
+Stdout:
+
+Stderr:
+
+# Plot Taxonomy Summary command
+plot_taxa_summary.py -i summarize_taxa_through_plots_mapping/otu_table_L2.txt,summarize_taxa_through_plots_mapping/otu_table_L3.txt,summarize_taxa_through_plots_mapping/otu_table_L4.txt,summarize_taxa_through_plots_mapping/otu_table_L5.txt,summarize_taxa_through_plots_mapping/otu_table_L6.txt -o summarize_taxa_through_plots_mapping/taxa_summary_plots/
+
+Stdout:
+
+Stderr:
+/Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
+ if self._edgecolors == str('face'):
+
+
+Logging stopped at 13:09:49 on 01 May 2017

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping/otu_table_L2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping/otu_table_L2.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,3 @@
+# Constructed from biom file
+#OTU ID PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+Root;k__Bacteria 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping/otu_table_L2_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping/otu_table_L2_json.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping/otu_table_L3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping/otu_table_L3.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,10 @@
+# Constructed from biom file
+#OTU ID PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+Root;k__Bacteria;Other 0.0202702702703 0.0469798657718 0.0266666666667 0.027397260274 0.0134228187919 0.0134228187919 0.0136054421769 0.0469798657718 0.02
+Root;k__Bacteria;p__Actinobacteria 0.00675675675676 0.00671140939597 0.0 0.00684931506849 0.0 0.0 0.0 0.0201342281879 0.02
+Root;k__Bacteria;p__Bacteroidetes 0.695945945946 0.523489932886 0.193333333333 0.143835616438 0.0738255033557 0.389261744966 0.285714285714 0.275167785235 0.653333333333
+Root;k__Bacteria;p__Deferribacteres 0.0472972972973 0.0134228187919 0.0 0.0 0.0 0.0 0.0 0.0201342281879 0.0333333333333
+Root;k__Bacteria;p__Firmicutes 0.209459459459 0.395973154362 0.773333333333 0.787671232877 0.89932885906 0.41610738255 0.700680272109 0.456375838926 0.22
+Root;k__Bacteria;p__Proteobacteria 0.00675675675676 0.00671140939597 0.0 0.0 0.0 0.0335570469799 0.0 0.0201342281879 0.0133333333333
+Root;k__Bacteria;p__TM7 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0133333333333
+Root;k__Bacteria;p__Tenericutes 0.0135135135135 0.00671140939597 0.00666666666667 0.0342465753425 0.0134228187919 0.147651006711 0.0 0.161073825503 0.0266666666667
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping/otu_table_L3_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping/otu_table_L3_json.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping/otu_table_L4.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping/otu_table_L4.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,14 @@
+# Constructed from biom file
+#OTU ID PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+Root;k__Bacteria;Other;Other 0.0202702702703 0.0469798657718 0.0266666666667 0.027397260274 0.0134228187919 0.0134228187919 0.0136054421769 0.0469798657718 0.02
+Root;k__Bacteria;p__Actinobacteria;c__Actinobacteria 0.00675675675676 0.00671140939597 0.0 0.00684931506849 0.0 0.0 0.0 0.0201342281879 0.02
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia 0.695945945946 0.523489932886 0.193333333333 0.143835616438 0.0738255033557 0.389261744966 0.285714285714 0.275167785235 0.653333333333
+Root;k__Bacteria;p__Deferribacteres;c__Deferribacteres 0.0472972972973 0.0134228187919 0.0 0.0 0.0 0.0 0.0 0.0201342281879 0.0333333333333
+Root;k__Bacteria;p__Firmicutes;Other 0.0 0.0 0.0 0.0 0.00671140939597 0.0 0.0 0.0268456375839 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli 0.0202702702703 0.0 0.0933333333333 0.0890410958904 0.107382550336 0.0335570469799 0.0136054421769 0.00671140939597 0.02
+Root;k__Bacteria;p__Firmicutes;c__Clostridia 0.189189189189 0.395973154362 0.68 0.698630136986 0.785234899329 0.38255033557 0.687074829932 0.422818791946 0.2
+Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria 0.00675675675676 0.00671140939597 0.0 0.0 0.0 0.0 0.0 0.00671140939597 0.0133333333333
+Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria 0.0 0.0 0.0 0.0 0.0 0.0335570469799 0.0 0.0134228187919 0.0
+Root;k__Bacteria;p__TM7;c__TM7-3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0133333333333
+Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi 0.0135135135135 0.00671140939597 0.0 0.0342465753425 0.0134228187919 0.147651006711 0.0 0.154362416107 0.0266666666667
+Root;k__Bacteria;p__Tenericutes;c__Mollicutes 0.0 0.0 0.00666666666667 0.0 0.0 0.0 0.0 0.00671140939597 0.0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping/otu_table_L4_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping/otu_table_L4_json.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping/otu_table_L5.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping/otu_table_L5.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,16 @@
+# Constructed from biom file
+#OTU ID PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+Root;k__Bacteria;Other;Other;Other 0.0202702702703 0.0469798657718 0.0266666666667 0.027397260274 0.0134228187919 0.0134228187919 0.0136054421769 0.0469798657718 0.02
+Root;k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Coriobacteriales 0.00675675675676 0.00671140939597 0.0 0.00684931506849 0.0 0.0 0.0 0.0201342281879 0.02
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales 0.695945945946 0.523489932886 0.193333333333 0.143835616438 0.0738255033557 0.389261744966 0.285714285714 0.275167785235 0.653333333333
+Root;k__Bacteria;p__Deferribacteres;c__Deferribacteres;o__Deferribacterales 0.0472972972973 0.0134228187919 0.0 0.0 0.0 0.0 0.0 0.0201342281879 0.0333333333333
+Root;k__Bacteria;p__Firmicutes;Other;Other 0.0 0.0 0.0 0.0 0.00671140939597 0.0 0.0 0.0268456375839 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales 0.0202702702703 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales 0.0 0.0 0.0933333333333 0.027397260274 0.107382550336 0.0335570469799 0.0136054421769 0.00671140939597 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales 0.0 0.0 0.0 0.0616438356164 0.0 0.0 0.0 0.0 0.02
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales 0.189189189189 0.395973154362 0.68 0.698630136986 0.785234899329 0.38255033557 0.687074829932 0.422818791946 0.2
+Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales 0.00675675675676 0.00671140939597 0.0 0.0 0.0 0.0 0.0 0.00671140939597 0.0133333333333
+Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales 0.0 0.0 0.0 0.0 0.0 0.0335570469799 0.0 0.0134228187919 0.0
+Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0133333333333
+Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales 0.0135135135135 0.00671140939597 0.0 0.0342465753425 0.0134228187919 0.147651006711 0.0 0.154362416107 0.0266666666667
+Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39 0.0 0.0 0.00666666666667 0.0 0.0 0.0 0.0 0.00671140939597 0.0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping/otu_table_L5_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping/otu_table_L5_json.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping/otu_table_L6.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping/otu_table_L6.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,29 @@
+# Constructed from biom file
+#OTU ID PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+Root;k__Bacteria;Other;Other;Other;Other 0.0202702702703 0.0469798657718 0.0266666666667 0.027397260274 0.0134228187919 0.0134228187919 0.0136054421769 0.0469798657718 0.02
+Root;k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Coriobacteriales;f__Coriobacteriaceae 0.00675675675676 0.00671140939597 0.0 0.00684931506849 0.0 0.0 0.0 0.0201342281879 0.02
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;Other 0.00675675675676 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__ 0.466216216216 0.308724832215 0.173333333333 0.0753424657534 0.0536912751678 0.362416107383 0.136054421769 0.201342281879 0.186666666667
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae 0.168918918919 0.0469798657718 0.0 0.013698630137 0.0134228187919 0.0268456375839 0.12925170068 0.0 0.273333333333
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae 0.0135135135135 0.0268456375839 0.0 0.00684931506849 0.0 0.0 0.00680272108844 0.0 0.08
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae 0.0 0.00671140939597 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae 0.0405405405405 0.134228187919 0.02 0.0479452054795 0.00671140939597 0.0 0.0136054421769 0.0738255033557 0.113333333333
+Root;k__Bacteria;p__Deferribacteres;c__Deferribacteres;o__Deferribacterales;f__Deferribacteraceae 0.0472972972973 0.0134228187919 0.0 0.0 0.0 0.0 0.0 0.0201342281879 0.0333333333333
+Root;k__Bacteria;p__Firmicutes;Other;Other;Other 0.0 0.0 0.0 0.0 0.00671140939597 0.0 0.0 0.0268456375839 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae 0.0202702702703 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae 0.0 0.0 0.0933333333333 0.027397260274 0.107382550336 0.0335570469799 0.0136054421769 0.0 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.00671140939597 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales;f__Turicibacteraceae 0.0 0.0 0.0 0.0616438356164 0.0 0.0 0.0 0.0 0.02
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;Other 0.0 0.0201342281879 0.02 0.00684931506849 0.00671140939597 0.00671140939597 0.0 0.0134228187919 0.00666666666667
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__ 0.0 0.00671140939597 0.00666666666667 0.0 0.00671140939597 0.00671140939597 0.0204081632653 0.00671140939597 0.0
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Catabacteriaceae 0.00675675675676 0.0 0.0 0.0 0.0 0.0 0.0 0.0268456375839 0.0
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae 0.0 0.0 0.0 0.0 0.00671140939597 0.0671140939597 0.00680272108844 0.0 0.02
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales Family XIII. Incertae Sedis 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.00671140939597 0.00666666666667
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae 0.114864864865 0.268456375839 0.58 0.650684931507 0.718120805369 0.275167785235 0.65306122449 0.268456375839 0.113333333333
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptococcaceae 0.0 0.00671140939597 0.0 0.0 0.00671140939597 0.00671140939597 0.0 0.00671140939597 0.0
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae 0.0675675675676 0.0939597315436 0.0733333333333 0.041095890411 0.0402684563758 0.0201342281879 0.00680272108844 0.0939597315436 0.0533333333333
+Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae 0.00675675675676 0.00671140939597 0.0 0.0 0.0 0.0 0.0 0.00671140939597 0.0133333333333
+Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae 0.0 0.0 0.0 0.0 0.0 0.0335570469799 0.0 0.0134228187919 0.0
+Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;f__F16 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0133333333333
+Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae 0.0135135135135 0.00671140939597 0.0 0.0342465753425 0.0134228187919 0.147651006711 0.0 0.154362416107 0.0266666666667
+Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;f__ 0.0 0.0 0.00666666666667 0.0 0.0 0.0 0.0 0.00671140939597 0.0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping/otu_table_L6_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping/otu_table_L6_json.biom Thu May 18 09:38:55 2017 -0400

[

@@ -0,0 +1,1 @@
+{"id": "No Table ID","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-05-01T13:26:26.770739","type": "OTU table","matrix_element_type": "float","shape": [27, 9],"data": [[0,0,0.020270270270270271],[0,1,0.046979865771812075],[0,2,0.026666666666666668],[0,3,0.027397260273972601],[0,4,0.013422818791946308],[0,5,0.013422818791946308],[0,6,0.013605442176870748],[0,7,0.046979865771812075],[0,8,0.02],[1,0,0.0067567567567567571],[1,1,0.0067114093959731542],[1,3,0.0068493150684931503],[1,7,0.020134228187919462],[1,8,0.02],[2,0,0.0067567567567567571],[3,0,0.46621621621621612],[3,1,0.30872483221476499],[3,2,0.17333333333333331],[3,3,0.075342465753424653],[3,4,0.053691275167785227],[3,5,0.36241610738255031],[3,6,0.13605442176870747],[3,7,0.20134228187919456],[3,8,0.18666666666666668],[4,0,0.16891891891891891],[4,1,0.046979865771812082],[4,3,0.013698630136986301],[4,4,0.013422818791946308],[4,5,0.026845637583892617],[4,6,0.12925170068027211],[4,8,0.27333333333333332],[5,0,0.013513513513513514],[5,1,0.026845637583892617],[5,3,0.0068493150684931503],[5,6,0.0068027210884353739],[5,8,0.080000000000000002],[6,1,0.0067114093959731542],[7,0,0.040540540540540543],[7,1,0.13422818791946309],[7,2,0.02],[7,3,0.047945205479452052],[7,4,0.0067114093959731542],[7,6,0.013605442176870748],[7,7,0.073825503355704702],[7,8,0.11333333333333334],[8,0,0.0472972972972973],[8,1,0.013422818791946308],[8,7,0.020134228187919462],[8,8,0.033333333333333333],[9,4,0.0067114093959731542],[9,7,0.026845637583892617],[10,0,0.020270270270270271],[11,2,0.093333333333333338],[11,3,0.027397260273972601],[11,4,0.10738255033557048],[11,5,0.033557046979865772],[11,6,0.013605442176870748],[12,7,0.0067114093959731542],[13,3,0.061643835616438353],[13,8,0.02],[14,1,0.020134228187919462],[14,2,0.02],[14,3,0.0068493150684931503],[14,4,0.0067114093959731542],[14,5,0.0067114093959731542],[14,7,0.013422818791946308],[14,8,0.0066666666666666671],[15,1,0.0067114093959731542],[15,2,0.0066666666666666671],[15,4,0.0067114093959731542],[15,5,0.0067114093959731542],[15,6,0.020408163265306121],[15,7,0.0067114093959731542],[16,0,0.0067567567567567571],[16,7,0.026845637583892617],[17,4,0.0067114093959731542],[17,5,0.067114093959731544],[17,6,0.0068027210884353739],[17,8,0.02],[18,7,0.0067114093959731542],[18,8,0.0066666666666666671],[19,0,0.11486486486486487],[19,1,0.26845637583892606],[19,2,0.57999999999999996],[19,3,0.65068493150684981],[19,4,0.71812080536912726],[19,5,0.27516778523489921],[19,6,0.65306122448979598],[19,7,0.26845637583892612],[19,8,0.11333333333333334],[20,1,0.0067114093959731542],[20,4,0.0067114093959731542],[20,5,0.0067114093959731542],[20,7,0.0067114093959731542],[21,0,0.067567567567567571],[21,1,0.093959731543624178],[21,2,0.073333333333333334],[21,3,0.041095890410958902],[21,4,0.040268456375838924],[21,5,0.020134228187919462],[21,6,0.0068027210884353739],[21,7,0.093959731543624178],[21,8,0.053333333333333337],[22,0,0.0067567567567567571],[22,1,0.0067114093959731542],[22,7,0.0067114093959731542],[22,8,0.013333333333333334],[23,5,0.033557046979865772],[23,7,0.013422818791946308],[24,8,0.013333333333333334],[25,0,0.013513513513513514],[25,1,0.0067114093959731542],[25,3,0.034246575342465752],[25,4,0.013422818791946308],[25,5,0.1476510067114094],[25,7,0.15436241610738255],[25,8,0.026666666666666668],[26,2,0.0066666666666666671],[26,7,0.0067114093959731542]],"rows": [{"id": "Root;k__Bacteria;Other;Other;Other;Other", "metadata": null},{"id": "Root;k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Coriobacteriales;f__Coriobacteriaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;Other", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Deferribacteres;c__Deferribacteres;o__Deferribacterales;f__Deferribacteraceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;Other;Other;Other", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales;f__Turicibacteraceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;Other", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Catabacteriaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales Family XIII. Incertae Sedis", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptococcaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae", "metadata": null},{"id": "Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;f__F16", "metadata": null},{"id": "Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;f__", "metadata": null}],"columns": [{"id": "PC.636", "metadata": null},{"id": "PC.635", "metadata": null},{"id": "PC.356", "metadata": null},{"id": "PC.481", "metadata": null},{"id": "PC.354", "metadata": null},{"id": "PC.593", "metadata": null},{"id": "PC.355", "metadata": null},{"id": "PC.607", "metadata": null},{"id": "PC.634", "metadata": null}]}
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_categories/Treatment_map.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_categories/Treatment_map.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,3 @@
+#SampleID original-sample-ids BarcodeSequence LinkerPrimerSequence DOB Description
+Control (PC.354, PC.355, PC.356, PC.481, PC.593) (AGCACGAGCCTA, AACTCGTCGATG, ACAGACCACTCA, ACCAGCGACTAG, AGCAGCACTTGT) YATGCTGCCTCCCGTAGGAGT (20061218, 20061218, 20061126, 20070314, 20071210) (Control_mouse_I.D._354, Control_mouse_I.D._355, Control_mouse_I.D._356, Control_mouse_I.D._481, Control_mouse_I.D._593)
+Fast (PC.607, PC.634, PC.635, PC.636) (AACTGTGCGTAC, ACAGAGTCGGCT, ACCGCAGAGTCA, ACGGTGAGTGTC) YATGCTGCCTCCCGTAGGAGT (20071112, 20080116, 20080116, 20080116) (Fasting_mouse_I.D._607, Fasting_mouse_I.D._634, Fasting_mouse_I.D._635, Fasting_mouse_I.D._636)
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L2.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,3 @@
+# Constructed from biom file
+#OTU ID Control Fast
+Root;k__Bacteria 1.0 1.0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L2_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L2_json.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L3.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,10 @@
+# Constructed from biom file
+#OTU ID Control Fast
+Root;k__Bacteria;Other 0.0188933873144 0.0335570469799
+Root;k__Bacteria;p__Actinobacteria 0.00134952766532 0.0134228187919
+Root;k__Bacteria;p__Bacteroidetes 0.217273954116 0.536912751678
+Root;k__Bacteria;p__Deferribacteres 0.0 0.0285234899329
+Root;k__Bacteria;p__Firmicutes 0.715249662618 0.320469798658
+Root;k__Bacteria;p__Proteobacteria 0.00674763832659 0.011744966443
+Root;k__Bacteria;p__TM7 0.0 0.00335570469799
+Root;k__Bacteria;p__Tenericutes 0.0404858299595 0.0520134228188
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L3_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L3_json.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L4.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L4.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,14 @@
+# Constructed from biom file
+#OTU ID Control Fast
+Root;k__Bacteria;Other;Other 0.0188933873144 0.0335570469799
+Root;k__Bacteria;p__Actinobacteria;c__Actinobacteria 0.00134952766532 0.0134228187919
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia 0.217273954116 0.536912751678
+Root;k__Bacteria;p__Deferribacteres;c__Deferribacteres 0.0 0.0285234899329
+Root;k__Bacteria;p__Firmicutes;Other 0.00134952766532 0.00671140939597
+Root;k__Bacteria;p__Firmicutes;c__Bacilli 0.0674763832659 0.011744966443
+Root;k__Bacteria;p__Firmicutes;c__Clostridia 0.646423751687 0.302013422819
+Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria 0.0 0.00838926174497
+Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria 0.00674763832659 0.00335570469799
+Root;k__Bacteria;p__TM7;c__TM7-3 0.0 0.00335570469799
+Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi 0.0391363022942 0.0503355704698
+Root;k__Bacteria;p__Tenericutes;c__Mollicutes 0.00134952766532 0.00167785234899
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L4_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L4_json.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L5.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L5.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,16 @@
+# Constructed from biom file
+#OTU ID Control Fast
+Root;k__Bacteria;Other;Other;Other 0.0188933873144 0.0335570469799
+Root;k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Coriobacteriales 0.00134952766532 0.0134228187919
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales 0.217273954116 0.536912751678
+Root;k__Bacteria;p__Deferribacteres;c__Deferribacteres;o__Deferribacterales 0.0 0.0285234899329
+Root;k__Bacteria;p__Firmicutes;Other;Other 0.00134952766532 0.00671140939597
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales 0.0 0.00503355704698
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales 0.055330634278 0.00167785234899
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales 0.0121457489879 0.00503355704698
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales 0.646423751687 0.302013422819
+Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales 0.0 0.00838926174497
+Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales 0.00674763832659 0.00335570469799
+Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040 0.0 0.00335570469799
+Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales 0.0391363022942 0.0503355704698
+Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39 0.00134952766532 0.00167785234899
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L5_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L5_json.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L6.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L6.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,29 @@
+# Constructed from biom file
+#OTU ID Control Fast
+Root;k__Bacteria;Other;Other;Other;Other 0.0188933873144 0.0335570469799
+Root;k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Coriobacteriales;f__Coriobacteriaceae 0.00134952766532 0.0134228187919
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;Other 0.0 0.00167785234899
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__ 0.160593792173 0.290268456376
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae 0.0364372469636 0.122483221477
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae 0.00269905533063 0.0302013422819
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae 0.0 0.00167785234899
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae 0.0175438596491 0.0906040268456
+Root;k__Bacteria;p__Deferribacteres;c__Deferribacteres;o__Deferribacterales;f__Deferribacteraceae 0.0 0.0285234899329
+Root;k__Bacteria;p__Firmicutes;Other;Other;Other 0.00134952766532 0.00671140939597
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae 0.0 0.00503355704698
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae 0.055330634278 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae 0.0 0.00167785234899
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales;f__Turicibacteraceae 0.0121457489879 0.00503355704698
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;Other 0.0080971659919 0.010067114094
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__ 0.0080971659919 0.00335570469799
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Catabacteriaceae 0.0 0.00838926174497
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae 0.0161943319838 0.00503355704698
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales Family XIII. Incertae Sedis 0.0 0.00335570469799
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae 0.574898785425 0.191275167785
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptococcaceae 0.00269905533063 0.00335570469799
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae 0.0364372469636 0.0771812080537
+Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae 0.0 0.00838926174497
+Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae 0.00674763832659 0.00335570469799
+Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;f__F16 0.0 0.00335570469799
+Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae 0.0391363022942 0.0503355704698
+Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;f__ 0.00134952766532 0.00167785234899
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L6_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_categories/Treatment_otu_table_L6_json.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_categories/area_charts.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_categories/area_charts.html Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,202 @@\n+\n+<html>\n+<head>\n+<link rel="stylesheet" href="./css/qiime_style.css" type="text/css">\n+<script type="text/javascript" src="./js/overlib.js"></script>\n+\n+<script type="text/javascript">\n+\n+</script>\n+<title>Taxa Summaries</title>\n+</head>\n+<body>\n+<div id="overDiv" style="position:absolute; visibility:hidden; z-index:1000;"></div>\n+<table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: </td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/S54w6N70dF4ht1ZrOg3MZOJ5441wnc.pdf\' target="_blank">View Figure (.pdf)</a>  <a href=\'charts/24xlHyndkg9tNJZzl7aiC05fcCAz2F_legend.pdf\' target="_blank">View Legend (.pdf)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/24xlHyndkg9tNJZzl7aiC05fcCAz2F.png\' border=1 ismap usemap="#pointsrect1" /><br></td>\n+</tr>\n+</table>\n+\n+<MAP name="pointsrect1">\n+<AREA shape="rect" coords="118.1400%,432.0000%,121.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'Control:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="862.1400%,432.0000%,865.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'Fast:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+\n+</MAP>\n+\n+<table><tr class=ntitle><td><a href="raw_data/Treatment_otu_table_L2.txt" target="_blank">View Table (.txt)</a></td></tr></table><table cellpadding=1 cellspacing=1 border=1 style="text-align:center;border-color:white;border-style:groove;"><tr class="ntitle"><td class="header" colspan="2"></td><td valign="bottom" class="header">Total</td><td valign=bottom class=header>Control</td><td valign=bottom class=header>Fast</td></tr><tr class=ntitle><td valign="bottom" class="header">Legend</td><td valign="bottom" class="header">Taxonomy</td><td class="header">%</td><td class="header">%</td><td class="header">%</td></tr><tr><td class="normal" bgcolor="#ff0000">  </td><td style="text-align:left;" class="normal">Root;<a href=javascript:gg(\'k__Bacteria\');>k__Bacteria</a></td><td class="normal">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td></tr></table><table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: </td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/LBfTHN72y1QCQlsHz0FiFq33pigq0n.pdf\' target="_blank">View Figure (.pdf)</a>  <a href=\'charts/UtWyleSZEECBbFXGPAr7wcn7skEzWF_legend.pdf\' target="_blank">View Legend (.pdf)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/UtWyleSZEECBbFXGPAr7wcn7skEzWF.png\' border=1 ismap usemap="#pointsrect2" /><br></td>\n+</tr>\n+</table>\n+\n+<MAP name="pointsrect2">\n+<AREA shape="rect" coords="118.1400%,432.0000%,121.8600%,424.7449%" href="#Root;k__Bacteria;Other" onmouseover="return overlib(\'Control:Root;k__Bacteria;Other (1.89%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="862.1400%,432.0000%,865.8600%,419.1141%" href="#Root;k__Bacteria;Other" onmouseover="return overlib(\'Fast:Root;k__Bacteria;Other (3.36%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="118.1400%,424.7449%,121.8600%,424.2267%" href="#Root;k__Bacteria;p__Actinobacteria" onmouseover="return overlib(\'Control:Root;k__Bacteria;p__Actinobacteria (0.13%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="862.1400%,419.1141%,865.8600%,413.9597%" href="#Root;k__Bacteria;p__Actinobacteria" onmouseover="return overlib(\'Fas'..b' bgcolor="#fff899">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;<a href=javascript:gg(\'f__Clostridiaceae\');>f__Clostridiaceae</a></td><td class="normal"> 1.1%</td><td class="normal" style="border-color:#fff899;"> 1.6%</td><td class="normal" style="border-color:#fff899;"> 0.5%</td></tr><tr><td class="normal" bgcolor="#c0c0c0">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;<a href=javascript:gg(\'f__Clostridiales+Family+XIII.+Incertae+Sedis\');>f__Clostridiales Family XIII. Incertae Sedis</a></td><td class="normal"> 0.2%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#c0c0c0;"> 0.3%</td></tr><tr><td class="normal" bgcolor="#ed008a">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;<a href=javascript:gg(\'f__Lachnospiraceae\');>f__Lachnospiraceae</a></td><td class="normal"> 38.3%</td><td class="normal" style="border-color:#ed008a;"> 57.5%</td><td class="normal" style="border-color:#ed008a;"> 19.1%</td></tr><tr><td class="normal" bgcolor="#00b6ff">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;<a href=javascript:gg(\'f__Peptococcaceae\');>f__Peptococcaceae</a></td><td class="normal"> 0.3%</td><td class="normal" style="border-color:#00b6ff;"> 0.3%</td><td class="normal" style="border-color:#00b6ff;"> 0.3%</td></tr><tr><td class="normal" bgcolor="#c49c6b">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;<a href=javascript:gg(\'f__Ruminococcaceae\');>f__Ruminococcaceae</a></td><td class="normal"> 5.7%</td><td class="normal" style="border-color:#c49c6b;"> 3.6%</td><td class="normal" style="border-color:#c49c6b;"> 7.7%</td></tr><tr><td class="normal" bgcolor="#808000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;<a href=javascript:gg(\'f__Desulfovibrionaceae\');>f__Desulfovibrionaceae</a></td><td class="normal"> 0.4%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#808000;"> 0.8%</td></tr><tr><td class="normal" bgcolor="#8c3fff">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;<a href=javascript:gg(\'f__Helicobacteraceae\');>f__Helicobacteraceae</a></td><td class="normal"> 0.5%</td><td class="normal" style="border-color:#8c3fff;"> 0.7%</td><td class="normal" style="border-color:#8c3fff;"> 0.3%</td></tr><tr><td class="normal" bgcolor="#bc828d">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;<a href=javascript:gg(\'f__F16\');>f__F16</a></td><td class="normal"> 0.2%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#bc828d;"> 0.3%</td></tr><tr><td class="normal" bgcolor="#008080">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;<a href=javascript:gg(\'f__Erysipelotrichaceae\');>f__Erysipelotrichaceae</a></td><td class="normal"> 4.5%</td><td class="normal" style="border-color:#008080;"> 3.9%</td><td class="normal" style="border-color:#008080;"> 5.0%</td></tr><tr><td class="normal" bgcolor="#800000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;<a href=javascript:gg(\'f__\');>f__</a></td><td class="normal"> 0.2%</td><td class="normal" style="border-color:#800000;"> 0.1%</td><td class="normal" style="border-color:#800000;"> 0.2%</td></tr></table>\n+</body>\n+</html>\n'

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_categories/bar_charts.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_categories/bar_charts.html Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,202 @@\n+\n+<html>\n+<head>\n+<link rel="stylesheet" href="./css/qiime_style.css" type="text/css">\n+<script type="text/javascript" src="./js/overlib.js"></script>\n+\n+<script type="text/javascript">\n+\n+</script>\n+<title>Taxa Summaries</title>\n+</head>\n+<body>\n+<div id="overDiv" style="position:absolute; visibility:hidden; z-index:1000;"></div>\n+<table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: </td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/FyUk6Y8OGQPD0p2cWBZqiis5p6BXZL.pdf\' target="_blank">View Figure (.pdf)</a>  <a href=\'charts/EUOZxnh2FQQus4sZrTJBoWqDfaMzn8_legend.pdf\' target="_blank">View Legend (.pdf)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/EUOZxnh2FQQus4sZrTJBoWqDfaMzn8.png\' border=1 ismap usemap="#pointsrect1" /><br></td>\n+</tr>\n+</table>\n+\n+<MAP name="pointsrect1">\n+<AREA shape="rect" coords="130.3333%,432.0000%,440.3333%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'Control:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="543.6667%,432.0000%,853.6667%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'Fast:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+\n+</MAP>\n+\n+<table><tr class=ntitle><td><a href="raw_data/Treatment_otu_table_L2.txt" target="_blank">View Table (.txt)</a></td></tr></table><table cellpadding=1 cellspacing=1 border=1 style="text-align:center;border-color:white;border-style:groove;"><tr class="ntitle"><td class="header" colspan="2"></td><td valign="bottom" class="header">Total</td><td valign=bottom class=header>Control</td><td valign=bottom class=header>Fast</td></tr><tr class=ntitle><td valign="bottom" class="header">Legend</td><td valign="bottom" class="header">Taxonomy</td><td class="header">%</td><td class="header">%</td><td class="header">%</td></tr><tr><td class="normal" bgcolor="#ff0000">  </td><td style="text-align:left;" class="normal">Root;<a href=javascript:gg(\'k__Bacteria\');>k__Bacteria</a></td><td class="normal">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td><td class="normal" style="border-color:#ff0000;">100.0%</td></tr></table><table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: </td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/mIwpGq0fHZlfrhjuyiydRq5tDe3a3X.pdf\' target="_blank">View Figure (.pdf)</a>  <a href=\'charts/xzA2ZkzTKBytSp30OZZCIKLywEpqg3_legend.pdf\' target="_blank">View Legend (.pdf)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/xzA2ZkzTKBytSp30OZZCIKLywEpqg3.png\' border=1 ismap usemap="#pointsrect2" /><br></td>\n+</tr>\n+</table>\n+\n+<MAP name="pointsrect2">\n+<AREA shape="rect" coords="130.3333%,432.0000%,440.3333%,424.7449%" href="#Root;k__Bacteria;Other" onmouseover="return overlib(\'Control:Root;k__Bacteria;Other (1.89%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="543.6667%,432.0000%,853.6667%,419.1141%" href="#Root;k__Bacteria;Other" onmouseover="return overlib(\'Fast:Root;k__Bacteria;Other (3.36%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="130.3333%,424.7449%,440.3333%,424.2267%" href="#Root;k__Bacteria;p__Actinobacteria" onmouseover="return overlib(\'Control:Root;k__Bacteria;p__Actinobacteria (0.13%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="543.6667%,419.1141%,853.6667%,413.9597%" href="#Root;k__Bacteria;p__Actinobacteria" onmouseover="return overlib(\'Fas'..b' bgcolor="#fff899">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;<a href=javascript:gg(\'f__Clostridiaceae\');>f__Clostridiaceae</a></td><td class="normal"> 1.1%</td><td class="normal" style="border-color:#fff899;"> 1.6%</td><td class="normal" style="border-color:#fff899;"> 0.5%</td></tr><tr><td class="normal" bgcolor="#c0c0c0">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;<a href=javascript:gg(\'f__Clostridiales+Family+XIII.+Incertae+Sedis\');>f__Clostridiales Family XIII. Incertae Sedis</a></td><td class="normal"> 0.2%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#c0c0c0;"> 0.3%</td></tr><tr><td class="normal" bgcolor="#ed008a">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;<a href=javascript:gg(\'f__Lachnospiraceae\');>f__Lachnospiraceae</a></td><td class="normal"> 38.3%</td><td class="normal" style="border-color:#ed008a;"> 57.5%</td><td class="normal" style="border-color:#ed008a;"> 19.1%</td></tr><tr><td class="normal" bgcolor="#00b6ff">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;<a href=javascript:gg(\'f__Peptococcaceae\');>f__Peptococcaceae</a></td><td class="normal"> 0.3%</td><td class="normal" style="border-color:#00b6ff;"> 0.3%</td><td class="normal" style="border-color:#00b6ff;"> 0.3%</td></tr><tr><td class="normal" bgcolor="#c49c6b">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;<a href=javascript:gg(\'f__Ruminococcaceae\');>f__Ruminococcaceae</a></td><td class="normal"> 5.7%</td><td class="normal" style="border-color:#c49c6b;"> 3.6%</td><td class="normal" style="border-color:#c49c6b;"> 7.7%</td></tr><tr><td class="normal" bgcolor="#808000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;<a href=javascript:gg(\'f__Desulfovibrionaceae\');>f__Desulfovibrionaceae</a></td><td class="normal"> 0.4%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#808000;"> 0.8%</td></tr><tr><td class="normal" bgcolor="#8c3fff">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;<a href=javascript:gg(\'f__Helicobacteraceae\');>f__Helicobacteraceae</a></td><td class="normal"> 0.5%</td><td class="normal" style="border-color:#8c3fff;"> 0.7%</td><td class="normal" style="border-color:#8c3fff;"> 0.3%</td></tr><tr><td class="normal" bgcolor="#bc828d">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;<a href=javascript:gg(\'f__F16\');>f__F16</a></td><td class="normal"> 0.2%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#bc828d;"> 0.3%</td></tr><tr><td class="normal" bgcolor="#008080">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;<a href=javascript:gg(\'f__Erysipelotrichaceae\');>f__Erysipelotrichaceae</a></td><td class="normal"> 4.5%</td><td class="normal" style="border-color:#008080;"> 3.9%</td><td class="normal" style="border-color:#008080;"> 5.0%</td></tr><tr><td class="normal" bgcolor="#800000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;<a href=javascript:gg(\'f__\');>f__</a></td><td class="normal"> 0.2%</td><td class="normal" style="border-color:#800000;"> 0.1%</td><td class="normal" style="border-color:#800000;"> 0.2%</td></tr></table>\n+</body>\n+</html>\n'

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_categories/log_20170501132849.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_categories/log_20170501132849.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,50 @@
+Logging started at 13:28:49 on 01 May 2017
+QIIME version: 1.9.1
+
+qiime_config values:
+pick_otus_reference_seqs_fp /Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
+sc_queue all.q
+pynast_template_alignment_fp /Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta
+cluster_jobs_fp start_parallel_jobs.py
+assign_taxonomy_reference_seqs_fp /Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
+torque_queue friendlyq
+jobs_to_start 1
+denoiser_min_per_core 50
+assign_taxonomy_id_to_taxonomy_fp /Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
+temp_dir /var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/
+blastall_fp blastall
+seconds_to_sleep 1
+
+parameter file values:
+
+Input file md5 sums:
+test-data/summarize_taxa_through_plots/otu_table.biom: dda91090fbdc0f69056852247bcd924f
+test-data/summarize_taxa_through_plots/Fasting_Map.txt: e16159d7122035797076d66b1a287962
+
+Executing commands.
+
+# Collapse samples in OTU table by categories command
+collapse_samples.py -m test-data/summarize_taxa_through_plots/Fasting_Map.txt -b test-data/summarize_taxa_through_plots/otu_table.biom --output_biom_fp summarize_taxa_through_plots_mapping_categories/Treatment_otu_table.biom --output_mapping_fp summarize_taxa_through_plots_mapping_categories/Treatment_map.txt --collapse_fields 'Treatment'
+
+Stdout:
+
+Stderr:
+
+# Summarize Taxonomy command
+summarize_taxa.py -i summarize_taxa_through_plots_mapping_categories/Treatment_otu_table.biom -o summarize_taxa_through_plots_mapping_categories
+
+Stdout:
+
+Stderr:
+
+# Plot Taxonomy Summary command
+plot_taxa_summary.py -i summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L2.txt,summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L3.txt,summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L4.txt,summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L5.txt,summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L6.txt -o summarize_taxa_through_plots_mapping_categories/taxa_summary_plots/
+
+Stdout:
+
+Stderr:
+/Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
+ if self._edgecolors == str('face'):
+
+
+Logging stopped at 13:29:07 on 01 May 2017

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_sort/area_charts.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_sort/area_charts.html Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,400 @@\n+\n+<html>\n+<head>\n+<link rel="stylesheet" href="./css/qiime_style.css" type="text/css">\n+<script type="text/javascript" src="./js/overlib.js"></script>\n+\n+<script type="text/javascript">\n+\n+</script>\n+<title>Taxa Summaries</title>\n+</head>\n+<body>\n+<div id="overDiv" style="position:absolute; visibility:hidden; z-index:1000;"></div>\n+<table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: </td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/8O0a5ben1NfyyzAXszfhN89kTG6EUO.pdf\' target="_blank">View Figure (.pdf)</a>  <a href=\'charts/ZqWSDENX2buCIEF0fU8UJzjaYsit0u_legend.pdf\' target="_blank">View Legend (.pdf)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/ZqWSDENX2buCIEF0fU8UJzjaYsit0u.png\' border=1 ismap usemap="#pointsrect1" /><br></td>\n+</tr>\n+</table>\n+\n+<MAP name="pointsrect1">\n+<AREA shape="rect" coords="118.1400%,432.0000%,121.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.354:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="211.1400%,432.0000%,214.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.355:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="304.1400%,432.0000%,307.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.356:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="397.1400%,432.0000%,400.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.481:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="490.1400%,432.0000%,493.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.593:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="583.1400%,432.0000%,586.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.607:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="676.1400%,432.0000%,679.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.634:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="769.1400%,432.0000%,772.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.635:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="862.1400%,432.0000%,865.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.636:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+\n+</MAP>\n+\n+<table><tr class=ntitle><td><a href="raw_data/otu_table_sorted_L2.txt" target="_blank">View Table (.txt)</a></td></tr></table><table cellpadding=1 cellspacing=1 border=1 style="text-align:center;border-color:white;border-style:groove;"><tr class="ntitle"><td class="header" colspan="2"></td><td valign="bottom" class="header">Total</td><td valign=bottom class=header>PC.354</td><td valign=bottom class=header>PC.355</td><td valign=bottom class=header>PC.356</td><td valign=bottom class=header>PC.481</td><td valign=bottom class=header>PC.593</td><td valign=bottom class=header>PC.607</td><td valign=bottom class=header>PC.634</td><td valign=bottom class=header>PC.635</td><td valign=bottom class=header>PC.636</td></tr><tr class=ntitle><td valign="bottom" class="header">Legend</td><td valign="bottom" class="header">Taxonomy</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="'..b'mal"> 5.4%</td><td class="normal" style="border-color:#c49c6b;"> 4.0%</td><td class="normal" style="border-color:#c49c6b;"> 0.7%</td><td class="normal" style="border-color:#c49c6b;"> 7.3%</td><td class="normal" style="border-color:#c49c6b;"> 4.1%</td><td class="normal" style="border-color:#c49c6b;"> 2.0%</td><td class="normal" style="border-color:#c49c6b;"> 9.4%</td><td class="normal" style="border-color:#c49c6b;"> 5.3%</td><td class="normal" style="border-color:#c49c6b;"> 9.4%</td><td class="normal" style="border-color:#c49c6b;"> 6.8%</td></tr><tr><td class="normal" bgcolor="#808000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;<a href=javascript:gg(\'f__Desulfovibrionaceae\');>f__Desulfovibrionaceae</a></td><td class="normal"> 0.4%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal" style="border-color:#808000;"> 1.3%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal" style="border-color:#808000;"> 0.7%</td></tr><tr><td class="normal" bgcolor="#8c3fff">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;<a href=javascript:gg(\'f__Helicobacteraceae\');>f__Helicobacteraceae</a></td><td class="normal"> 0.5%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#8c3fff;"> 3.4%</td><td class="normal" style="border-color:#8c3fff;"> 1.3%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td></tr><tr><td class="normal" bgcolor="#bc828d">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;<a href=javascript:gg(\'f__F16\');>f__F16</a></td><td class="normal"> 0.1%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#bc828d;"> 1.3%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td></tr><tr><td class="normal" bgcolor="#008080">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;<a href=javascript:gg(\'f__Erysipelotrichaceae\');>f__Erysipelotrichaceae</a></td><td class="normal"> 4.4%</td><td class="normal" style="border-color:#008080;"> 1.3%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#008080;"> 3.4%</td><td class="normal" style="border-color:#008080;"> 14.8%</td><td class="normal" style="border-color:#008080;"> 15.4%</td><td class="normal" style="border-color:#008080;"> 2.7%</td><td class="normal" style="border-color:#008080;"> 0.7%</td><td class="normal" style="border-color:#008080;"> 1.4%</td></tr><tr><td class="normal" bgcolor="#800000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;<a href=javascript:gg(\'f__\');>f__</a></td><td class="normal"> 0.1%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#800000;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#800000;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td></tr></table>\n+</body>\n+</html>\n'

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_sort/bar_charts.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_sort/bar_charts.html Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,400 @@\n+\n+<html>\n+<head>\n+<link rel="stylesheet" href="./css/qiime_style.css" type="text/css">\n+<script type="text/javascript" src="./js/overlib.js"></script>\n+\n+<script type="text/javascript">\n+\n+</script>\n+<title>Taxa Summaries</title>\n+</head>\n+<body>\n+<div id="overDiv" style="position:absolute; visibility:hidden; z-index:1000;"></div>\n+<table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: </td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/ZRYX0w0bghEmxuS0oI1z9HPCzLSKXn.pdf\' target="_blank">View Figure (.pdf)</a>  <a href=\'charts/znQC4AIr5bY4hlOkLYZn6BAkQEGPjM_legend.pdf\' target="_blank">View Legend (.pdf)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/znQC4AIr5bY4hlOkLYZn6BAkQEGPjM.png\' border=1 ismap usemap="#pointsrect1" /><br></td>\n+</tr>\n+</table>\n+\n+<MAP name="pointsrect1">\n+<AREA shape="rect" coords="166.5000%,432.0000%,222.3000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.354:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="240.9000%,432.0000%,296.7000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.355:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="315.3000%,432.0000%,371.1000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.356:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="389.7000%,432.0000%,445.5000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.481:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="464.1000%,432.0000%,519.9000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.593:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="538.5000%,432.0000%,594.3000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.607:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="612.9000%,432.0000%,668.7000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.634:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="687.3000%,432.0000%,743.1000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.635:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="761.7000%,432.0000%,817.5000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.636:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+\n+</MAP>\n+\n+<table><tr class=ntitle><td><a href="raw_data/otu_table_sorted_L2.txt" target="_blank">View Table (.txt)</a></td></tr></table><table cellpadding=1 cellspacing=1 border=1 style="text-align:center;border-color:white;border-style:groove;"><tr class="ntitle"><td class="header" colspan="2"></td><td valign="bottom" class="header">Total</td><td valign=bottom class=header>PC.354</td><td valign=bottom class=header>PC.355</td><td valign=bottom class=header>PC.356</td><td valign=bottom class=header>PC.481</td><td valign=bottom class=header>PC.593</td><td valign=bottom class=header>PC.607</td><td valign=bottom class=header>PC.634</td><td valign=bottom class=header>PC.635</td><td valign=bottom class=header>PC.636</td></tr><tr class=ntitle><td valign="bottom" class="header">Legend</td><td valign="bottom" class="header">Taxonomy</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="'..b'mal"> 5.4%</td><td class="normal" style="border-color:#c49c6b;"> 4.0%</td><td class="normal" style="border-color:#c49c6b;"> 0.7%</td><td class="normal" style="border-color:#c49c6b;"> 7.3%</td><td class="normal" style="border-color:#c49c6b;"> 4.1%</td><td class="normal" style="border-color:#c49c6b;"> 2.0%</td><td class="normal" style="border-color:#c49c6b;"> 9.4%</td><td class="normal" style="border-color:#c49c6b;"> 5.3%</td><td class="normal" style="border-color:#c49c6b;"> 9.4%</td><td class="normal" style="border-color:#c49c6b;"> 6.8%</td></tr><tr><td class="normal" bgcolor="#808000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;<a href=javascript:gg(\'f__Desulfovibrionaceae\');>f__Desulfovibrionaceae</a></td><td class="normal"> 0.4%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal" style="border-color:#808000;"> 1.3%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal" style="border-color:#808000;"> 0.7%</td></tr><tr><td class="normal" bgcolor="#8c3fff">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;<a href=javascript:gg(\'f__Helicobacteraceae\');>f__Helicobacteraceae</a></td><td class="normal"> 0.5%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#8c3fff;"> 3.4%</td><td class="normal" style="border-color:#8c3fff;"> 1.3%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td></tr><tr><td class="normal" bgcolor="#bc828d">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;<a href=javascript:gg(\'f__F16\');>f__F16</a></td><td class="normal"> 0.1%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#bc828d;"> 1.3%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td></tr><tr><td class="normal" bgcolor="#008080">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;<a href=javascript:gg(\'f__Erysipelotrichaceae\');>f__Erysipelotrichaceae</a></td><td class="normal"> 4.4%</td><td class="normal" style="border-color:#008080;"> 1.3%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#008080;"> 3.4%</td><td class="normal" style="border-color:#008080;"> 14.8%</td><td class="normal" style="border-color:#008080;"> 15.4%</td><td class="normal" style="border-color:#008080;"> 2.7%</td><td class="normal" style="border-color:#008080;"> 0.7%</td><td class="normal" style="border-color:#008080;"> 1.4%</td></tr><tr><td class="normal" bgcolor="#800000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;<a href=javascript:gg(\'f__\');>f__</a></td><td class="normal"> 0.1%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#800000;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#800000;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td></tr></table>\n+</body>\n+</html>\n'

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_sort/log_20170501134214.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_sort/log_20170501134214.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,50 @@
+Logging started at 13:42:14 on 01 May 2017
+QIIME version: 1.9.1
+
+qiime_config values:
+pick_otus_reference_seqs_fp /Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
+sc_queue all.q
+pynast_template_alignment_fp /Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta
+cluster_jobs_fp start_parallel_jobs.py
+assign_taxonomy_reference_seqs_fp /Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
+torque_queue friendlyq
+jobs_to_start 1
+denoiser_min_per_core 50
+assign_taxonomy_id_to_taxonomy_fp /Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
+temp_dir /var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/
+blastall_fp blastall
+seconds_to_sleep 1
+
+parameter file values:
+
+Input file md5 sums:
+test-data/summarize_taxa_through_plots/otu_table.biom: dda91090fbdc0f69056852247bcd924f
+test-data/summarize_taxa_through_plots/Fasting_Map.txt: e16159d7122035797076d66b1a287962
+
+Executing commands.
+
+# Sort OTU Table command
+sort_otu_table.py -i test-data/summarize_taxa_through_plots/otu_table.biom -o summarize_taxa_through_plots_mapping_sort/otu_table_sorted.biom
+
+Stdout:
+
+Stderr:
+
+# Summarize Taxonomy command
+summarize_taxa.py -i summarize_taxa_through_plots_mapping_sort/otu_table_sorted.biom -o summarize_taxa_through_plots_mapping_sort
+
+Stdout:
+
+Stderr:
+
+# Plot Taxonomy Summary command
+plot_taxa_summary.py -i summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L2.txt,summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L3.txt,summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L4.txt,summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L5.txt,summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L6.txt -o summarize_taxa_through_plots_mapping_sort/taxa_summary_plots/
+
+Stdout:
+
+Stderr:
+/Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
+ if self._edgecolors == str('face'):
+
+
+Logging stopped at 13:42:34 on 01 May 2017

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L2.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,3 @@
+# Constructed from biom file
+#OTU ID PC.354 PC.355 PC.356 PC.481 PC.593 PC.607 PC.634 PC.635 PC.636
+Root;k__Bacteria 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L2_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L2_json.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L3.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,10 @@
+# Constructed from biom file
+#OTU ID PC.354 PC.355 PC.356 PC.481 PC.593 PC.607 PC.634 PC.635 PC.636
+Root;k__Bacteria;Other 0.0134228187919 0.0136054421769 0.0266666666667 0.027397260274 0.0134228187919 0.0469798657718 0.02 0.0469798657718 0.0202702702703
+Root;k__Bacteria;p__Actinobacteria 0.0 0.0 0.0 0.00684931506849 0.0 0.0201342281879 0.02 0.00671140939597 0.00675675675676
+Root;k__Bacteria;p__Bacteroidetes 0.0738255033557 0.285714285714 0.193333333333 0.143835616438 0.389261744966 0.275167785235 0.653333333333 0.523489932886 0.695945945946
+Root;k__Bacteria;p__Deferribacteres 0.0 0.0 0.0 0.0 0.0 0.0201342281879 0.0333333333333 0.0134228187919 0.0472972972973
+Root;k__Bacteria;p__Firmicutes 0.89932885906 0.700680272109 0.773333333333 0.787671232877 0.41610738255 0.456375838926 0.22 0.395973154362 0.209459459459
+Root;k__Bacteria;p__Proteobacteria 0.0 0.0 0.0 0.0 0.0335570469799 0.0201342281879 0.0133333333333 0.00671140939597 0.00675675675676
+Root;k__Bacteria;p__TM7 0.0 0.0 0.0 0.0 0.0 0.0 0.0133333333333 0.0 0.0
+Root;k__Bacteria;p__Tenericutes 0.0134228187919 0.0 0.00666666666667 0.0342465753425 0.147651006711 0.161073825503 0.0266666666667 0.00671140939597 0.0135135135135
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L3_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L3_json.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L4.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L4.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,14 @@
+# Constructed from biom file
+#OTU ID PC.354 PC.355 PC.356 PC.481 PC.593 PC.607 PC.634 PC.635 PC.636
+Root;k__Bacteria;Other;Other 0.0134228187919 0.0136054421769 0.0266666666667 0.027397260274 0.0134228187919 0.0469798657718 0.02 0.0469798657718 0.0202702702703
+Root;k__Bacteria;p__Actinobacteria;c__Actinobacteria 0.0 0.0 0.0 0.00684931506849 0.0 0.0201342281879 0.02 0.00671140939597 0.00675675675676
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia 0.0738255033557 0.285714285714 0.193333333333 0.143835616438 0.389261744966 0.275167785235 0.653333333333 0.523489932886 0.695945945946
+Root;k__Bacteria;p__Deferribacteres;c__Deferribacteres 0.0 0.0 0.0 0.0 0.0 0.0201342281879 0.0333333333333 0.0134228187919 0.0472972972973
+Root;k__Bacteria;p__Firmicutes;Other 0.00671140939597 0.0 0.0 0.0 0.0 0.0268456375839 0.0 0.0 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli 0.107382550336 0.0136054421769 0.0933333333333 0.0890410958904 0.0335570469799 0.00671140939597 0.02 0.0 0.0202702702703
+Root;k__Bacteria;p__Firmicutes;c__Clostridia 0.785234899329 0.687074829932 0.68 0.698630136986 0.38255033557 0.422818791946 0.2 0.395973154362 0.189189189189
+Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria 0.0 0.0 0.0 0.0 0.0 0.00671140939597 0.0133333333333 0.00671140939597 0.00675675675676
+Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria 0.0 0.0 0.0 0.0 0.0335570469799 0.0134228187919 0.0 0.0 0.0
+Root;k__Bacteria;p__TM7;c__TM7-3 0.0 0.0 0.0 0.0 0.0 0.0 0.0133333333333 0.0 0.0
+Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi 0.0134228187919 0.0 0.0 0.0342465753425 0.147651006711 0.154362416107 0.0266666666667 0.00671140939597 0.0135135135135
+Root;k__Bacteria;p__Tenericutes;c__Mollicutes 0.0 0.0 0.00666666666667 0.0 0.0 0.00671140939597 0.0 0.0 0.0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L4_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L4_json.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L5.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L5.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,16 @@
+# Constructed from biom file
+#OTU ID PC.354 PC.355 PC.356 PC.481 PC.593 PC.607 PC.634 PC.635 PC.636
+Root;k__Bacteria;Other;Other;Other 0.0134228187919 0.0136054421769 0.0266666666667 0.027397260274 0.0134228187919 0.0469798657718 0.02 0.0469798657718 0.0202702702703
+Root;k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Coriobacteriales 0.0 0.0 0.0 0.00684931506849 0.0 0.0201342281879 0.02 0.00671140939597 0.00675675675676
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales 0.0738255033557 0.285714285714 0.193333333333 0.143835616438 0.389261744966 0.275167785235 0.653333333333 0.523489932886 0.695945945946
+Root;k__Bacteria;p__Deferribacteres;c__Deferribacteres;o__Deferribacterales 0.0 0.0 0.0 0.0 0.0 0.0201342281879 0.0333333333333 0.0134228187919 0.0472972972973
+Root;k__Bacteria;p__Firmicutes;Other;Other 0.00671140939597 0.0 0.0 0.0 0.0 0.0268456375839 0.0 0.0 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0202702702703
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales 0.107382550336 0.0136054421769 0.0933333333333 0.027397260274 0.0335570469799 0.00671140939597 0.0 0.0 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales 0.0 0.0 0.0 0.0616438356164 0.0 0.0 0.02 0.0 0.0
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales 0.785234899329 0.687074829932 0.68 0.698630136986 0.38255033557 0.422818791946 0.2 0.395973154362 0.189189189189
+Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales 0.0 0.0 0.0 0.0 0.0 0.00671140939597 0.0133333333333 0.00671140939597 0.00675675675676
+Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales 0.0 0.0 0.0 0.0 0.0335570469799 0.0134228187919 0.0 0.0 0.0
+Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040 0.0 0.0 0.0 0.0 0.0 0.0 0.0133333333333 0.0 0.0
+Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales 0.0134228187919 0.0 0.0 0.0342465753425 0.147651006711 0.154362416107 0.0266666666667 0.00671140939597 0.0135135135135
+Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39 0.0 0.0 0.00666666666667 0.0 0.0 0.00671140939597 0.0 0.0 0.0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L5_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L5_json.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L6.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L6.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,29 @@
+# Constructed from biom file
+#OTU ID PC.354 PC.355 PC.356 PC.481 PC.593 PC.607 PC.634 PC.635 PC.636
+Root;k__Bacteria;Other;Other;Other;Other 0.0134228187919 0.0136054421769 0.0266666666667 0.027397260274 0.0134228187919 0.0469798657718 0.02 0.0469798657718 0.0202702702703
+Root;k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Coriobacteriales;f__Coriobacteriaceae 0.0 0.0 0.0 0.00684931506849 0.0 0.0201342281879 0.02 0.00671140939597 0.00675675675676
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;Other 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.00675675675676
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__ 0.0536912751678 0.136054421769 0.173333333333 0.0753424657534 0.362416107383 0.201342281879 0.186666666667 0.308724832215 0.466216216216
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae 0.0134228187919 0.12925170068 0.0 0.013698630137 0.0268456375839 0.0 0.273333333333 0.0469798657718 0.168918918919
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae 0.0 0.00680272108844 0.0 0.00684931506849 0.0 0.0 0.08 0.0268456375839 0.0135135135135
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.00671140939597 0.0
+Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae 0.00671140939597 0.0136054421769 0.02 0.0479452054795 0.0 0.0738255033557 0.113333333333 0.134228187919 0.0405405405405
+Root;k__Bacteria;p__Deferribacteres;c__Deferribacteres;o__Deferribacterales;f__Deferribacteraceae 0.0 0.0 0.0 0.0 0.0 0.0201342281879 0.0333333333333 0.0134228187919 0.0472972972973
+Root;k__Bacteria;p__Firmicutes;Other;Other;Other 0.00671140939597 0.0 0.0 0.0 0.0 0.0268456375839 0.0 0.0 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0202702702703
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae 0.107382550336 0.0136054421769 0.0933333333333 0.027397260274 0.0335570469799 0.0 0.0 0.0 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae 0.0 0.0 0.0 0.0 0.0 0.00671140939597 0.0 0.0 0.0
+Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales;f__Turicibacteraceae 0.0 0.0 0.0 0.0616438356164 0.0 0.0 0.02 0.0 0.0
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;Other 0.00671140939597 0.0 0.02 0.00684931506849 0.00671140939597 0.0134228187919 0.00666666666667 0.0201342281879 0.0
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__ 0.00671140939597 0.0204081632653 0.00666666666667 0.0 0.00671140939597 0.00671140939597 0.0 0.00671140939597 0.0
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Catabacteriaceae 0.0 0.0 0.0 0.0 0.0 0.0268456375839 0.0 0.0 0.00675675675676
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae 0.00671140939597 0.00680272108844 0.0 0.0 0.0671140939597 0.0 0.02 0.0 0.0
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales Family XIII. Incertae Sedis 0.0 0.0 0.0 0.0 0.0 0.00671140939597 0.00666666666667 0.0 0.0
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae 0.718120805369 0.65306122449 0.58 0.650684931507 0.275167785235 0.268456375839 0.113333333333 0.268456375839 0.114864864865
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptococcaceae 0.00671140939597 0.0 0.0 0.0 0.00671140939597 0.00671140939597 0.0 0.00671140939597 0.0
+Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae 0.0402684563758 0.00680272108844 0.0733333333333 0.041095890411 0.0201342281879 0.0939597315436 0.0533333333333 0.0939597315436 0.0675675675676
+Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae 0.0 0.0 0.0 0.0 0.0 0.00671140939597 0.0133333333333 0.00671140939597 0.00675675675676
+Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae 0.0 0.0 0.0 0.0 0.0335570469799 0.0134228187919 0.0 0.0 0.0
+Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;f__F16 0.0 0.0 0.0 0.0 0.0 0.0 0.0133333333333 0.0 0.0
+Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae 0.0134228187919 0.0 0.0 0.0342465753425 0.147651006711 0.154362416107 0.0266666666667 0.00671140939597 0.0135135135135
+Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;f__ 0.0 0.0 0.00666666666667 0.0 0.0 0.00671140939597 0.0 0.0 0.0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L6_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/mapping_sort/otu_table_sorted_L6_json.biom Thu May 18 09:38:55 2017 -0400

[

@@ -0,0 +1,1 @@
+{"id": "No Table ID","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-05-01T13:44:27.158771","type": "OTU table","matrix_element_type": "float","shape": [27, 9],"data": [[0,0,0.013422818791946308],[0,1,0.013605442176870748],[0,2,0.026666666666666668],[0,3,0.027397260273972601],[0,4,0.013422818791946308],[0,5,0.046979865771812075],[0,6,0.02],[0,7,0.046979865771812075],[0,8,0.020270270270270271],[1,3,0.0068493150684931503],[1,5,0.020134228187919462],[1,6,0.02],[1,7,0.0067114093959731542],[1,8,0.0067567567567567571],[2,8,0.0067567567567567571],[3,0,0.053691275167785227],[3,1,0.13605442176870747],[3,2,0.17333333333333331],[3,3,0.075342465753424653],[3,4,0.36241610738255031],[3,5,0.20134228187919456],[3,6,0.18666666666666668],[3,7,0.30872483221476499],[3,8,0.46621621621621612],[4,0,0.013422818791946308],[4,1,0.12925170068027211],[4,3,0.013698630136986301],[4,4,0.026845637583892617],[4,6,0.27333333333333332],[4,7,0.046979865771812082],[4,8,0.16891891891891891],[5,1,0.0068027210884353739],[5,3,0.0068493150684931503],[5,6,0.080000000000000002],[5,7,0.026845637583892617],[5,8,0.013513513513513514],[6,7,0.0067114093959731542],[7,0,0.0067114093959731542],[7,1,0.013605442176870748],[7,2,0.02],[7,3,0.047945205479452052],[7,5,0.073825503355704702],[7,6,0.11333333333333334],[7,7,0.13422818791946309],[7,8,0.040540540540540543],[8,5,0.020134228187919462],[8,6,0.033333333333333333],[8,7,0.013422818791946308],[8,8,0.0472972972972973],[9,0,0.0067114093959731542],[9,5,0.026845637583892617],[10,8,0.020270270270270271],[11,0,0.10738255033557048],[11,1,0.013605442176870748],[11,2,0.093333333333333338],[11,3,0.027397260273972601],[11,4,0.033557046979865772],[12,5,0.0067114093959731542],[13,3,0.061643835616438353],[13,6,0.02],[14,0,0.0067114093959731542],[14,2,0.02],[14,3,0.0068493150684931503],[14,4,0.0067114093959731542],[14,5,0.013422818791946308],[14,6,0.0066666666666666671],[14,7,0.020134228187919462],[15,0,0.0067114093959731542],[15,1,0.020408163265306121],[15,2,0.0066666666666666671],[15,4,0.0067114093959731542],[15,5,0.0067114093959731542],[15,7,0.0067114093959731542],[16,5,0.026845637583892617],[16,8,0.0067567567567567571],[17,0,0.0067114093959731542],[17,1,0.0068027210884353739],[17,4,0.067114093959731544],[17,6,0.02],[18,5,0.0067114093959731542],[18,6,0.0066666666666666671],[19,0,0.71812080536912726],[19,1,0.65306122448979598],[19,2,0.57999999999999996],[19,3,0.65068493150684981],[19,4,0.27516778523489921],[19,5,0.26845637583892612],[19,6,0.11333333333333334],[19,7,0.26845637583892606],[19,8,0.11486486486486487],[20,0,0.0067114093959731542],[20,4,0.0067114093959731542],[20,5,0.0067114093959731542],[20,7,0.0067114093959731542],[21,0,0.040268456375838924],[21,1,0.0068027210884353739],[21,2,0.073333333333333334],[21,3,0.041095890410958902],[21,4,0.020134228187919462],[21,5,0.093959731543624178],[21,6,0.053333333333333337],[21,7,0.093959731543624178],[21,8,0.067567567567567571],[22,5,0.0067114093959731542],[22,6,0.013333333333333334],[22,7,0.0067114093959731542],[22,8,0.0067567567567567571],[23,4,0.033557046979865772],[23,5,0.013422818791946308],[24,6,0.013333333333333334],[25,0,0.013422818791946308],[25,3,0.034246575342465752],[25,4,0.1476510067114094],[25,5,0.15436241610738255],[25,6,0.026666666666666668],[25,7,0.0067114093959731542],[25,8,0.013513513513513514],[26,2,0.0066666666666666671],[26,5,0.0067114093959731542]],"rows": [{"id": "Root;k__Bacteria;Other;Other;Other;Other", "metadata": null},{"id": "Root;k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Coriobacteriales;f__Coriobacteriaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;Other", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Deferribacteres;c__Deferribacteres;o__Deferribacterales;f__Deferribacteraceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;Other;Other;Other", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales;f__Turicibacteraceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;Other", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Catabacteriaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales Family XIII. Incertae Sedis", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptococcaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae", "metadata": null},{"id": "Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;f__F16", "metadata": null},{"id": "Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;f__", "metadata": null}],"columns": [{"id": "PC.354", "metadata": null},{"id": "PC.355", "metadata": null},{"id": "PC.356", "metadata": null},{"id": "PC.481", "metadata": null},{"id": "PC.593", "metadata": null},{"id": "PC.607", "metadata": null},{"id": "PC.634", "metadata": null},{"id": "PC.635", "metadata": null},{"id": "PC.636", "metadata": null}]}
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/otu_table.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/without_mapping/area_charts.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/without_mapping/area_charts.html Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,400 @@\n+\n+<html>\n+<head>\n+<link rel="stylesheet" href="./css/qiime_style.css" type="text/css">\n+<script type="text/javascript" src="./js/overlib.js"></script>\n+\n+<script type="text/javascript">\n+\n+</script>\n+<title>Taxa Summaries</title>\n+</head>\n+<body>\n+<div id="overDiv" style="position:absolute; visibility:hidden; z-index:1000;"></div>\n+<table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: </td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/g3HlKnyEByotQgq9I03pIcolCoNmGc.pdf\' target="_blank">View Figure (.pdf)</a>  <a href=\'charts/PjlIwOCDP3xYuZFb2U7i5jHPzk2IWd_legend.pdf\' target="_blank">View Legend (.pdf)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/PjlIwOCDP3xYuZFb2U7i5jHPzk2IWd.png\' border=1 ismap usemap="#pointsrect1" /><br></td>\n+</tr>\n+</table>\n+\n+<MAP name="pointsrect1">\n+<AREA shape="rect" coords="118.1400%,432.0000%,121.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.636:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="211.1400%,432.0000%,214.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.635:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="304.1400%,432.0000%,307.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.356:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="397.1400%,432.0000%,400.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.481:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="490.1400%,432.0000%,493.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.354:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="583.1400%,432.0000%,586.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.593:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="676.1400%,432.0000%,679.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.355:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="769.1400%,432.0000%,772.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.607:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="862.1400%,432.0000%,865.8600%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.634:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+\n+</MAP>\n+\n+<table><tr class=ntitle><td><a href="raw_data/otu_table_L2.txt" target="_blank">View Table (.txt)</a></td></tr></table><table cellpadding=1 cellspacing=1 border=1 style="text-align:center;border-color:white;border-style:groove;"><tr class="ntitle"><td class="header" colspan="2"></td><td valign="bottom" class="header">Total</td><td valign=bottom class=header>PC.636</td><td valign=bottom class=header>PC.635</td><td valign=bottom class=header>PC.356</td><td valign=bottom class=header>PC.481</td><td valign=bottom class=header>PC.354</td><td valign=bottom class=header>PC.593</td><td valign=bottom class=header>PC.355</td><td valign=bottom class=header>PC.607</td><td valign=bottom class=header>PC.634</td></tr><tr class=ntitle><td valign="bottom" class="header">Legend</td><td valign="bottom" class="header">Taxonomy</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header"'..b'mal"> 5.4%</td><td class="normal" style="border-color:#c49c6b;"> 6.8%</td><td class="normal" style="border-color:#c49c6b;"> 9.4%</td><td class="normal" style="border-color:#c49c6b;"> 7.3%</td><td class="normal" style="border-color:#c49c6b;"> 4.1%</td><td class="normal" style="border-color:#c49c6b;"> 4.0%</td><td class="normal" style="border-color:#c49c6b;"> 2.0%</td><td class="normal" style="border-color:#c49c6b;"> 0.7%</td><td class="normal" style="border-color:#c49c6b;"> 9.4%</td><td class="normal" style="border-color:#c49c6b;"> 5.3%</td></tr><tr><td class="normal" bgcolor="#808000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;<a href=javascript:gg(\'f__Desulfovibrionaceae\');>f__Desulfovibrionaceae</a></td><td class="normal"> 0.4%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal" style="border-color:#808000;"> 1.3%</td></tr><tr><td class="normal" bgcolor="#8c3fff">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;<a href=javascript:gg(\'f__Helicobacteraceae\');>f__Helicobacteraceae</a></td><td class="normal"> 0.5%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#8c3fff;"> 3.4%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#8c3fff;"> 1.3%</td><td class="normal"> 0.0%</td></tr><tr><td class="normal" bgcolor="#bc828d">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;<a href=javascript:gg(\'f__F16\');>f__F16</a></td><td class="normal"> 0.1%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#bc828d;"> 1.3%</td></tr><tr><td class="normal" bgcolor="#008080">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;<a href=javascript:gg(\'f__Erysipelotrichaceae\');>f__Erysipelotrichaceae</a></td><td class="normal"> 4.4%</td><td class="normal" style="border-color:#008080;"> 1.4%</td><td class="normal" style="border-color:#008080;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#008080;"> 3.4%</td><td class="normal" style="border-color:#008080;"> 1.3%</td><td class="normal" style="border-color:#008080;"> 14.8%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#008080;"> 15.4%</td><td class="normal" style="border-color:#008080;"> 2.7%</td></tr><tr><td class="normal" bgcolor="#800000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;<a href=javascript:gg(\'f__\');>f__</a></td><td class="normal"> 0.1%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#800000;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#800000;"> 0.7%</td><td class="normal"> 0.0%</td></tr></table>\n+</body>\n+</html>\n'

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/without_mapping/bar_charts.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/without_mapping/bar_charts.html Thu May 18 09:38:55 2017 -0400

b'@@ -0,0 +1,400 @@\n+\n+<html>\n+<head>\n+<link rel="stylesheet" href="./css/qiime_style.css" type="text/css">\n+<script type="text/javascript" src="./js/overlib.js"></script>\n+\n+<script type="text/javascript">\n+\n+</script>\n+<title>Taxa Summaries</title>\n+</head>\n+<body>\n+<div id="overDiv" style="position:absolute; visibility:hidden; z-index:1000;"></div>\n+<table cellpadding=2 cellspacing=2 border=0>\n+<tr><td class="normal" colspan=2> </td></tr>\n+<tr><td class="header" colspan=2>Taxonomy Summary. Current Level: </td></tr>\n+<tr><td class="ntitle">  <a href=\'charts/4kgnTcfo0boZgR2GGSiHNT0X49kJQQ.pdf\' target="_blank">View Figure (.pdf)</a>  <a href=\'charts/XqNpgcidrHgEM0y7w2feSJLjYK2zJ0_legend.pdf\' target="_blank">View Legend (.pdf)</a><br></td>\n+<td class="ntitle"> </td>\n+</tr>\n+<tr><td class="ntitle"><img src=\'charts/XqNpgcidrHgEM0y7w2feSJLjYK2zJ0.png\' border=1 ismap usemap="#pointsrect1" /><br></td>\n+</tr>\n+</table>\n+\n+<MAP name="pointsrect1">\n+<AREA shape="rect" coords="166.5000%,432.0000%,222.3000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.636:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="240.9000%,432.0000%,296.7000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.635:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="315.3000%,432.0000%,371.1000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.356:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="389.7000%,432.0000%,445.5000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.481:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="464.1000%,432.0000%,519.9000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.354:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="538.5000%,432.0000%,594.3000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.593:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="612.9000%,432.0000%,668.7000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.355:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="687.3000%,432.0000%,743.1000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.607:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+<AREA shape="rect" coords="761.7000%,432.0000%,817.5000%,48.0000%" href="#Root;k__Bacteria" onmouseover="return overlib(\'PC.634:Root;k__Bacteria (100.00%)\');" onmouseout="return nd();">\n+\n+</MAP>\n+\n+<table><tr class=ntitle><td><a href="raw_data/otu_table_L2.txt" target="_blank">View Table (.txt)</a></td></tr></table><table cellpadding=1 cellspacing=1 border=1 style="text-align:center;border-color:white;border-style:groove;"><tr class="ntitle"><td class="header" colspan="2"></td><td valign="bottom" class="header">Total</td><td valign=bottom class=header>PC.636</td><td valign=bottom class=header>PC.635</td><td valign=bottom class=header>PC.356</td><td valign=bottom class=header>PC.481</td><td valign=bottom class=header>PC.354</td><td valign=bottom class=header>PC.593</td><td valign=bottom class=header>PC.355</td><td valign=bottom class=header>PC.607</td><td valign=bottom class=header>PC.634</td></tr><tr class=ntitle><td valign="bottom" class="header">Legend</td><td valign="bottom" class="header">Taxonomy</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header">%</td><td class="header"'..b'mal"> 5.4%</td><td class="normal" style="border-color:#c49c6b;"> 6.8%</td><td class="normal" style="border-color:#c49c6b;"> 9.4%</td><td class="normal" style="border-color:#c49c6b;"> 7.3%</td><td class="normal" style="border-color:#c49c6b;"> 4.1%</td><td class="normal" style="border-color:#c49c6b;"> 4.0%</td><td class="normal" style="border-color:#c49c6b;"> 2.0%</td><td class="normal" style="border-color:#c49c6b;"> 0.7%</td><td class="normal" style="border-color:#c49c6b;"> 9.4%</td><td class="normal" style="border-color:#c49c6b;"> 5.3%</td></tr><tr><td class="normal" bgcolor="#808000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;<a href=javascript:gg(\'f__Desulfovibrionaceae\');>f__Desulfovibrionaceae</a></td><td class="normal"> 0.4%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#808000;"> 0.7%</td><td class="normal" style="border-color:#808000;"> 1.3%</td></tr><tr><td class="normal" bgcolor="#8c3fff">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;<a href=javascript:gg(\'f__Helicobacteraceae\');>f__Helicobacteraceae</a></td><td class="normal"> 0.5%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#8c3fff;"> 3.4%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#8c3fff;"> 1.3%</td><td class="normal"> 0.0%</td></tr><tr><td class="normal" bgcolor="#bc828d">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;<a href=javascript:gg(\'f__F16\');>f__F16</a></td><td class="normal"> 0.1%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#bc828d;"> 1.3%</td></tr><tr><td class="normal" bgcolor="#008080">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;<a href=javascript:gg(\'f__Erysipelotrichaceae\');>f__Erysipelotrichaceae</a></td><td class="normal"> 4.4%</td><td class="normal" style="border-color:#008080;"> 1.4%</td><td class="normal" style="border-color:#008080;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#008080;"> 3.4%</td><td class="normal" style="border-color:#008080;"> 1.3%</td><td class="normal" style="border-color:#008080;"> 14.8%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#008080;"> 15.4%</td><td class="normal" style="border-color:#008080;"> 2.7%</td></tr><tr><td class="normal" bgcolor="#800000">  </td><td style="text-align:left;" class="normal">Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;<a href=javascript:gg(\'f__\');>f__</a></td><td class="normal"> 0.1%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#800000;"> 0.7%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal"> 0.0%</td><td class="normal" style="border-color:#800000;"> 0.7%</td><td class="normal"> 0.0%</td></tr></table>\n+</body>\n+</html>\n'

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/without_mapping/log_20170501134810.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/without_mapping/log_20170501134810.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,42 @@
+Logging started at 13:48:10 on 01 May 2017
+QIIME version: 1.9.1
+
+qiime_config values:
+pick_otus_reference_seqs_fp /Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
+sc_queue all.q
+pynast_template_alignment_fp /Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta
+cluster_jobs_fp start_parallel_jobs.py
+assign_taxonomy_reference_seqs_fp /Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
+torque_queue friendlyq
+jobs_to_start 1
+denoiser_min_per_core 50
+assign_taxonomy_id_to_taxonomy_fp /Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
+temp_dir /var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/
+blastall_fp blastall
+seconds_to_sleep 1
+
+parameter file values:
+
+Input file md5 sums:
+test-data/summarize_taxa_through_plots/otu_table.biom: dda91090fbdc0f69056852247bcd924f
+
+Executing commands.
+
+# Summarize Taxonomy command
+summarize_taxa.py -i test-data/summarize_taxa_through_plots/otu_table.biom -o summarize_taxa_through_plots_without_mapping
+
+Stdout:
+
+Stderr:
+
+# Plot Taxonomy Summary command
+plot_taxa_summary.py -i summarize_taxa_through_plots_without_mapping/otu_table_L2.txt,summarize_taxa_through_plots_without_mapping/otu_table_L3.txt,summarize_taxa_through_plots_without_mapping/otu_table_L4.txt,summarize_taxa_through_plots_without_mapping/otu_table_L5.txt,summarize_taxa_through_plots_without_mapping/otu_table_L6.txt -o summarize_taxa_through_plots_without_mapping/taxa_summary_plots/
+
+Stdout:
+
+Stderr:
+/Users/bebatut/miniconda3/envs/qiime/lib/python2.7/site-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
+ if self._edgecolors == str('face'):
+
+
+Logging stopped at 13:48:24 on 01 May 2017

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/without_mapping/otu_table_L2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/without_mapping/otu_table_L2.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,3 @@
+# Constructed from biom file
+#OTU ID PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+Root;k__Bacteria 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/without_mapping/otu_table_L2_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/without_mapping/otu_table_L2_json.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/without_mapping/otu_table_L3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/without_mapping/otu_table_L3.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/without_mapping/otu_table_L3_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/without_mapping/otu_table_L3_json.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/without_mapping/otu_table_L4.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/without_mapping/otu_table_L4.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/without_mapping/otu_table_L4_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/without_mapping/otu_table_L4_json.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/without_mapping/otu_table_L5.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/without_mapping/otu_table_L5.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/without_mapping/otu_table_L5_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/without_mapping/otu_table_L5_json.biom Thu May 18 09:38:55 2017 -0400

[

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/without_mapping/otu_table_L6.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/without_mapping/otu_table_L6.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/summarize_taxa_through_plots/without_mapping/otu_table_L6_json.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_taxa_through_plots/without_mapping/otu_table_L6_json.biom Thu May 18 09:38:55 2017 -0400

[

@@ -0,0 +1,1 @@
+{"id": "No Table ID","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-05-01T13:49:51.006003","type": "OTU table","matrix_element_type": "float","shape": [27, 9],"data": [[0,0,0.020270270270270271],[0,1,0.046979865771812075],[0,2,0.026666666666666668],[0,3,0.027397260273972601],[0,4,0.013422818791946308],[0,5,0.013422818791946308],[0,6,0.013605442176870748],[0,7,0.046979865771812075],[0,8,0.02],[1,0,0.0067567567567567571],[1,1,0.0067114093959731542],[1,3,0.0068493150684931503],[1,7,0.020134228187919462],[1,8,0.02],[2,0,0.0067567567567567571],[3,0,0.46621621621621612],[3,1,0.30872483221476499],[3,2,0.17333333333333331],[3,3,0.075342465753424653],[3,4,0.053691275167785227],[3,5,0.36241610738255031],[3,6,0.13605442176870747],[3,7,0.20134228187919456],[3,8,0.18666666666666668],[4,0,0.16891891891891891],[4,1,0.046979865771812082],[4,3,0.013698630136986301],[4,4,0.013422818791946308],[4,5,0.026845637583892617],[4,6,0.12925170068027211],[4,8,0.27333333333333332],[5,0,0.013513513513513514],[5,1,0.026845637583892617],[5,3,0.0068493150684931503],[5,6,0.0068027210884353739],[5,8,0.080000000000000002],[6,1,0.0067114093959731542],[7,0,0.040540540540540543],[7,1,0.13422818791946309],[7,2,0.02],[7,3,0.047945205479452052],[7,4,0.0067114093959731542],[7,6,0.013605442176870748],[7,7,0.073825503355704702],[7,8,0.11333333333333334],[8,0,0.0472972972972973],[8,1,0.013422818791946308],[8,7,0.020134228187919462],[8,8,0.033333333333333333],[9,4,0.0067114093959731542],[9,7,0.026845637583892617],[10,0,0.020270270270270271],[11,2,0.093333333333333338],[11,3,0.027397260273972601],[11,4,0.10738255033557048],[11,5,0.033557046979865772],[11,6,0.013605442176870748],[12,7,0.0067114093959731542],[13,3,0.061643835616438353],[13,8,0.02],[14,1,0.020134228187919462],[14,2,0.02],[14,3,0.0068493150684931503],[14,4,0.0067114093959731542],[14,5,0.0067114093959731542],[14,7,0.013422818791946308],[14,8,0.0066666666666666671],[15,1,0.0067114093959731542],[15,2,0.0066666666666666671],[15,4,0.0067114093959731542],[15,5,0.0067114093959731542],[15,6,0.020408163265306121],[15,7,0.0067114093959731542],[16,0,0.0067567567567567571],[16,7,0.026845637583892617],[17,4,0.0067114093959731542],[17,5,0.067114093959731544],[17,6,0.0068027210884353739],[17,8,0.02],[18,7,0.0067114093959731542],[18,8,0.0066666666666666671],[19,0,0.11486486486486487],[19,1,0.26845637583892606],[19,2,0.57999999999999996],[19,3,0.65068493150684981],[19,4,0.71812080536912726],[19,5,0.27516778523489921],[19,6,0.65306122448979598],[19,7,0.26845637583892612],[19,8,0.11333333333333334],[20,1,0.0067114093959731542],[20,4,0.0067114093959731542],[20,5,0.0067114093959731542],[20,7,0.0067114093959731542],[21,0,0.067567567567567571],[21,1,0.093959731543624178],[21,2,0.073333333333333334],[21,3,0.041095890410958902],[21,4,0.040268456375838924],[21,5,0.020134228187919462],[21,6,0.0068027210884353739],[21,7,0.093959731543624178],[21,8,0.053333333333333337],[22,0,0.0067567567567567571],[22,1,0.0067114093959731542],[22,7,0.0067114093959731542],[22,8,0.013333333333333334],[23,5,0.033557046979865772],[23,7,0.013422818791946308],[24,8,0.013333333333333334],[25,0,0.013513513513513514],[25,1,0.0067114093959731542],[25,3,0.034246575342465752],[25,4,0.013422818791946308],[25,5,0.1476510067114094],[25,7,0.15436241610738255],[25,8,0.026666666666666668],[26,2,0.0066666666666666671],[26,7,0.0067114093959731542]],"rows": [{"id": "Root;k__Bacteria;Other;Other;Other;Other", "metadata": null},{"id": "Root;k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Coriobacteriales;f__Coriobacteriaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;Other", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Deferribacteres;c__Deferribacteres;o__Deferribacterales;f__Deferribacteraceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;Other;Other;Other", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales;f__Turicibacteraceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;Other", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Catabacteriaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiales Family XIII. Incertae Sedis", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptococcaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae", "metadata": null},{"id": "Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;f__F16", "metadata": null},{"id": "Root;k__Bacteria;p__Tenericutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae", "metadata": null},{"id": "Root;k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;f__", "metadata": null}],"columns": [{"id": "PC.636", "metadata": null},{"id": "PC.635", "metadata": null},{"id": "PC.356", "metadata": null},{"id": "PC.481", "metadata": null},{"id": "PC.354", "metadata": null},{"id": "PC.593", "metadata": null},{"id": "PC.355", "metadata": null},{"id": "PC.607", "metadata": null},{"id": "PC.634", "metadata": null}]}
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/upgma_cluster/beta_div_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/upgma_cluster/beta_div_1.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,10 @@
+ PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+PC.636 0.0 36.7287353444 49.9599839872 48.3528696149 58.7792480387 56.4003546088 53.2634959423 50.3884907494 46.7332857822
+PC.635 36.7287353444 0.0 32.3264597505 29.7825452237 44.4747119159 42.3792402008 36.7967389859 31.5594676761 29.6141857899
+PC.356 49.9599839872 32.3264597505 0.0 30.8220700148 30.8382878902 38.3536178215 36.5102725271 37.0270171631 39.9749921826
+PC.481 48.3528696149 29.7825452237 30.8220700148 0.0 41.3400532172 40.5832477754 33.8378486314 32.8785644455 37.8153408024
+PC.354 58.7792480387 44.4747119159 30.8382878902 41.3400532172 0.0 48.6415460281 45.9347363114 47.6235235992 49.6487663492
+PC.593 56.4003546088 42.3792402008 38.3536178215 40.5832477754 48.6415460281 0.0 48.1456124688 38.2883794382 48.3632091574
+PC.355 53.2634959423 36.7967389859 36.5102725271 33.8378486314 45.9347363114 48.1456124688 0.0 42.8719022205 34.7419055321
+PC.607 50.3884907494 31.5594676761 37.0270171631 32.8785644455 47.6235235992 38.2883794382 42.8719022205 0.0 40.3360880602
+PC.634 46.7332857822 29.6141857899 39.9749921826 37.8153408024 49.6487663492 48.3632091574 34.7419055321 40.3360880602 0.0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/upgma_cluster/beta_div_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/upgma_cluster/beta_div_2.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/upgma_cluster/beta_div_3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/upgma_cluster/beta_div_3.txt Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/upgma_cluster/beta_div_4.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/upgma_cluster/beta_div_4.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,10 @@
+ PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+PC.636 0.0 0.275683407854 0.453169793694 0.463169006849 0.530075154635 0.316693638219 0.367507936661 0.367668532106 0.207390851351
+PC.635 0.275683407854 0.0 0.332995003579 0.341452795348 0.411631543624 0.262879798658 0.301005982286 0.221100536913 0.240434181208
+PC.356 0.453169793694 0.332995003579 0.0 0.154091373516 0.144798193736 0.332624051454 0.186403568707 0.322076019239 0.443208
+PC.481 0.463169006849 0.341452795348 0.154091373516 0.0 0.168675520364 0.329334425393 0.192866592582 0.318716145536 0.433075579909
+PC.354 0.530075154635 0.411631543624 0.144798193736 0.168675520364 0.0 0.395430805369 0.237877518605 0.396216241611 0.510311668456
+PC.593 0.316693638219 0.262879798658 0.332624051454 0.329334425393 0.395430805369 0.0 0.322882191481 0.220838053691 0.340061936913
+PC.355 0.367507936661 0.301005982286 0.186403568707 0.192866592582 0.237877518605 0.322882191481 0.0 0.324959266311 0.360463247619
+PC.607 0.367668532106 0.221100536913 0.322076019239 0.318716145536 0.396216241611 0.220838053691 0.324959266311 0.0 0.356951809843
+PC.634 0.207390851351 0.240434181208 0.443208 0.433075579909 0.510311668456 0.340061936913 0.360463247619 0.356951809843 0.0
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/validate_mapping_file/corrected_map.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/validate_mapping_file/corrected_map.tabular Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 test-data/validate_mapping_file/log.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/validate_mapping_file/log.txt Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,1 @@
+No errors or warnings found in mapping file.
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 test-data/validate_mapping_file/map.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/validate_mapping_file/map.tsv Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 tool-data/qiime_rep_set.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/qiime_rep_set.loc.sample Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,6 @@
+#<unique_id> <name> <database_caption> <fasta_file_path>
+#
+#For each reference database, you need to download the fasta file in qiime path
+#
+#List of useful db for qiime: http://qiime.org/home_static/dataFiles.html
+#
\ No newline at end of file

diff -r 000000000000 -r c11972e98d44 tool-data/qiime_rep_set_aligned.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/qiime_rep_set_aligned.loc.sample Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 tool-data/qiime_taxonomy.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/qiime_taxonomy.loc.sample Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 tool-data/qiime_trees.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/qiime_trees.loc.sample Thu May 18 09:38:55 2017 -0400

diff -r 000000000000 -r c11972e98d44 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu May 18 09:38:55 2017 -0400

@@ -0,0 +1,18 @@
+<tables>
+    <table name="qiime_rep_set" comment_char="#">
+        <columns>value, name, dbkey, path</columns>
+        <file path="tool-data/qiime_rep_set.loc" />
+    </table>
+    <table name="qiime_rep_set_aligned" comment_char="#">
+        <columns>value, name, dbkey, path</columns>
+        <file path="tool-data/qiime_rep_set_aligned.loc" />
+    </table>
+    <table name="qiime_taxonomy" comment_char="#">
+        <columns>value, name, dbkey, path</columns>
+        <file path="tool-data/qiime_taxonomy.loc" />
+    </table>
+    <table name="qiime_trees" comment_char="#">
+        <columns>value, name, dbkey, path</columns>
+        <file path="tool-data/qiime_trees.loc" />
+    </table>
+</tables>
\ No newline at end of file