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Changeset 0:f9df45b8425a (2017-05-18)

Next changeset 1:c5a99b5e2c19 (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 f9df45b8425a README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Thu May 18 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a generate_test_data.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_test_data.sh Thu May 18 09:31:46 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 f9df45b8425a jackknifed_beta_diversity.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/jackknifed_beta_diversity.xml Thu May 18 09:31:46 2017 -0400

[

b'@@ -0,0 +1,223 @@\n+<tool id="qiime_jackknifed_beta_diversity" name="Perform jackknifed UPGMA clustering" version="@WRAPPER_VERSION@.0">\n+ <description>and building jackknifed PCoA plots</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <stdio>\n+ <regex match="VisibleDeprecationWarning" source="both" level="warning" description="VisibleDeprecationWarning on numpy for `rank`"/>\n+ <regex match="RuntimeWarning: The result contains negative eigenvalues" source="both" level="warning" description="Presence of negative eigenvalues"/>\n+ </stdio>\n+ <version_command>jackknifed_beta_diversity.py --version</version_command>\n+ <command detect_errors="aggressive"><![CDATA[\n+ jackknifed_beta_diversity.py\n+ --otu_table_fp \'$otu_table_fp\'\n+ --mapping_fp \'$mapping_fp\'\n+ -o jackknifed_beta_diversity\n+ --seqs_per_sample \'$seqs_per_sample\'\n+ #if $tree_fp\n+ --tree_fp \'$tree_fp\'\n+ #end if\n+ #if $parameter_fp\n+ --parameter_fp \'$parameter_fp\'\n+ #end if\n+ --master_tree \'$master_tree\'\n+ $parallel\n+ -O "\\${GALAXY_SLOTS:-4}"\n+\n+ && python $__tool_directory__/jackknifed_beta_diversity_output_management.py\n+ --data_directory jackknifed_beta_diversity\n+ --html_file \'$jackknifed_beta_diversity_report\'\n+ --html_dir \'$jackknifed_beta_diversity_report.files_path\'\n+ ]]></command>\n+ <inputs>\n+ <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" label="OTU table" multiple="True"/>\n+ <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file" multiple="True"/>\n+ <param argument="--seqs_per_sample" type="integer" value="" label="Number of sequences to include in each jackknifed subset"/>\n+ <param argument="--tree_fp" type="data" format="txt" label="Tree file" help="It is required for phylogenetic measures" optional="True"/>\n+ <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior, e.g. beta diversity metrics" optional="true"/>\n+ <param argument="--master_tree" type="select" label="Method for computing master trees in jackknife analysis">\n+ <option value="consensus" selected="True">Consensus of trees from jackknifed otu tables</option>\n+ <option value="full">Tree generated from input (unsubsambled) otu table</option>\n+ </param>\n+ <param argument="--parallel" type="boolean" label="Run in parallel where available?" truevalue="--parallel" falsevalue="" checked="true"/>\n+ </inputs>\n+ <outputs>\n+ <collection name="unrarefied_beta_div_dist_matrix" type="list" label="${tool.name} on ${on_string}: Distance matrix for unrarefied beta diversity">\n+ <discover_datasets pattern="(?P<designation>.+)\\.txt" directory="jackknifed_beta_diversity/unrarefied_bdiv/"/>\n+ </collection>\n+ <collection name="unrarefied_beta_div_tree" type="list" label="${tool.name} on ${on_string}: UPGMA trees for unrarefied beta diversity">\n+ <discover_datasets pattern="(?P<designation>.+)\\.tre" directory="jackknifed_beta_diversity/unrarefied_bdiv/"/>\n+ </collection>\n+ <collection name="rarefaction" type="list" label="${tool.name} on ${on_string}: Rarefied OTU tables">\n+ <discover_datasets pattern="rarefaction_(?P<designation>.+)\\.biom" directory="jackknifed_beta_diversity/rarefaction/"/>\n+ </collection>\n+ <collection name="pcoa" type="list:list" label="${tool.name} on ${on_string}: PCoA">\n+ <discover_datasets pattern="pcoa_(?P<identifier_0>.+)_rarefaction_(?P<identifier_1>.+)\\.txt" ext="txt" directory="jackknifed_beta_diversity/pcoa/"/>\n+ </collection>\n+ <collection name="r'..b'_text text="PC.355" />\n+ <has_text text="PC.607" />\n+ <has_text text="PC.634" />\n+ </assert_contents>\n+ </element>\n+ </element>\n+ </output_collection>\n+ <output_collection name="rare_upgma" type="list:list">\n+ <element name="unweighted_unifrac">\n+ <element name="10_0">\n+ <assert_contents>\n+ <has_text text="PC.636" />\n+ <has_text text="PC.635" />\n+ <has_text text="PC.356" />\n+ <has_text text="PC.481" />\n+ <has_text text="PC.354" />\n+ <has_text text="PC.593" />\n+ <has_text text="PC.355" />\n+ <has_text text="PC.607" />\n+ <has_text text="PC.634" />\n+ </assert_contents>\n+ </element>\n+ </element>\n+ <element name="weighted_unifrac">\n+ <element name="10_0">\n+ <assert_contents>\n+ <has_text text="PC.636" />\n+ <has_text text="PC.635" />\n+ <has_text text="PC.356" />\n+ <has_text text="PC.481" />\n+ <has_text text="PC.354" />\n+ <has_text text="PC.593" />\n+ <has_text text="PC.355" />\n+ <has_text text="PC.607" />\n+ <has_text text="PC.634" />\n+ </assert_contents>\n+ </element>\n+ </element>\n+ </output_collection>\n+ <output_collection name="rare_upgma_consensus" type="list" count="2">\n+ <element name="unweighted_unifrac">\n+ <assert_contents>\n+ <has_text text="PC.636" />\n+ <has_text text="PC.635" />\n+ <has_text text="PC.356" />\n+ <has_text text="PC.481" />\n+ <has_text text="PC.354" />\n+ <has_text text="PC.593" />\n+ <has_text text="PC.355" />\n+ <has_text text="PC.607" />\n+ <has_text text="PC.634" />\n+ </assert_contents>\n+ </element>\n+ <element name="weighted_unifrac">\n+ <assert_contents>\n+ <has_text text="PC.636" />\n+ <has_text text="PC.635" />\n+ <has_text text="PC.356" />\n+ <has_text text="PC.481" />\n+ <has_text text="PC.354" />\n+ <has_text text="PC.593" />\n+ <has_text text="PC.355" />\n+ <has_text text="PC.607" />\n+ <has_text text="PC.634" />\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ <output name="jackknifed_beta_diversity_report">\n+ <assert_contents>\n+ <has_text text="unweighted_unifrac" />\n+ <has_text text="weighted_unifrac" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**What it does**\n+\n+This tool performs jackknifing (repeatedly resampling a subset of the available data from each sample) to measure robustness of individual UPGMA clusters and clusters in PCoA plots.\n+\n+More information about this tool is available on\n+`QIIME documentation <http://qiime.org/scripts/jackknifed_beta_diversity.html>`_.\n+ ]]></help>\n+ <citations>\n+ <expand macro="citations"/>\n+ </citations>\n+</tool>\n'

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu May 18 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a test-data/alpha_diversity/alphadiv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alpha_diversity/alphadiv Thu May 18 09:31:46 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 f9df45b8425a 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 09:31:46 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": 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"float"}\n\\ No newline at end of file\n'

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

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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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

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

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a test-data/compare_categories/dbrda_plot.pdf

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

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

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

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

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

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

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

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

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

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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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file\n'

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

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

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

[

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

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

[

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

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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": [[0,6,1.0],[1,2,1.0],[1,5,1.0],[2,3,2.0],[2,4,2.0],[2,5,5.0],[2,6,1.0],[3,6,1.0],[4,6,1.0],[5,5,1.0],[6,5,1.0],[7,1,1.0],[7,3,9.0],[7,4,1.0],[7,5,1.0],[7,6,3.0],[8,6,1.0],[9,2,1.0],[9,5,8.0],[9,6,29.0],[10,0,1.0],[10,1,2.0],[10,2,2.0],[10,3,1.0],[10,4,6.0],[10,5,2.0],[10,6,4.0],[11,6,2.0],[12,1,1.0],[12,4,3.0],[12,5,1.0],[12,6,1.0],[13,2,1.0],[13,5,1.0],[14,5,1.0],[15,5,3.0],[17,4,5.0],[18,1,2.0],[18,2,4.0],[18,4,5.0],[18,5,5.0],[19,5,1.0],[19,6,1.0],[20,5,1.0],[21,5,2.0],[21,6,3.0],[22,6,1.0],[23,5,1.0],[24,6,1.0],[25,5,1.0],[25,6,1.0],[26,6,5.0],[27,4,1.0],[28,1,1.0],[29,1,1.0],[29,2,1.0],[29,3,1.0],[29,6,4.0],[30,3,9.0],[30,4,1.0],[31,5,1.0],[32,4,2.0],[35,4,1.0],[36,6,1.0],[37,6,1.0],[38,5,1.0],[39,2,1.0],[40,0,6.0],[40,3,1.0],[42,0,1.0],[42,1,1.0],[43,3,1.0],[44,3,2.0],[45,4,5.0],[45,5,5.0],[45,6,3.0],[46,1,1.0],[49,3,3.0],[50,6,1.0],[53,4,2.0],[54,1,1.0],[55,5,1.0],[56,5,1.0],[58,3,1.0],[59,6,1.0],[60,3,2.0],[60,5,6.0],[61,1,2.0],[61,2,1.0],[61,5,1.0],[63,1,1.0],[64,0,5.0],[64,1,9.0],[64,2,3.0],[64,5,2.0],[65,1,2.0],[65,4,1.0],[66,1,1.0],[67,1,1.0],[67,3,3.0],[68,0,1.0],[68,4,1.0],[69,4,1.0],[70,4,1.0],[71,2,1.0],[71,5,1.0],[72,5,1.0],[73,1,16.0],[73,3,1.0],[74,0,2.0],[74,1,1.0],[74,2,2.0],[74,3,24.0],[74,5,1.0],[74,6,1.0],[75,4,2.0],[75,5,1.0],[76,3,1.0],[77,1,1.0],[77,6,2.0],[78,2,1.0],[79,4,7.0],[80,2,1.0],[80,5,2.0],[80,6,19.0],[81,2,2.0],[82,1,1.0],[82,2,2.0],[82,5,1.0],[82,6,1.0],[83,1,1.0],[85,3,1.0],[86,6,1.0],[88,1,4.0],[88,3,1.0],[88,4,2.0],[88,5,1.0],[88,6,1.0],[89,2,1.0],[90,3,1.0],[92,2,1.0],[92,5,1.0],[93,5,1.0],[93,6,1.0],[94,5,1.0],[96,5,2.0],[96,6,2.0],[97,4,1.0],[98,4,1.0],[99,5,1.0],[100,1,1.0],[100,6,1.0],[101,2,1.0],[102,5,1.0],[103,1,1.0],[107,2,2.0],[109,4,6.0],[109,5,3.0],[110,4,1.0],[110,5,1.0],[111,0,1.0],[111,2,5.0],[111,3,17.0],[111,4,14.0],[112,4,3.0],[112,5,2.0],[112,6,5.0],[113,1,4.0],[113,2,1.0],[113,4,2.0],[114,0,1.0],[116,0,1.0],[116,1,3.0],[117,1,1.0],[117,3,1.0],[118,0,2.0],[118,1,1.0],[118,2,5.0],[118,4,1.0],[119,1,1.0],[119,2,4.0],[119,5,1.0],[120,1,1.0],[120,6,1.0],[121,1,1.0],[121,2,1.0],[121,3,1.0],[121,6,3.0],[122,0,1.0],[122,4,4.0],[123,6,1.0],[124,0,1.0],[125,1,1.0],[125,2,3.0],[126,1,2.0],[127,1,1.0],[128,3,1.0],[129,2,1.0],[132,4,1.0],[134,2,1.0],[136,4,1.0],[137,0,1.0],[138,2,2.0],[139,1,1.0],[140,4,1.0],[141,0,1.0],[142,0,1.0],[143,0,1.0],[143,2,2.0],[143,3,4.0],[144,1,2.0],[145,0,2.0],[145,1,4.0],[145,3,1.0],[146,0,1.0],[146,4,4.0],[147,6,1.0],[148,0,1.0],[149,5,1.0],[150,2,1.0],[151,0,1.0],[152,6,1.0],[153,0,1.0],[153,2,1.0],[154,1,3.0],[154,3,1.0],[155,5,1.0],[156,2,1.0],[157,5,1.0],[160,1,1.0],[160,2,3.0],[160,5,1.0],[162,0,16.0],[162,3,9.0],[163,4,1.0],[164,2,1.0],[165,2,1.0],[166,0,1.0],[166,3,1.0],[167,0,1.0],[167,1,4.0],[167,2,6.0],[168,4,1.0],[171,4,2.0],[171,5,1.0],[172,0,29.0],[172,1,1.0],[173,3,1.0],[174,0,5.0],[174,3,1.0],[176,5,1.0],[176,6,1.0],[177,2,1.0],[178,0,1.0],[179,1,1.0],[180,0,2.0],[180,2,1.0],[181,0,1.0],[182,2,4.0],[183,0,1.0],[183,3,10.0],[184,3,1.0],[186,2,1.0],[186,5,1.0],[189,2,1.0],[190,2,1.0],[193,4,1.0],[194,5,1.0],[195,4,1.0],[196,4,1.0],[197,5,1.0],[199,5,1.0],[200,4,1.0],[201,0,1.0],[201,3,1.0],[202,1,1.0],[203,4,1.0],[204,6,1.0],[205,4,1.0],[206,4,2.0],[207,2,1.0],[208,0,1.0],[209,2,1.0],[210,4,1.0],[212,2,1.0],[213,5,1.0],[214,4,7.0],[214,5,2.0],[214,6,2.0],[215,5,2.0],[216,6,1.0],[217,4,1.0],[217,5,1.0],[218,0,2.0],[218,1,18.0],[218,2,1.0],[218,5,4.0],[218,6,4.0],[219,3,1.0],[220,0,1.0],[220,3,1.0],[221,5,1.0],[222,3,1.0],[223,2,1.0],[223,4,2.0],[223,5,1.0],[223,6,1.0],[225,0,1.0],[226,4,1.0],[226,6,1.0],[227,5,1.0],[228,4,2.0],[229,2,1.0],[230,5,1.0],[231,5,1.0],[232,0,1.0],[233,2,4.0],[233,5,1.0],[234,0,1.0],[235,5,1.0],[236,3,1.0],[237,0,'..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.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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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": [{"id": "0", "metadata": {"taxonomy": ["Root", "Bacteria", "Actinobacteria", "Actinobacteria", "Coriobacteridae", "Coriobacteriales", "Coriobacterineae", "C'..b'inococcaceae\\""]}},{"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.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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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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null},{"id": "PC.634", "metadata": null}]}
\ No newline at end of file

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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"]}}, {"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__Tenericutes", "c__Erysipelotrichi", "o__Erysipelotrichales", "f__Erysipelotrichaceae"]}}, {"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__Ruminococcaceae"]}}, {"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__Bacilli", "o__Lactobacillales", "f__Streptococcaceae"]}}, 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"int"}\n\\ No newline at end of file\n'

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a test-data/make_otu_heatmap/basic_heatmap.pdf

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

diff -r 000000000000 -r f9df45b8425a test-data/make_otu_heatmap/basic_heatmap.png

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

diff -r 000000000000 -r f9df45b8425a test-data/make_otu_heatmap/basic_heatmap.svg
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diff -r 000000000000 -r f9df45b8425a test-data/make_otu_heatmap/mapping_file.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r f9df45b8425a test-data/make_otu_heatmap/otu_table.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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[

diff -r 000000000000 -r f9df45b8425a test-data/make_otu_heatmap/rep_set.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r f9df45b8425a test-data/make_otu_heatmap/treatment_sample_sorted_heatmap.pdf

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diff -r 000000000000 -r f9df45b8425a test-data/make_phylogeny/aligned.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r f9df45b8425a test-data/make_phylogeny/clustalw.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r f9df45b8425a 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 f9df45b8425a test-data/make_phylogeny/fasttree_tree_method_default.tre
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+++ b/test-data/make_phylogeny/fasttree_tree_method_default.tre Thu May 18 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a test-data/map.tsv.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/map.tsv.html Thu May 18 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

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

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

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

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

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

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

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

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 f9df45b8425a 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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
+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

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

[

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

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

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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 f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 2017 -0400

diff -r 000000000000 -r f9df45b8425a 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 09:31:46 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