| Next changeset 1:e93e39c121b1 (2019-01-29) |
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Commit message:
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 |
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added:
correct_replicates.xml counttable-addsums.xml krona_mothur.xml macros.xml make_multi_otutable.xml mycrobiota.py otutable_add_blast_links.xml otutable_split_by_sample.xml qcreport.xml recover_samples_discarded_by_subsample.xml test-data/DX01.otutable test-data/example.mothur.shared test-data/fasta_after_subsample_small.fasta test-data/fasta_before_subsample_small.fasta test-data/groups_after_subsample_small.groups test-data/groups_before_subsample_small.groups test-data/krona.test1.mothur.cons.taxonomy test-data/multisample.otutable test-data/multisample.taxonomy test-data/otureps.fasta test-data/otutable_tocorrect.taxonomy test-data/otutable_with_blast.tsv test-data/otutable_without_blast.tsv test-data/recovered.fasta test-data/recovered.groups test-data/shared_dereplicated.tsv test-data/shared_mock.tsv test-data/shared_tocorrect.tsv test-data/shared_with_taxonomy.tsv test-data/summarylog1.txt test-data/summarylog2.txt test-data/summarylog3.txt test-data/test-out.count_table test-data/test.count_table test-data/test2.count_table |
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| diff -r 000000000000 -r 607c5e7e0a64 correct_replicates.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/correct_replicates.xml Wed Dec 13 10:09:50 2017 -0500 |
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| @@ -0,0 +1,46 @@ +<tool id="mycrobiota-correct-replicates" name="Correct counts" version="0.6"> + <description>in a mothur shared file for replicates and negative controls</description> + <macros> + <import>macros.xml</import> + </macros> + <command detect_errors="aggressive"><![CDATA[ + python '$__tool_directory__/mycrobiota.py' + --command correct_replicates + --shared '$shared' + --taxonomy '$taxonomy' + --replicate_suffix '$replicate_suffix' + --negative_control '$negative_control' + --nc_copies '$nc_copies' + --copies '$copies' + --negative_control_species '$negative_control_species' + ]]></command> + <inputs> + <param argument="--shared" type="data" format="mothur.shared" label="Select shared file"/> + <param argument="--taxonomy" type="data" format="mothur.ref.taxonomy,mothur.seq.taxonomy,mothur.cons.taxonomy" label="Select taxonomy file"/> + <param argument="--replicate_suffix" type="text" size="100" value="_replicate" label="Suffix used to indicated replicates" help="e.g. _R if files are named [sample]_R1, [sample]_R2 etc"/> + <param argument="--negative_control" type="text" optional="True" size="100" value="" label="sample name for your negative control (optional)" help="e.g. negative_control"/> + <param argument="--negative_control_species" type="text" optional="True" size="100" value="Oscillatoria" label="taxonomy of negative control" help="e.g. Oscillatoria"/> + <param argument="--nc_copies" type="integer" value="100" min="0" label="number of copies of control species in the negative control sample"/> + <param argument="--copies" type="integer" value="1000" min="0" label="number of copies of control species in the real samples"/> + </inputs> + <outputs> + <data name="corrected_out" format="mothur.shared" from_work_dir="shared_corrected.tsv" label="${tool.name} on ${on_string}: corrected shared file"/> + <data name="corrected_tax" format_source="taxonomy" from_work_dir="taxonomy_corrected.tsv" label="${tool.name} on ${on_string}: corrected taxonomy file"/> + <data name="corrected_out_avg" format="mothur.shared" from_work_dir="shared_averaged.tsv" label="${tool.name} on ${on_string}: averaged only shared file"/> + </outputs> + <tests> + <test> + <param name="shared" value="shared_tocorrect.tsv" ftype="mothur.shared"/> + <param name="taxonomy" value="otutable_tocorrect.taxonomy" ftype="mothur.cons.taxonomy"/> + <param name="replicate_suffix" value="_replicate"/> + <param name="negative_control" value="NC"/> + <output name="corrected_out" md5="a7bafe98a383b308b4f1f1681483091d" ftype="mothur.shared"/> + <output name="corrected_tax" md5="9cc44bec811b868bde9acbe5d857e4c9" ftype="mothur.cons.taxonomy"/> + </test> + </tests> + <help><![CDATA[ +**What it does** +averages the counts over all replicates of a sample in a mothur shared file + ]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 607c5e7e0a64 counttable-addsums.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/counttable-addsums.xml Wed Dec 13 10:09:50 2017 -0500 |
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| @@ -0,0 +1,28 @@ +<tool id="mycrobiota-counttable-totals" name="Counttable totals" version="0.1"> + <description>add line with total counts to your mothur count table</description> + <macros> + <import>macros.xml</import> + </macros> + <command detect_errors="aggressive"><![CDATA[ + python '$__tool_directory__/mycrobiota.py' + --command counttable_totals + -ct '$count_in' + -o '$count_out' + ]]></command> + <inputs> + <param name="count_in" type="data" format="mothur.count_table" label="Select count file"/> + </inputs> + <outputs> + <data name="count_out" format="tabular" label="Count table with totals on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="count_in" value="test.count_table" ftype="mothur.count_table"/> + <output name="count_out" file="test-out.count_table" ftype="tabular"/> + </test> + </tests> + <help><![CDATA[ + Takes a Mothur count table and adds a line to the end with the total counts per sample + ]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 607c5e7e0a64 krona_mothur.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/krona_mothur.xml Wed Dec 13 10:09:50 2017 -0500 |
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| @@ -0,0 +1,113 @@ +<tool id="mycrobiota-krona-mothur" name="Krona" version="1"> + <description>for mothur datasets</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="2.7">krona</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ + ## create symlinks to taxonomy files for nicer display names in output + #if $input.haveshared == 'no': + #for $tax in $input.taxonomy: + ln -s '$tax' '$tax.name' && + #end for + #end if + + python '$__tool_directory__/mycrobiota.py' + #if $input.haveshared == 'yes': + --command create_krona_plot_multisample + --shared_file '$input.shared_file' + #if $input.level == 'None': + --level '$input.taxonomy.name' + #else: + --level '$input.level' + #end if + --taxonomy $input.taxonomy + #else: + --command create_krona_plot + #for $tax in $input.taxonomy: + --taxonomy '$tax.name' + #end for + #end if + ${with_otu} + ]]></command> + <inputs> + <conditional name="input"> + <param name="haveshared" type="select" label="Would you like to supply a mothur shared file?" + help="This will create a multisample plot. If you select 'no', you can still create a multisample plot by providing a taxonomy file per sample"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <param argument="--taxonomy" type="data" multiple="true" format="mothur.ref.taxonomy,mothur.seq.taxonomy,mothur.cons.taxonomy" label="Select mothur taxonomy file" help=""/> + </when> + <when value="yes"> + <param argument="--taxonomy" type="data" format="mothur.ref.taxonomy,mothur.seq.taxonomy,mothur.cons.taxonomy" label="Select mothur taxonomy file" help=""/> + <param argument="--shared_file" type="data" optional="true" format="mothur.shared" label="Supply a mothur shared file" help=""/> + <param argument="--level" type="select" optional="true" label="label - pick (one) OTU Label" help="leave blank for collections, will try to determine level from element names"> + <options> + <filter type="data_meta" ref="shared_file" key="labels"/> + </options> + </param> + </when> + </conditional> + <param argument="--with_otu" type="boolean" checked="false" truevalue="--with-otu" falsevalue="" label="differentiate between different OTUs of same taxonomy?" help=""/> + </inputs> + <outputs> + <data name="krona_plot" format="html" from_work_dir="text.krona.html" label="Krona plot of ${on_string}: HTML"/> + </outputs> + <tests> + <test> <!-- test single sample --> + <param name="haveshared" value="no"/> + <param name="taxonomy" value="multisample.taxonomy"/> + <param name="with_otu" value="--with-otu"/> + <output name="krona_plot"> + <assert_contents> + <has_text text="Krona"/> + <has_text text="Actinobacteria"/> + <not_has_text text="F3D0"/> + <not_has_text text="F3D148"/> + <not_has_text text="krona.test1.mothur.cons"/> + <has_text text="Otu0127"/> + </assert_contents> + </output> + </test> + <test> <!-- test multi samples (multiple single-sample taxonomy files) --> + <param name="haveshared" value="no"/> + <param name="taxonomy" value="multisample.taxonomy,krona.test1.mothur.cons.taxonomy"/> + <param name="with_otu" value=""/> + <output name="krona_plot"> + <assert_contents> + <has_text text="Krona"/> + <has_text text="krona.test1.mothur.cons"/> + <has_text text="Actinobacteria"/> + <not_has_text text="F3D0"/> + <not_has_text text="F3D148"/> + <not_has_text text="Otu0127"/> + </assert_contents> + </output> + </test> + <test> <!-- test multi sample (single multisample taxonomy file with shared file) --> + <param name="haveshared" value="yes"/> + <param name="taxonomy" value="multisample.taxonomy"/> + <param name="shared_file" ftype="mothur.shared" value="example.mothur.shared"/> + <param name="with_otu" value="--with-otu"/> + <param name="level" value="0.03"/> + <output name="krona_plot"> + <assert_contents> + <has_text text="Krona"/> + <has_text text="Actinobacteria"/> + <has_text text="F3D0"/> + <has_text text="F3D148"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**What it does** + ]]></help> + <expand macro="citations"> + <citation type="doi">10.1007/978-1-4614-6418-1_802-1</citation> + </expand> +</tool> |
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| diff -r 000000000000 -r 607c5e7e0a64 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Dec 13 10:09:50 2017 -0500 |
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| @@ -0,0 +1,9 @@ +<macros> + <xml name="citations"> + <citations> + <citation type="doi">10.1128/AEM.01541-09</citation> <!-- mothur --> + <!-- TODO: MYcrobiota paper --> + <yield/> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 607c5e7e0a64 make_multi_otutable.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/make_multi_otutable.xml Wed Dec 13 10:09:50 2017 -0500 |
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| @@ -0,0 +1,37 @@ +<tool id="mycrobiota-make-multi-otutable" name="Make multisample OTUtable" version="0.1"> + <description>from a shared and taxonomy file</description> + <macros> + <import>macros.xml</import> + </macros> + <command detect_errors="aggressive"><![CDATA[ + python '$__tool_directory__/mycrobiota.py' + --command make_multi_otutable + --shared_file '$shared_file' + --taxonomy '$taxonomy' + --level $level + ]]></command> + <inputs> + <param argument="--taxonomy" type="data" format="mothur.ref.taxonomy,mothur.seq.taxonomy,mothur.cons.taxonomy" label="Select mothur taxonomy file" help=""/> + <param argument="--shared_file" type="data" optional="true" format="mothur.shared" label="Supply a mothur shared file" help=""/> + <param argument="--level" type="select" optional="true" label="label - pick (one) OTU Label" help="leave blank for collections, will try to determine level from element names"> + <options> + <filter type="data_meta" ref="shared_file" key="labels"/> + </options> + </param> + </inputs> + <outputs> + <data name="multi_otutable" format="tabular" from_work_dir="multi_otutable.tsv" label="Multisample otutable on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="taxonomy" value="multisample.taxonomy"/> + <param name="shared_file" ftype="mothur.shared" value="example.mothur.shared"/> + <param name="level" value="0.03"/> + <output name="multi_otutable" file="shared_with_taxonomy.tsv"/> + </test> + </tests> + <help><![CDATA[ + help text goes here + ]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 607c5e7e0a64 mycrobiota.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mycrobiota.py Wed Dec 13 10:09:50 2017 -0500 |
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| b'@@ -0,0 +1,553 @@\n+import argparse\n+import csv\n+import math\n+import os\n+from subprocess import call\n+\n+\n+def main():\n+ print("Welcome to the MYcrobiota suite")\n+ parser = argparse.ArgumentParser()\n+ parser.add_argument(\'-c\', \'--command\', required=True,\n+ help="What action to perform")\n+ parser.add_argument(\'-ct\', \'--count_table\', action=\'append\',\n+ help="mothur count table")\n+ parser.add_argument(\'-cp\', \'--copies\', help="copies of NC for samples")\n+ parser.add_argument(\'-nccp\', \'--nc_copies\', help="copies of NC for itself")\n+ parser.add_argument(\'-t\', \'--taxonomy\', action=\'append\',\n+ help="mothur taxonomy file")\n+ parser.add_argument(\'-s\', \'--shared_file\', action=\'append\',\n+ help="mothur shared file")\n+ parser.add_argument(\'-otu\', \'--otutable\', action=\'append\',\n+ help="mothur OTU table")\n+ parser.add_argument(\'-f\', \'--fasta\', action=\'append\', help="fasta")\n+ parser.add_argument(\'-sl\', \'--summary_log\', action=\'append\',\n+ help="mothur summary log file")\n+ parser.add_argument(\'-o\', \'--outfile\', help="output file")\n+ parser.add_argument(\'-od\', \'--outdir\', help="output directory", default="")\n+ parser.add_argument(\'-lv\', \'--level\', help="taxonomy level")\n+ parser.add_argument(\'-nc\', \'--negative_control\',\n+ help="sample name of the negative control")\n+ parser.add_argument(\'-ncs\', \'--negative_control_species\',\n+ help="species name of the negative control",\n+ default="Oscillatoria")\n+ parser.add_argument(\'-r\', \'--replicate_suffix\',\n+ help="suffix to identify replicates")\n+ parser.add_argument(\'-l\', \'--label\', action=\'append\',\n+ help="label for count table")\n+ parser.add_argument(\'--with-otu\', dest=\'with_otu\', action=\'store_true\',\n+ default=False)\n+ args = parser.parse_args()\n+\n+ try:\n+ os.mkdir(args.outdir)\n+ except OSError:\n+ pass\n+\n+ print("Running command: "+args.command)\n+\n+ if args.command == \'counttable_totals\':\n+ count_table_totals(args.count_table[0], args.outdir, args.outfile)\n+\n+ elif args.command == \'qc_report\':\n+ if args.count_table:\n+ qc_report(args.count_table, args.label, \'counttables\', args.outdir)\n+ elif args.summary_log:\n+ qc_report(args.summary_log, args.label, \'summarylogs\', args.outdir)\n+\n+ elif args.command == \'create_krona_plot\':\n+ create_krona_plot(args.taxonomy, args.outdir, args.with_otu)\n+\n+ elif args.command == \'create_krona_plot_multisample\':\n+ create_krona_plot_multisample(args.taxonomy, args.shared_file,\n+ args.level, args.outdir, args.with_otu)\n+\n+ elif args.command == \'correct_replicates\':\n+ correct_replicates(args.shared_file, args.taxonomy, args.outdir,\n+ args.replicate_suffix, args.copies,\n+ args.negative_control, args.nc_copies,\n+ args.negative_control_species)\n+\n+ elif args.command == \'make_multi_otutable\':\n+ make_multi_otutable(args.taxonomy, args.shared_file, args.level,\n+ args.outdir)\n+\n+ elif args.command == \'otutable_add_blast_links\':\n+ otutable_add_blast_links(args.otutable, args.fasta)\n+\n+ elif args.command == \'split_multi_otutable\':\n+ split_multi_otutable(args.otutable)\n+\n+ else:\n+ print("unknown command. exiting")\n+\n+\n+def make_url(seq, baseurl):\n+ return baseurl+"?DATABASE=nr&PERC_IDENT=97&EXCLUDE_SEQ_UNCULT=on&" \\\n+ "HITLIST_SIZE=10&FILTER=L&FILTER=m&FILTER=R&EXPECT=10&" \\\n+ "FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&" \\\n+ "SERVICE=megablast&PAGE=Nucleotides&CMD=Put&QUERY=" \\\n+ + seq.lower()\n+\n+\n+def mak'..b'[0])\n+ lst = map(list, zip(*lst))\n+ writelines2 = [[writelines[i][0]] + lst[i] + writelines[i][-6:]\n+ for i in range(0, len(writelines))]\n+\n+ # output corrected shared file\n+ write_output(outdir, "multi_otutable.tsv", writelines2)\n+\n+\n+def split_multi_otutable(otutable, with_avg=True):\n+ fulltable = [line.strip().split(\'\\t\')\n+ for line in open(otutable[0], \'r\') if line]\n+ samples = [s.split(\'_\')[0] for s in fulltable[0][1:-6]]\n+ numcols = len(fulltable[0])\n+ numreplicates = (numcols - 7) / len(set(samples))\n+\n+ for sample in set(samples):\n+ outlines = []\n+ cols = [0] + [i+1 for i, s in enumerate(samples) if sample in s] \\\n+ + [i for i in range(numcols-6, numcols)]\n+ for i, line in enumerate(fulltable):\n+ out = [line[j] for j in cols]\n+ if out[1:-6] != [\'0\'] * numreplicates:\n+ out.insert(-6, \'mean\' if i == 0\n+ else int(round(mean(map(int, out[1:-6])))))\n+ outlines.append(out)\n+\n+ write_output(\'.\', sample+\'.otutable\', outlines)\n+\n+\n+def create_krona_plot_multisample(taxonomy_file, shared_file, level, outdir,\n+ with_otu):\n+ """\n+ Create krona plots from a multisample taxonomy plot and a shared file.\n+ Create one multisample plot and a plot per individual sample\n+\n+ :param taxonomy_file:\n+ :param shared_file:\n+ :param level: which level to use, e.g. unique/0.03/..\n+ :param with_otu:\n+ :return:\n+ """\n+\n+ taxonomies = []\n+\n+ # create taxonomy file per sample\n+ with open(taxonomy_file[0], \'r\') as tax, open(shared_file[0]) as sh:\n+ taxonomy = csv.reader(tax, delimiter=\'\\t\')\n+ shared = csv.reader(sh, delimiter=\'\\t\')\n+ shared_header = next(shared)\n+\n+ for i, row in enumerate(shared):\n+ tax.seek(0) # make sure to start at beginning of file each time\n+ if row[0] == level:\n+ sample = row[1]\n+\n+ outfile = os.path.join(outdir, sample+".tsv")\n+ taxonomies.append(outfile)\n+ with open(outfile, \'w+\') as of:\n+ out_table = csv.writer(of, delimiter=\'\\t\')\n+ out_table.writerow(next(taxonomy)) # header line\n+ for j, t in enumerate(taxonomy):\n+ assert t[0] == shared_header[j+3], \\\n+ "OTU mismatch between taxonomy and shared file"\n+ t[1] = row[j+3]\n+ out_table.writerow(t + [shared_header[j+3]])\n+\n+ # make krona plot\n+ create_krona_plot(taxonomies, outdir, with_otu)\n+\n+\n+def create_krona_plot(taxonomy_files, outdir, with_otu):\n+ """\n+ Create a krona plot from one or more mothur taxonomy files\n+\n+ :param taxonomy_files: mothur taxonomy file (output from classify.otu)\n+ :param outdir: directory to store krona-formatted outputs. Default=cwd\n+ :param with_otu: add OTU number as a level in the Krona plot? Default=True\n+ :return:\n+ """\n+ krona_input_files = []\n+\n+ # convert taxonomy files to krona input.\n+ for tax in taxonomy_files:\n+ with open(tax, \'r\') as f:\n+ taxonomy = csv.reader(f, delimiter=\'\\t\')\n+ out_rows = []\n+\n+ next(taxonomy) # skip header line\n+ for row in taxonomy:\n+ out_rows.append(\n+ filter(None, [row[1]] + row[2].rstrip(";\\n").split(\';\') +\n+ [row[0] if with_otu else None]))\n+\n+ outfile = os.path.join(outdir, tax.split("/")[-1]+"krona")\n+ krona_input_files.append(outfile)\n+\n+ with open(outfile, \'w+\') as f2:\n+ out_table = csv.writer(f2, delimiter=\'\\t\')\n+ for row in out_rows:\n+ out_table.writerow(row)\n+\n+ # execute krona command\n+ call(["ktImportText"] + krona_input_files)\n+\n+\n+if __name__ == "__main__":\n+ main()\n' |
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| diff -r 000000000000 -r 607c5e7e0a64 otutable_add_blast_links.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/otutable_add_blast_links.xml Wed Dec 13 10:09:50 2017 -0500 |
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| @@ -0,0 +1,31 @@ +<tool id="mycrobiota-otutable_add_blast" name="Add BLAST links" version="0.1"> + <description>to a mothur OTU table</description> + <macros> + <import>macros.xml</import> + </macros> + <command detect_errors="aggressive"><![CDATA[ + python '$__tool_directory__/mycrobiota.py' + --command otutable_add_blast_links + --otutable '$otutable' + --fasta '$fasta' + ]]></command> + <inputs> + <param argument="--otutable" type="data" format="tabular" label="OTU table" help=""/> + <param argument="--fasta" type="data" format="fasta" label="OTU representatives fasta file" help=""/> + </inputs> + <outputs> + <data name="otutable_with_blast" format="tabular" from_work_dir="otutable_with_blast.tsv" label="OTUtable with blast links on ${on_string}"/> + <data name="filtered_otureps" format="fasta" from_work_dir="filtered_otureps.fasta" label="OTUtable with blast links on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="otutable" value="otutable_without_blast.tsv"/> + <param name="fasta" value="otureps.fasta"/> + <output name="otutable_with_blast" file="otutable_with_blast.tsv"/> + </test> + </tests> + <help><![CDATA[ + help text goes here + ]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 607c5e7e0a64 otutable_split_by_sample.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/otutable_split_by_sample.xml Wed Dec 13 10:09:50 2017 -0500 |
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| @@ -0,0 +1,31 @@ +<tool id="mycrobiota-split-multi-otutable" name="Split multisample OTUtable" version="0.1"> + <description>into a table persample</description> + <macros> + <import>macros.xml</import> + </macros> + <command detect_errors="aggressive"><![CDATA[ + python '$__tool_directory__/mycrobiota.py' + --command split_multi_otutable + --otutable '$otutable' + ]]></command> + <inputs> + <param argument="--otutable" type="data" format="tabular" label="Supply a multisaple OTU table" help="expects sample as first part of name e.g. samplename_replicate2_rest"/> + </inputs> + <outputs> + <collection name="sample_otutables" type="list" label="${tool.name} on ${on_string}: per-sample otu tables"> + <discover_datasets pattern="(?P<designation>.*)\.otutable" format="tabular"/> + </collection> + </outputs> + <tests> + <test> + <param name="otutable" value="multisample.otutable" ftype="tabular"/> + <output_collection name="sample_otutables" count="3"> + <element name="DX01" file="DX01.otutable" ftype="tabular"/> + </output_collection> + </test> + </tests> + <help><![CDATA[ + help text goes here + ]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 607c5e7e0a64 qcreport.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qcreport.xml Wed Dec 13 10:09:50 2017 -0500 |
| [ |
| @@ -0,0 +1,89 @@ +<tool id="mycrobiota-qc-report" name="QC report" version="1"> + <description>from count tables</description> + <macros> + <import>macros.xml</import> + </macros> + <command detect_errors="aggressive"><![CDATA[ + python '$__tool_directory__/mycrobiota.py' + --command qc_report + #if $input.filetype == 'summarylog': + #for $i, $c in enumerate($input.summaryfiles): + --summary_log '${c.summary}' + --label '${c.label}' + #end for + #elif $input.filetype == 'counttable': + #for $i, $c in enumerate($input.counttables): + --count_table '${c.count_table}' + --label '${c.label}' + #end for + #end if + ]]></command> + <inputs> + <conditional name="input"> + <param name="filetype" type="select" label="Generate QC table from" help=""> + <option value="counttable">count tables</option> + <option value="summarylog">summary.seqs log outputs</option> + </param> + <when value="counttable"> + <repeat name="counttables" title="Count Table" default="1" > + <param argument="--count_table" type="data" format="mothur.count_table" label="Coumt Table" help=""/> + <param argument="--label" type="text" size="100" value="" label="Enter a label for this step" help="e.g. trimmed by length"/> + </repeat> + </when> + <when value="summarylog"> + <repeat name="summaryfiles" title="Summary.seqs output log" default="1" > + <param argument="--summary" type="data" format="text" label="Summary File" help="logfile output of summary.seqs command"/> + <param argument="--label" type="text" size="100" value="" label="Enter a label for this step" help="e.g. trimmed by length"/> + </repeat> + </when> + </conditional> + </inputs> + <outputs> + <data name="allsamples" format="tabular" from_work_dir="all_qctable.tsv" label="${tool.name} on ${on_string}: QC table total counts"/> + <collection name="persample" type="list" label="${tool.name} on ${on_string}: per-sample QC tables"> + <discover_datasets pattern=".*?persample_qctable_(?P<designation>.*)\.tsv" format="tabular"/> + <filter> input['filetype'] == 'counttable' </filter> + </collection> + </outputs> + <tests> + <test><!-- test with count tables --> + <param name="filetype" value="counttable"/> + <repeat name="counttables"> + <param name="count_table" value="test2.count_table"/> + <param name="label" value="step1"/> + </repeat> + <repeat name="counttables"> + <param name="count_table" value="test.count_table"/> + <param name="label" value="step2"/> + </repeat> + <output name="allsamples" md5="97725d04b9927724729f6cd902e10317" ftype="tabular"/> + <output_collection name="persample" count="9"> + <element name="F3D144" md5="d86e633358e8f1518a4a8c2782a358ec"/> + </output_collection> + </test> + <test><!-- test with summary logfiles --> + <param name="filetype" value="summarylog"/> + <repeat name="summaryfiles"> + <param name="summary" value="summarylog1.txt"/> + <param name="label" value="step1"/> + </repeat> + <repeat name="summaryfiles"> + <param name="summary" value="summarylog2.txt"/> + <param name="label" value="step2"/> + </repeat> + <repeat name="summaryfiles"> + <param name="summary" value="summarylog3.txt"/> + <param name="label" value="step 3"/> + </repeat> + <output name="allsamples" md5="7e092deb126c537247e63a36def1d8fb" ftype="tabular"/> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +Given a set of count tables, make a summary table describing the differences in number of sequences. +]]> + </help> + <expand macro="citations"/> +</tool> |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 recover_samples_discarded_by_subsample.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/recover_samples_discarded_by_subsample.xml Wed Dec 13 10:09:50 2017 -0500 |
| [ |
| @@ -0,0 +1,63 @@ +<tool id="mycrobiota_subsample_add_discarded_samples" name="Recover samples" version="0.1" profile="16.07"> + <description> discarded by sub.sample</description> + <requirements> + <requirement type="package" version="1.36.1">mothur</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ + ln -s "$in_fasta" fasta.dat && + ln -s "$in_group" group.dat && + ln -s "$in_fasta_subsampled" fasta2.dat && + ln -s "$in_group_subsampled" group2.dat + + ## mothur count.groups on in_fasta + && echo 'count.groups(group=group.dat)' | sed 's/ //g' | mothur + + ## get group names with fewer than threshold reads and make a dash-separated list + && samples=`python -c "print('-'.join([g[0] for g in [ l.strip().split('\t') for l in open('group.count.summary').readlines() ] if int(g[1]) < $threshold]))"` + + ## get.groups on in_fasta with this list of groups, if list not empty, otherwise create empty file + && + if [ -z "\$samples"]; + then + touch fasta.pick.dat; + touch group.pick.dat; + else + echo "get.groups(fasta=fasta.dat, group=group.dat, groups=\$samples)" | sed 's/ //g' | mothur; + fi + + ## merge selected reads (fasta.pick.dat) with the fasta file from after sub.sample + && echo "merge.files(input=fasta2.dat-fasta.pick.dat, output=final_fasta)" | sed 's/ //g' | mothur + + ## merge group files + && echo "merge.files(input=group2.dat-group.pick.dat, output=final_group)" | sed 's/ //g' | mothur + + ]]></command> + <inputs> + <param name="in_fasta" type="data" format="fasta" label="Fasta before subsample"/> + <param name="in_fasta_subsampled" type="data" format="fasta" label="Fasta after subsample"/> + <param name="in_group" type="data" format="mothur.groups" label="Group file before subsample"/> + <param name="in_group_subsampled" type="data" format="mothur.groups" label="Group file after subsample"/> + <param name="threshold" type="integer" value="" min="0" label="Subsample level - cutoff value used in the subsampling" help="any samples with fewer reads than this value would have been discarded by sub.sample, but we want to add them back in" /> + </inputs> + <outputs> + <data name="out_fasta" format="fasta" from_work_dir="final_fasta" label="${tool.name} on ${on_string}: fasta"/> + <data name="out_group" format="mothur.groups" from_work_dir="final_group" label="${tool.name} on ${on_string}: group"/> + </outputs> + <tests> + <test> + <param name="in_fasta" value="fasta_before_subsample_small.fasta" ftype="fasta"/> + <param name="in_fasta_subsampled" value="fasta_after_subsample_small.fasta" ftype="fasta"/> + <param name="in_group" value="groups_before_subsample_small.groups" ftype="mothur.groups"/> + <param name="in_group_subsampled" value="groups_after_subsample_small.groups" ftype="mothur.groups"/> + <param name="threshold" value="3"/> + <output name="out_fasta" file="recovered.fasta"/> + <output name="out_group" file="recovered.groups"/> + </test> + </tests> + <help><![CDATA[ +**What it does** +filter fasta file by group based on number of sequences in the group. + ]]></help> + <citations> + </citations> +</tool> |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/DX01.otutable --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DX01.otutable Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,19 @@ +OTU DX01_replicate1 DX01_replicate2 DX01_replicate3 mean Kingdom Phylum Class Order Family Genus +Otu0001 1025 930 1769 1241 Bacteria Cyanobacteria Cyanobacteria SubsectionIII FamilyI Oscillatoria +Otu0003 7700 5150 11678 8176 Bacteria Firmicutes Clostridia Clostridiales Family_XI Anaerococcus +Otu0004 0 3 0 1 Bacteria Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Alloprevotella +Otu0005 0 2 0 1 Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus +Otu0006 1333 1123 2015 1490 Bacteria Firmicutes Clostridia Clostridiales Family_XI Peptoniphilus +Otu0007 1335 853 1941 1376 Bacteria Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Prevotella +Otu0008 946 761 1909 1205 Bacteria Firmicutes Clostridia Clostridiales Family_XI Parvimonas +Otu0009 1 8 23 11 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus +Otu0010 897 614 1397 969 Bacteria Firmicutes Clostridia Clostridiales Family_XI Peptoniphilus +Otu0011 33 10 40 28 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter +Otu0012 833 459 1020 771 Bacteria Proteobacteria Epsilonproteobacteria Campylobacterales Campylobacteraceae Campylobacter +Otu0013 715 454 1121 763 Bacteria Bacteroidetes Bacteroidia Bacteroidales Porphyromonadaceae Porphyromonas +Otu0014 443 409 671 508 Bacteria Actinobacteria Actinobacteria Corynebacteriales Corynebacteriaceae unclassified +Otu0015 388 422 1015 608 Bacteria Bacteroidetes Bacteroidia Bacteroidales Porphyromonadaceae Porphyromonas +Otu0016 585 390 839 605 Bacteria Firmicutes Clostridia Clostridiales Family_XI Peptoniphilus +Otu0017 0 1 0 0 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acetobacter +Otu0018 45 1 144 63 Bacteria Firmicutes Bacilli Lactobacillales Streptococcaceae Streptococcus +Otu0019 374 352 645 457 Bacteria Firmicutes Clostridia Clostridiales Family_XI Anaerococcus |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/example.mothur.shared --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.mothur.shared Wed Dec 13 10:09:50 2017 -0500 |
| b |
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\t1\t0\t2\t1\t1\t1\t2\t1\t3\t0\t1\t2\t0\t1\t2\t2\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\n' |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/fasta_after_subsample_small.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_after_subsample_small.fasta Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,12 @@ +>read1 +ACTG +>read2 +ACTG +>read3 +ACTG +>read6 +ACTG +>read7 +ACTG +>read8 +ACTG |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/fasta_before_subsample_small.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_before_subsample_small.fasta Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,20 @@ +>read1 +ACTG +>read2 +ACTG +>read3 +ACTG +>read4 +ACTG +>read5 +ACTG +>read6 +ACTG +>read7 +ACTG +>read8 +ACTG +>read9 +ACTG +>read10 +ACTG |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/groups_after_subsample_small.groups --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/groups_after_subsample_small.groups Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,6 @@ +read1 group1 +read2 group1 +read3 group1 +read6 group2 +read7 group2 +read8 group2 |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/groups_before_subsample_small.groups --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/groups_before_subsample_small.groups Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,10 @@ +read1 group1 +read2 group1 +read3 group1 +read4 group1 +read5 group1 +read6 group2 +read7 group2 +read8 group2 +read9 group3 +read10 group3 |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/krona.test1.mothur.cons.taxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/krona.test1.mothur.cons.taxonomy Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,47 @@ +OTU Size Taxonomy +Otu01 89 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +Otu02 67 Bacteria;Firmicutes;Bacilli;Lactobacillales;Carnobacteriaceae;Dolosigranulum; +Otu03 66 Bacteria;Firmicutes;Bacilli;Lactobacillales;Aerococcaceae;Abiotrophia; +Otu04 57 Bacteria;Firmicutes;Bacilli;Bacillales;Staphylococcaceae;Staphylococcus; +Otu05 42 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Moraxellaceae;Moraxella; +Otu06 31 Bacteria;Actinobacteria;Actinobacteria;Corynebacteriales;Corynebacteriaceae;Corynebacterium_1; +Otu07 29 Bacteria;Actinobacteria;Actinobacteria;Corynebacteriales;Corynebacteriaceae;Corynebacterium_1; +Otu08 28 Bacteria;Firmicutes;Negativicutes;Selenomonadales;Veillonellaceae;Veillonella; +Otu09 14 Bacteria;Actinobacteria;Actinobacteria;Corynebacteriales;Corynebacteriaceae;Corynebacterium_1; +Otu10 11 Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella_7; +Otu11 5 Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;unclassified; +Otu12 5 Bacteria;Actinobacteria;Actinobacteria;Corynebacteriales;Corynebacteriaceae;Corynebacterium_1; +Otu13 5 Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Stomatobaculum; +Otu14 5 Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia-Shigella; +Otu15 4 Bacteria;Actinobacteria;Actinobacteria;unclassified;unclassified;unclassified; +Otu16 4 Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Neisseria; +Otu17 3 Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;unclassified; +Otu18 2 Bacteria;Proteobacteria;Gammaproteobacteria;unclassified;unclassified;unclassified; +Otu19 2 Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Tepidimonas; +Otu20 2 Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Aquabacterium; +Otu21 2 Bacteria;Firmicutes;Negativicutes;Selenomonadales;Veillonellaceae;Selenomonas; +Otu22 2 Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Lachnoanaerobaculum; +Otu23 1 Bacteria;Actinobacteria;Actinobacteria;Bifidobacteriales;Bifidobacteriaceae;Scardovia; +Otu24 1 Bacteria;Deinococcus-Thermus;Deinococci;Deinococcales;Deinococcaceae;Deinococcus; +Otu25 1 Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella; +Otu26 1 Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;Coriobacteriaceae;Atopobium; +Otu27 1 Bacteria;Actinobacteria;Actinobacteria;Corynebacteriales;Corynebacteriaceae;Corynebacterium_1; +Otu28 1 Bacteria;Firmicutes;Bacilli;Bacillales;Listeriaceae;Listeria; +Otu29 1 Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;Coriobacteriaceae;Olsenella; +Otu30 1 Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella_7; +Otu31 1 Bacteria;Firmicutes;Clostridia;Clostridiales;Family_XIII;Mogibacterium; +Otu32 1 Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Oribacterium; +Otu33 1 Bacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Anaerococcus; +Otu34 1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +Otu35 1 Bacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Peptoniphilus; +Otu36 1 Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella_6; +Otu37 1 Bacteria;Actinobacteria;Actinobacteria;Micrococcales;Micrococcaceae;Kocuria; +Otu38 1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Carnobacteriaceae;Granulicatella; +Otu39 1 Bacteria;Actinobacteria;Actinobacteria;Micrococcales;Micrococcaceae;Rothia; +Otu40 1 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Moraxellaceae;Moraxella; +Otu41 1 Bacteria;Cyanobacteria;unclassified;unclassified;unclassified;unclassified; +Otu42 1 Bacteria;Firmicutes;Negativicutes;Selenomonadales;Veillonellaceae;Dialister; +Otu43 1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +Otu44 1 Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;unclassified; +Otu45 1 Bacteria;Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;Eikenella; +Otu46 1 Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella; |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/multisample.otutable --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multisample.otutable Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,20 @@ +OTU DX01_replicate1 DX01_replicate2 DX01_replicate3 DX02_replicate1 DX02_replicate2 DX02_replicate3 NC_replicate1 NC_replicate2 NC_replicate3 Kingdom Phylum Class Order Family Genus +Otu0001 1025 930 1769 981 931 1154 3098 11487 7509 Bacteria Cyanobacteria Cyanobacteria SubsectionIII FamilyI Oscillatoria +Otu0002 0 0 0 8703 7578 9012 0 0 0 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Morganella +Otu0003 7700 5150 11678 1 0 1 2 0 1 Bacteria Firmicutes Clostridia Clostridiales Family_XI Anaerococcus +Otu0004 0 3 0 7401 5795 7061 0 0 353 Bacteria Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Alloprevotella +Otu0005 0 2 0 3978 3577 4362 0 0 0 Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus +Otu0006 1333 1123 2015 0 0 0 0 0 0 Bacteria Firmicutes Clostridia Clostridiales Family_XI Peptoniphilus +Otu0007 1335 853 1941 0 0 3 0 0 0 Bacteria Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Prevotella +Otu0008 946 761 1909 0 0 0 0 0 0 Bacteria Firmicutes Clostridia Clostridiales Family_XI Parvimonas +Otu0009 1 8 23 610 451 519 214 686 943 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus +Otu0010 897 614 1397 0 0 0 0 0 0 Bacteria Firmicutes Clostridia Clostridiales Family_XI Peptoniphilus +Otu0011 33 10 40 1 35 0 156 1205 874 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter +Otu0012 833 459 1020 0 0 0 0 0 0 Bacteria Proteobacteria Epsilonproteobacteria Campylobacterales Campylobacteraceae Campylobacter +Otu0013 715 454 1121 4 0 0 0 0 0 Bacteria Bacteroidetes Bacteroidia Bacteroidales Porphyromonadaceae Porphyromonas +Otu0014 443 409 671 10 2 0 0 0 398 Bacteria Actinobacteria Actinobacteria Corynebacteriales Corynebacteriaceae unclassified +Otu0015 388 422 1015 18 0 16 0 0 0 Bacteria Bacteroidetes Bacteroidia Bacteroidales Porphyromonadaceae Porphyromonas +Otu0016 585 390 839 0 0 0 0 0 0 Bacteria Firmicutes Clostridia Clostridiales Family_XI Peptoniphilus +Otu0017 0 1 0 0 1 0 0 1589 0 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acetobacter +Otu0018 45 1 144 12 3 8 0 23 1287 Bacteria Firmicutes Bacilli Lactobacillales Streptococcaceae Streptococcus +Otu0019 374 352 645 0 0 0 0 0 0 Bacteria Firmicutes Clostridia Clostridiales Family_XI Anaerococcus |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/multisample.taxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multisample.taxonomy Wed Dec 13 10:09:50 2017 -0500 |
| b |
| b'@@ -0,0 +1,335 @@\n+OTU\tSize\tTaxonomy\n+Otu0001\t6675\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0002\t5145\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0003\t4815\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0004\t4283\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0005\t4060\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0006\t3710\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0007\t2489\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);Bacteroidaceae(100);Bacteroides(100);\n+Otu0008\t2152\tBacteria(100);Firmicutes(100);Bacilli(100);Lactobacillales(100);Lactobacillaceae(100);Lactobacillus(100);\n+Otu0009\t1581\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0010\t1572\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);Rikenellaceae(100);Alistipes(100);\n+Otu0011\t1539\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0012\t1416\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0013\t1092\tBacteria(100);Firmicutes(100);Erysipelotrichia(100);Erysipelotrichales(100);Erysipelotrichaceae(100);Turicibacter(100);\n+Otu0014\t980\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0015\t632\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(100);\n+Otu0016\t553\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0017\t470\tBacteria(100);Firmicutes(100);Bacilli(100);Lactobacillales(100);Lactobacillaceae(100);Lactobacillus(100);\n+Otu0018\t462\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0019\t414\tBacteria(100);Firmicutes(100);Bacilli(100);Lactobacillales(100);Lactobacillaceae(100);Lactobacillus(94);\n+Otu0020\t395\tBacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);\n+Otu0021\t330\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0022\t316\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(100);\n+Otu0023\t308\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(96);\n+Otu0024\t304\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(100);\n+Otu0025\t259\tBacteria(100);Tenericutes(100);Mollicutes(100);RF9(100);unclassified(100);unclassified(100);\n+Otu0026\t259\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0027\t257\tBacteria(100);Firmicutes(96);Clostridia(96);Clostridiales(96);Lachnospiraceae(96);unclassified(96);\n+Otu0028\t229\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(99);\n+Otu0029\t222\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0030\t220\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);unclassified(62);\n+Otu0031\t205\tBacteria(100);Actinobacteria(100);Actinobacteria(100);Bifidobacteriales(100);Bifidobacteriaceae(100);Bifidobacterium(100);\n+Otu0032\t203\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Clostridiaceae_1(100);Clostridium_sensu_stricto_1(100);\n+Otu0033\t203\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0034\t180\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(10'..b'ales(100);S24-7(100);unclassified(100);\n+Otu0300\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0301\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0302\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0303\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0304\t1\tBacteria(100);Firmicutes(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);\n+Otu0305\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0306\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0307\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0308\t1\tBacteria(100);Firmicutes(100);Bacilli(100);Lactobacillales(100);Lactobacillaceae(100);unclassified(100);\n+Otu0309\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0310\t1\tBacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);\n+Otu0311\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0312\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(100);\n+Otu0313\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0314\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0315\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Eubacteriaceae(100);Anaerofustis(100);\n+Otu0316\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Anaerotruncus(100);\n+Otu0317\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0318\t1\tBacteria(100);Firmicutes(100);Bacilli(100);unclassified(100);unclassified(100);unclassified(100);\n+Otu0319\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);Bacteroidaceae(100);Bacteroides(100);\n+Otu0320\t1\tBacteria(100);Bacteroidetes(100);Flavobacteriia(100);Flavobacteriales(100);Cryomorphaceae(100);Fluviicola(100);\n+Otu0321\t1\tBacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);\n+Otu0322\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0323\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Oscillibacter(100);\n+Otu0324\t1\tBacteria(100);Firmicutes(100);Bacilli(100);unclassified(100);unclassified(100);unclassified(100);\n+Otu0325\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0326\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0327\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);unclassified(100);\n+Otu0328\t1\tBacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);\n+Otu0329\t1\tBacteria(100);Firmicutes(100);Bacilli(100);unclassified(100);unclassified(100);unclassified(100);\n+Otu0330\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0331\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0332\t1\tBacteria(100);Firmicutes(100);Bacilli(100);Bacillales(100);Listeriaceae(100);Listeria(100);\n+Otu0333\t1\tBacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);unclassified(100);\n+Otu0334\t1\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Marvinbryantia(100);\n' |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/otureps.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/otureps.fasta Wed Dec 13 10:09:50 2017 -0500 |
| b |
| b'@@ -0,0 +1,92 @@\n+>6186_496929\tOtu01|89\n+CACGCTGTAAACGATG-AGTGC-TAGGTG-TT-AG-ACC-CT---TT-CC---GG-GGTTTAGTG-CCGT--AGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATT-CGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATC-CCTCT-GACCG-CTCTA-GAGAT-A-GA-GTTT-T-----CC-T--TC-G-G-G---ACAGAGGTG-ACAGGTGGTGCATGGTT\n+>6186_156947\tOtu02|67\n+CACGCCGTAAACGATG-AGTGC-TAAGTG-TT-GG-GGG-CT---TT-CC---GG-CCCTCGGTG-CTGG--AGCTAACGTATTAAGCACTCCGCCTGGGGATTACGACCGCAAGGTTGAAACTCAAAAGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATT-CGAAGCAACGCGAAGAACCTTACCAGCTCTTGACATC--TTCT-GACAA-CTCTA-GAGAT-A-GA-GCGT-T-C---CC-T--TC-G-G-G--GACAGAA-TG-ACAGGTGGTGCATGGTT\n+>6186_449599\tOtu03|66\n+CACGCCGTAAACGATG-AGTGC-TAAGTG-TT-GG-AGG-GG---TT-CC---AC-CCTTCAGTG-CTGG--AGTTAACGCAATAAGCACTCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATT-CGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATC-CCGAC-GACCG-CTCTA-GAGAT-A-GA-GTTT-T-----TC-T--TC-G-G-A---ACGTCGGTG-ACAGGTGGTGCATGGTT\n+>6186_7388600\tOtu04|57\n+CACGCCGTAAACGATG-AGTGC-TAAGTG-TT-AG-GGG-GT---TT-CC---GC-CCCTTAGTG-CTGC--AGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATT-CGAAGCAACGCGAAGAACCTTACCAAATCTTGACATC--CTTT-GACCG-CTCTA-GAGAT-A-GA-GTCT-T-CC--CC-T--TC-G-G-G-GGACAAAG-TG-ACAGGTGGTGCATGGTT\n+>6186_7011166\tOtu05|42\n+CACGCCGTAAACGATG-TCTAC-CAGTCG-TT-GG-GTC-T---TTT-AA----A-GGCTTAGTG-ACGC--AGTTAACGCGATAAGTAGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATT-CGATGCAACGCGAAGAACCTTACCTGGTCTTGACATA--GTGA-GAGTC-TTGCA-GAGAT-G-CG-AGAG-T-G---CC-T--TT-G-G-G--AATTCAC-AT-ACAGGTGCTGCATGGCT\n+>6186_6532585\tOtu06|31\n+CATGCCGTAAACGGTG-GGCGC-TAGGTG-TG-AG-GGT-C--TTTC-TA-C--G-ACTTTCGTG-CCGT--AGCTAACGCATTAAGCGCCCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGCGGAGCATGTGGATTAATT-CGATGCAACGCGAAGAACCTTACCTGGGCTTGACATAC-ATCA-GATCG-CTGCA-GAGAT-G-TA-GTTT-------CC-CT-TT-GTG-G----TTGGT-GT-ACAGGTGGTGCATGGTT\n+>6186_372115\tOtu07|29\n+CATGCCGTAAACGGTG-GGCGC-TAGGTG-TA-GG-GGC-C---TTT-TG-G--G-GTTTCTGTG-CCGT--AGCTAACGCATTAAGCGCCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATT-CGATGCAACGCGAAGAACCTTACCTGGGCTTGACATAC-ACCG-GATCG-CTGCA-GAGAT-G-TA-GTTT-------CC-C--TT-GTG-G----CTGGT-GT-ACAGGTGGTGCATGGCT\n+>6186_433990\tOtu08|28\n+CTGGCCGTAAACGATG-GGTAC-TAGGTG-TA-GG-AGG----TATC-GA-CC---CCTTCTGTG-CCGG--AGTTAACGCAATAAGTACCCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGTATGTGGTTTAATT-CGACGCAACGCGAAGAACCTTACCAGGTCTTGACATT--GATG-GACAG-AACTA-GAGAT-A-GT-TCCT-C-T---TC-T--TC-G-G-A--AGCCAGA-AA-ACAGGTGGTGCACGGTT\n+>6186_93574\tOtu09|14\n+CATGCCGTAAACGGTG-GGCGC-TAGGTG-TG-AG-GGT-C--TTTC-TA-C--G-ACTTTCGTG-CCGT--AGCTAACGCATTAAGCGCCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATT-CGATGCAACGCGAAGAACCTTACCTGGGCTTGACATAC-ACCA-GATTG-GGCTA-GAGAT-A-GT-TCGT-------CC-CT-TT-GTG-G----TTGGT-GT-ACAGGTGGTGCATGGTT\n+>6186_545958\tOtu10|11\n+CGCACAGTAAACGATG-GATGC-CCGCTG-TT-GG-TA------CCT-GG-------TATCAGCG-GCTA--AGCGAAAGCATTAAGCATCCCACCTGGGGAGTACGCCGGCAACGGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGAGGAACATGTGGTTTAATT-CGATGATACGCGAGGAACCTTACCCGGGCTTGAATTGC-AGAG-GAAGG-ATTTA-GAGAT-A-AT-GACG-C-----CC-T--TC-G-G-G---GTCTCT-GT-GAAGGTGCTGCATGGTT\n+>6186_553777\tOtu11|5\n+CACGCCCTAAACGATG-ACAAT-TAGCTG-TT-GG-CCC-C---ATT-AA----G-GGGTGAGTA-GCGA--AGCTAACGCGTGAAATTGTCCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATT-CGATGCAACGCGAAGAACCTTACCTGGTCTTGACATG--TACA-GAAGG-TTTTA-GAGAT-A-AG-ACTG-T-G---CC-T--TC-G-G-G--AACTGTA-AC-ACAGGTGCTGCATGGCT\n+>6186_4347702\tOtu12|5\n+CATGCCGTAAACGGTG-GGCGC-TAGGTG-TG-GG-TTT-C--CTTC-CA-C--G-GGATCCGTG-CCGT--AGCTAACGCATTAAGCGCCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATT-CGATGCAACGCGAAGAACCTTACCTGGGCTTGACATGC-ACTG-GATGC-GGCCA-GAGAT-G-GT-TGTT-------CC-CT-TT-GTG-G----CTGGT-GT-GCAGGTGGTGCATGGTT\n+>6186_7681685\tOtu13|5\n+CACGCGGTAAACGATG-AATAC-TAGGTG-TT-GG-TGC-CC---AA-A----GG-GCATCGGTG-CCGT--CGCAAACGCAATAAGTATTCC'..b'ATGTGGTTTAATT-CGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATC-CTTCT-GACCG-GCCTA-GAGAT-A-GG-CTTT-C-----TC-T--TC-G-G-A---GCAGAAGTG-ACAGGTGGTGCATGGTT\n+>6186_735142\tOtu35|1\n+CACGCTGTAAACGATG-AGTGC-TAGGTG-TC-GG-C--------GA-AT--------GTCGGTG-CCGC--AGTTAACACAATAAGCACTCCGCCTGGGGAGTACGTGCGCAAGCATGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCAGCGGAGCATGTGGTTTAATT-CGAAGCAACGCGAAGAACCTTACCAGGGCTTGACATAC-TGAG-GACGT-ACTTA-GAGAT-A-AG-TATA-C-T---TC-T--TC-G-G-A--AGCCTCA-AT-ACAGGTGGTGCATGGTT\n+>6186_7042987\tOtu36|1\n+CGCACAGTAAACGATG-GATGC-CCGTTG-TT-AG-TTC-A---CTT-A-----A-GAATTAGCG-ACCA--AGCGAAAGCATTAAGCATCCCACCTGGGGAGTACGCCGGCAACGGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGAGGAACATGTGGTTTAATT-CGATGATACGCGAGGAACCTTACCCGGGCTTGAATTGC-AGAC-GAACG-ATTCA-GAGAT-G-AT-GAGG-C-----CC-T--TC-G-G-G---GCGTCT-GT-GAAGGTGCTGCATGGTT\n+>6186_6695219\tOtu37|1\n+CATGCCGTAAACGTTG-GGCAC-TAGGTG-TG-GG-GGA-C--ATTC-CA-C--G-TTTTCCGCG-CCGT--AGCTAACGCATTAAGTGCCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGCGGATTAATT-CGATGCAACGCGAAGAACCTTACCAAGGCTTGACATAT-ACCG-GATCG-TTCCA-GAGAT-G-GT-TCTT-C-----CC-C--TTTG-G-G---GTCGGT-AT-ACAGGTGGTGCATGGTT\n+>6186_6317358\tOtu38|1\n+CACGCCGTAAACGATG-AGTGC-TAAGTG-TT-GG-AGG-GT---TT-CC---GC-CCTTCAGTG-CTGC--AGTTAACGCATTAAGCACTCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATT-CGAAGCAACGCGAAGAACCTTACCAAGTCTTGACATC--CTTT-GACCA-CTCTA-GGGAT-A-GA-GCTT-T-C---CC-T--TC-G-G-G--GACAAAG-TG-ACAGGTGGTGCATGGTT\n+>6186_5975992\tOtu39|1\n+CATGCCGTAAACGTTG-GGCAC-TAGGTG-TG-GG-GGA-C--ATTC-CA-C--G-TTTTCCGCG-CCGT--AGCTAACGCATTAAGTGCCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGAAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGCGGATTAAT-TCGATGCAACGCGAAGAACCTTACCAAGGCTTGACATAT-ACTG-GACTG-CGTCA-GAGAT-G-GC-GTTT-C-----CC-T--TC-G-G-G---GCTGGT-AT-ACAGGTGGTGCATGGTT\n+>6186_2187574\tOtu40|1\n+CACGCCGTAAACGATG-TCTAC-CAGTCG-TT-GG-GTC-T---TTT-AA----A-GACTTAGTG-ACGC--AGTTAACGCAATAAGTAGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATT-CGATGCAACGCGAAGAACCTTACCTGGTCTTGACATA--TCTA-GAATC-CTGCA-GAGAT-G-CG-GGAG-T-G---CC-T--TC-G-G-G--AATTAGA-AT-ACAGGTGCTGCATGGCT\n+>6186_2825082\tOtu41|1\n+CTAGCCGTAAACGATG-GATAC-TAGGCG-CT-GC-GCGT----ATC-GACC----CGTGCAGTG-CTGT--AGCTAACGCGTTAAGTATCCCGCCTGGGGAGTACGTTCGCAAGAATGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATT-CGATGCAAAGCGAAGAACCTTACCAGGGCTTGACATG--CCGC-GAATC-CTCTT-GAAAG-A-GA-GGGG-T-G---CC-T--TC-G-G-G--AACGCGG-AC-ACAGGTGGTGCATGGCT\n+>6186_3293195\tOtu42|1\n+CACGCCGTAAACGATG-GATAC-TAGGTG-TA-GG-AGG----TATC-GA-CC---CCTCCTGTG-CCGG--AGTTAACGCAATAAGTATCCCGCCTGGGAAGTACGATCGCAAGATTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGTATGTGGTTTAATT-CGACGCAACGCGAAGAACCTTACCAGGTCTTGACATT--GATC-GCGAT-CTGCA-GAAAT-G-CG-GAGT-T-CT--TC-T--TC-G-G-A-AGACGAGA-AA-ACAGGTGGTGCACGGCT\n+>6186_3988839\tOtu43|1\n+CACGCCGTAAACGATG-AGTGC-TAGGTG-TT-GG-ATC-CT---TT-CC---GG-GATTCAGTG-CCGC--AGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATT-CGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATC-CCGAT-GCTAT-TTCTA-GAGAT-A-GA-AAGT-T-----AC-T--TC-G-G-T---ACATCGGTG-ACAGGTGGTGCATGGTT\n+>6186_4437514\tOtu44|1\n+CACGCGGTAAACGATG-AATAC-TAGGTG-TC-GG-GGG-A---CAT-AG----T-CTTTCGGTG-CCGC--CGCTAACGCATTAAGTATTCCACCTGGGGAGTACGTTCGCAAGAATGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATT-CGAAGCAACGCGAAGAACCTTACCAAGTCTTGACATA-CCGTT-GACGG-TTCCG-TAATG-G-GG-ACTT-T-----CC-T--TC-G-G-G---ACAACGGAT-ACAGGTGGTGCATGGTT\n+>6186_5203014\tOtu45|1\n+CACGCCCTAAACGATG-TCGAT-TAGCTG-TT-GG-GCA-A---CTT-GA----T-TGCTTAGTA-GCGT--AGCTAACGCGTGAAATCGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATT-CGATGCAACGCGAAGAACCTTACCTGGTCTTGACATG--TACG-GAACC-TTTCA-GAGAC-G-GA-AGGG-T-G---CC-T--TC-G-G-G--AGCCGTA-AC-ACAGGTGCTGCATGGCT\n+>6186_550524\tOtu46|1\n+CGCACAGTAAACGATG-GATGC-CCGCTG-TT-AG-CGC------CT-G-------GCGTTAGCG-GCTA--AGCGAAAGCATTAAGCATCCCACCTGGGGAGTACGCCGGCAACGGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGAGGAACATGTGGTTTAATT-CGATGATACGCGAGGAACCTTACCCGGGCTTGAATTGC-AGAG-GAATT-ATTTA-GAGAT-A-AA-TATG-C-----CC-T--TC-G-G-G---GTCTCT-GT-GAAGGTGCTGCATGGTT\n' |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/otutable_tocorrect.taxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/otutable_tocorrect.taxonomy Wed Dec 13 10:09:50 2017 -0500 |
| b |
| b'@@ -0,0 +1,597 @@\n+OTU\tSize\tTaxonomy\n+Otu0001\t29141\tBacteria;Cyanobacteria;Cyanobacteria;SubsectionIII;FamilyI;Oscillatoria;\n+Otu0002\t27843\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Anaerococcus;\n+Otu0003\t5121\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Peptoniphilus;\n+Otu0004\t4669\tBacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;\n+Otu0005\t4053\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Parvimonas;\n+Otu0006\t3278\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Peptoniphilus;\n+Otu0007\t2625\tBacteria;Proteobacteria;Epsilonproteobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;\n+Otu0008\t2596\tBacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;\n+Otu0009\t2574\tBacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Moraxellaceae;Acinetobacter;\n+Otu0010\t2194\tBacteria;Actinobacteria;Actinobacteria;Corynebacteriales;Corynebacteriaceae;unclassified;\n+Otu0011\t2119\tBacteria;Firmicutes;Bacilli;Bacillales;Staphylococcaceae;Staphylococcus;\n+Otu0012\t2066\tBacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;\n+Otu0013\t2028\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Peptoniphilus;\n+Otu0014\t1791\tBacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Acetobacteraceae;Acetobacter;\n+Otu0015\t1692\tBacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;\n+Otu0016\t1518\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Anaerococcus;\n+Otu0017\t1247\tBacteria;Actinobacteria;Actinobacteria;Corynebacteriales;Corynebacteriaceae;Corynebacterium_1;\n+Otu0018\t1028\tBacteria;Actinobacteria;Actinobacteria;Micrococcales;Dermabacteraceae;Brachybacterium;\n+Otu0019\t1004\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Peptoniphilus;\n+Otu0020\t955\tBacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Moraxellaceae;Moraxella;\n+Otu0021\t917\tBacteria;Actinobacteria;Actinobacteria;Corynebacteriales;Corynebacteriaceae;Corynebacterium_1;\n+Otu0022\t850\tBacteria;Actinobacteria;Actinobacteria;Corynebacteriales;Corynebacteriaceae;Corynebacterium;\n+Otu0023\t801\tBacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;\n+Otu0024\t772\tBacteria;Firmicutes;Clostridia;Clostridiales;Peptococcaceae;Peptococcus;\n+Otu0025\t761\tBacteria;Fusobacteria;Fusobacteriia;Fusobacteriales;Fusobacteriaceae;Fusobacterium;\n+Otu0026\t665\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Finegoldia;\n+Otu0027\t569\tBacteria;Proteobacteria;Alphaproteobacteria;Sphingomonadales;ORCA-3N101;unclassified;\n+Otu0028\t520\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;unclassified;\n+Otu0029\t457\tBacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus;\n+Otu0030\t452\tBacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Rhizobiales_Incertae_Sedis;Phreatobacter;\n+Otu0031\t429\tBacteria;Actinobacteria;Actinobacteria;unclassified;unclassified;unclassified;\n+Otu0032\t427\tBacteria;Proteobacteria;Alphaproteobacteria;Caulobacterales;Caulobacteraceae;Brevundimonas;\n+Otu0033\t410\tBacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Alloprevotella;\n+Otu0034\t370\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Peptoniphilus;\n+Otu0035\t349\tBacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;\n+Otu0036\t314\tBacteria;Actinobacteria;Actinobacteria;Corynebacteriales;Corynebacteriaceae;Turicella;\n+Otu0037\t234\tBacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Rikenellaceae;Rikenellaceae_RC9_gut_group;\n+Otu0038\t211\tBacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Actinomyces;\n+Otu0039\t200\tBacteria;Actinobacteria;Actinobacteria;Actinomycetales;Actinomycetaceae;Mobiluncus;\n+Otu0040\t185\tBacteria;Proteobacteria;Alphaproteobacteria;Sphingomonadales;Sphingomonadaceae;Sphingomonas;\n+Otu0041\t165\tBacteria;unclassified;unclassified;unclassified;unclassified;unclassified;\n+Otu0042\t159\tBacteria;Firmicutes;Bacilli'..b's;Clostridia;Clostridiales;Lachnospiraceae;Coprococcus_3;\n+Otu0551\t1\tBacteria;Firmicutes;Clostridia;unclassified;unclassified;unclassified;\n+Otu0552\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Anaerococcus;\n+Otu0553\t1\tBacteria;Firmicutes;Clostridia;unclassified;unclassified;unclassified;\n+Otu0554\t1\tBacteria;Firmicutes;unclassified;unclassified;unclassified;unclassified;\n+Otu0555\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Lachnospiraceae_UCG-010;\n+Otu0556\t1\tBacteria;Cyanobacteria;Cyanobacteria;SubsectionIII;FamilyI;unclassified;\n+Otu0557\t1\tBacteria;Cyanobacteria;Cyanobacteria;unclassified;unclassified;unclassified;\n+Otu0558\t1\tBacteria;Actinobacteria;Actinobacteria;Corynebacteriales;Nocardiaceae;Rhodococcus;\n+Otu0559\t1\tBacteria;Bacteroidetes;unclassified;unclassified;unclassified;unclassified;\n+Otu0560\t1\tBacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;\n+Otu0561\t1\tBacteria;Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;unclassified;\n+Otu0562\t1\tBacteria;Proteobacteria;Epsilonproteobacteria;unclassified;unclassified;unclassified;\n+Otu0563\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Anaerococcus;\n+Otu0564\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Anaerococcus;\n+Otu0565\t1\tBacteria;unclassified;unclassified;unclassified;unclassified;unclassified;\n+Otu0566\t1\tBacteria;Actinobacteria;Actinobacteria;Corynebacteriales;Corynebacteriaceae;Corynebacterium_1;\n+Otu0567\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Peptoniphilus;\n+Otu0568\t1\tBacteria;Bacteroidetes;unclassified;unclassified;unclassified;unclassified;\n+Otu0569\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Anaerococcus;\n+Otu0570\t1\tBacteria;Proteobacteria;Epsilonproteobacteria;unclassified;unclassified;unclassified;\n+Otu0571\t1\tBacteria;Bacteroidetes;Bacteroidia;unclassified;unclassified;unclassified;\n+Otu0572\t1\tBacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonas;\n+Otu0573\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Peptoniphilus;\n+Otu0574\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Anaerococcus;\n+Otu0575\t1\tBacteria;Proteobacteria;Alphaproteobacteria;unclassified;unclassified;unclassified;\n+Otu0576\t1\tBacteria;Bacteroidetes;Bacteroidia;Bacteroidales;unclassified;unclassified;\n+Otu0577\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;unclassified;unclassified;\n+Otu0578\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Anaerococcus;\n+Otu0579\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Anaerococcus;\n+Otu0580\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Peptoniphilus;\n+Otu0581\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Peptoniphilus;\n+Otu0582\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Peptoniphilus;\n+Otu0583\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Peptococcaceae;Peptococcus;\n+Otu0584\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Anaerococcus;\n+Otu0585\t1\tBacteria;unclassified;unclassified;unclassified;unclassified;unclassified;\n+Otu0586\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;unclassified;unclassified;\n+Otu0587\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Anaerococcus;\n+Otu0588\t1\tBacteria;Cyanobacteria;Cyanobacteria;SubsectionIII;FamilyI;Oscillatoria;\n+Otu0589\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;unclassified;\n+Otu0590\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Anaerococcus;\n+Otu0591\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;unclassified;\n+Otu0592\t1\tBacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Peptoniphilus;\n+Otu0593\t1\tBacteria;unclassified;unclassified;unclassified;unclassified;unclassified;\n+Otu0594\t1\tBacteria;Cyanobacteria;Cyanobacteria;unclassified;unclassified;unclassified;\n+Otu0595\t1\tBacteria;unclassified;unclassified;unclassified;unclassified;unclassified;\n+Otu0596\t1\tBacteria;unclassified;unclassified;unclassified;unclassified;unclassified;\n' |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/otutable_with_blast.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/otutable_with_blast.tsv Wed Dec 13 10:09:50 2017 -0500 |
| b |
| b'@@ -0,0 +1,47 @@\n+OTU\tSize\tPerc\tKingdom\tPhylum\tClass\tOrder\tFamily\tGenus\tBLAST\n+Otu01\t89\t17.8357%\tBacteria\tFirmicutes\tBacilli\tLactobacillales\tStreptococcaceae\tStreptococcus\t<a target="_blank" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?DATABASE=nr&EXCLUDE_SEQ_UNCULT=yes&FILTER=L&FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&SERVICE=megablast&PAGE=Nucleotides&CMD=Web&QUERY=cacgctgtaaacgatgagtgctaggtgttagaccctttccggggtttagtgccgtagctaacgcattaagcactccgcctggggagtacgaccgcaaggttgaaactcaaaggaattgacgggggcccgcacaagcggtggagcatgtggtttaattcgaagcaacgcgaagaaccttaccaggtcttgacatccctctgaccgctctagagatagagttttccttcgggacagaggtgacaggtggtgcatggtt">send to BLAST</a>\n+Otu02\t67\t13.4269%\tBacteria\tFirmicutes\tBacilli\tLactobacillales\tCarnobacteriaceae\tDolosigranulum\t<a target="_blank" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?DATABASE=nr&EXCLUDE_SEQ_UNCULT=yes&FILTER=L&FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&SERVICE=megablast&PAGE=Nucleotides&CMD=Web&QUERY=cacgccgtaaacgatgagtgctaagtgttgggggctttccggccctcggtgctggagctaacgtattaagcactccgcctggggattacgaccgcaaggttgaaactcaaaagaattgacggggacccgcacaagcggtggagcatgtggtttaattcgaagcaacgcgaagaaccttaccagctcttgacatcttctgacaactctagagatagagcgttcccttcggggacagaatgacaggtggtgcatggtt">send to BLAST</a>\n+Otu03\t66\t13.2265%\tBacteria\tFirmicutes\tBacilli\tLactobacillales\tAerococcaceae\tAbiotrophia\t<a target="_blank" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?DATABASE=nr&EXCLUDE_SEQ_UNCULT=yes&FILTER=L&FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&SERVICE=megablast&PAGE=Nucleotides&CMD=Web&QUERY=cacgccgtaaacgatgagtgctaagtgttggaggggttccacccttcagtgctggagttaacgcaataagcactccgcctggggagtacggccgcaaggctgaaactcaaaggaattgacggggacccgcacaagcggtggagcatgtggtttaattcgaagcaacgcgaagaaccttaccaggtcttgacatcccgacgaccgctctagagatagagtttttcttcggaacgtcggtgacaggtggtgcatggtt">send to BLAST</a>\n+Otu04\t57\t11.4228%\tBacteria\tFirmicutes\tBacilli\tBacillales\tStaphylococcaceae\tStaphylococcus\t<a target="_blank" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?DATABASE=nr&EXCLUDE_SEQ_UNCULT=yes&FILTER=L&FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&SERVICE=megablast&PAGE=Nucleotides&CMD=Web&QUERY=cacgccgtaaacgatgagtgctaagtgttagggggtttccgccccttagtgctgcagctaacgcattaagcactccgcctggggagtacgaccgcaaggttgaaactcaaaggaattgacggggacccgcacaagcggtggagcatgtggtttaattcgaagcaacgcgaagaaccttaccaaatcttgacatcctttgaccgctctagagatagagtcttccccttcgggggacaaagtgacaggtggtgcatggtt">send to BLAST</a>\n+Otu05\t42\t8.41683%\tBacteria\tProteobacteria\tGammaproteobacteria\tPseudomonadales\tMoraxellaceae\tMoraxella\t<a target="_blank" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?DATABASE=nr&EXCLUDE_SEQ_UNCULT=yes&FILTER=L&FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&SERVICE=megablast&PAGE=Nucleotides&CMD=Web&QUERY=cacgccgtaaacgatgtctaccagtcgttgggtcttttaaaggcttagtgacgcagttaacgcgataagtagaccgcctggggagtacggccgcaaggttaaaactcaaatgaattgacgggggcccgcacaagcggtggagcatgtggtttaattcgatgcaacgcgaagaaccttacctggtcttgacatagtgagagtcttgcagagatgcgagagtgcctttgggaattcacatacaggtgctgcatggct">send to BLAST</a>\n+Otu06\t31\t6.21242%\tBacteria\tActinobacteria\tActinobacteria\tCorynebacteriales\tCorynebacteriaceae\tCorynebacterium_1\t<a target="_blank" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?DATABASE=nr&EXCLUDE_SEQ_UNCULT=yes&FILTER=L&FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&SERVICE=megablast&PAGE=Nucleotides&CMD=Web&QUERY=catgccgtaaacggtgggcgctaggtgtgagggtctttctacgactttcgtgccgtagctaacgcattaagcgccccgcctggggagtacgaccgcaaggttgaaactcaaaggaattgacggggacccgcacaagcggcggagcatgtggattaattcgatgcaacgcgaagaaccttacctgggcttgacatacatcagatcgctgcagagatgtagtttccctttgtggttggtgtacaggtggtgcatggtt">send to BLAST</a>\n+Otu07\t29\t5.81162%\tBacteria\tActinobacteria\tActinobacteria\tCorynebacteriales\tCorynebacteriaceae\tCorynebacterium_1\t<a target="_blank" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?DATABASE=nr&EXCLUDE_SEQ_UNCULT=yes&FILTER=L&FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&SERVICE=megablast&PAGE=Nucleotides&CMD=Web&QUERY=catgccgtaaacggtgggcgctaggtgtaggggccttttggggtttctgtgccgtagctaacgcattaagcgccccgcctggggagtacggccgcaaggctaaaactcaaaggaattgacgggggcccgc'..b'obacteria\tGammaproteobacteria\tPseudomonadales\tMoraxellaceae\tMoraxella\t<a target="_blank" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?DATABASE=nr&EXCLUDE_SEQ_UNCULT=yes&FILTER=L&FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&SERVICE=megablast&PAGE=Nucleotides&CMD=Web&QUERY=cacgccgtaaacgatgtctaccagtcgttgggtcttttaaagacttagtgacgcagttaacgcaataagtagaccgcctggggagtacggccgcaaggttaaaactcaaatgaattgacgggggcccgcacaagcggtggagcatgtggtttaattcgatgcaacgcgaagaaccttacctggtcttgacatatctagaatcctgcagagatgcgggagtgccttcgggaattagaatacaggtgctgcatggct">send to BLAST</a>\n+Otu41\t1\t0.200401%\tBacteria\tCyanobacteria\tunclassified\tunclassified\tunclassified\tunclassified\t<a target="_blank" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?DATABASE=nr&EXCLUDE_SEQ_UNCULT=yes&FILTER=L&FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&SERVICE=megablast&PAGE=Nucleotides&CMD=Web&QUERY=ctagccgtaaacgatggatactaggcgctgcgcgtatcgacccgtgcagtgctgtagctaacgcgttaagtatcccgcctggggagtacgttcgcaagaatgaaactcaaaggaattgacgggggcccgcacaagcggtggagcatgtggtttaattcgatgcaaagcgaagaaccttaccagggcttgacatgccgcgaatcctcttgaaagagaggggtgccttcgggaacgcggacacaggtggtgcatggct">send to BLAST</a>\n+Otu42\t1\t0.200401%\tBacteria\tFirmicutes\tNegativicutes\tSelenomonadales\tVeillonellaceae\tDialister\t<a target="_blank" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?DATABASE=nr&EXCLUDE_SEQ_UNCULT=yes&FILTER=L&FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&SERVICE=megablast&PAGE=Nucleotides&CMD=Web&QUERY=cacgccgtaaacgatggatactaggtgtaggaggtatcgacccctcctgtgccggagttaacgcaataagtatcccgcctgggaagtacgatcgcaagattaaaactcaaaggaattgacgggggcccgcacaagcggtggagtatgtggtttaattcgacgcaacgcgaagaaccttaccaggtcttgacattgatcgcgatctgcagaaatgcggagttcttcttcggaagacgagaaaacaggtggtgcacggct">send to BLAST</a>\n+Otu43\t1\t0.200401%\tBacteria\tFirmicutes\tBacilli\tLactobacillales\tStreptococcaceae\tStreptococcus\t<a target="_blank" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?DATABASE=nr&EXCLUDE_SEQ_UNCULT=yes&FILTER=L&FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&SERVICE=megablast&PAGE=Nucleotides&CMD=Web&QUERY=cacgccgtaaacgatgagtgctaggtgttggatcctttccgggattcagtgccgcagctaacgcattaagcactccgcctggggagtacgaccgcaaggttgaaactcaaaggaattgacgggggcccgcacaagcggtggagcatgtggtttaattcgaagcaacgcgaagaaccttaccaggtcttgacatcccgatgctatttctagagatagaaagttacttcggtacatcggtgacaggtggtgcatggtt">send to BLAST</a>\n+Otu44\t1\t0.200401%\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tunclassified\t<a target="_blank" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?DATABASE=nr&EXCLUDE_SEQ_UNCULT=yes&FILTER=L&FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&SERVICE=megablast&PAGE=Nucleotides&CMD=Web&QUERY=cacgcggtaaacgatgaatactaggtgtcgggggacatagtctttcggtgccgccgctaacgcattaagtattccacctggggagtacgttcgcaagaatgaaactcaaaggaattgacggggacccgcacaagcggtggagcatgtggtttaattcgaagcaacgcgaagaaccttaccaagtcttgacataccgttgacggttccgtaatggggactttccttcgggacaacggatacaggtggtgcatggtt">send to BLAST</a>\n+Otu45\t1\t0.200401%\tBacteria\tProteobacteria\tBetaproteobacteria\tNeisseriales\tNeisseriaceae\tEikenella\t<a target="_blank" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?DATABASE=nr&EXCLUDE_SEQ_UNCULT=yes&FILTER=L&FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&SERVICE=megablast&PAGE=Nucleotides&CMD=Web&QUERY=cacgccctaaacgatgtcgattagctgttgggcaacttgattgcttagtagcgtagctaacgcgtgaaatcgaccgcctggggagtacggtcgcaagattaaaactcaaaggaattgacggggacccgcacaagcggtggatgatgtggattaattcgatgcaacgcgaagaaccttacctggtcttgacatgtacggaacctttcagagacggaagggtgccttcgggagccgtaacacaggtgctgcatggct">send to BLAST</a>\n+Otu46\t1\t0.200401%\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tPrevotellaceae\tPrevotella\t<a target="_blank" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?DATABASE=nr&EXCLUDE_SEQ_UNCULT=yes&FILTER=L&FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&SERVICE=megablast&PAGE=Nucleotides&CMD=Web&QUERY=cgcacagtaaacgatggatgcccgctgttagcgcctggcgttagcggctaagcgaaagcattaagcatcccacctggggagtacgccggcaacggtgaaactcaaaggaattgacgggggcccgcacaagcggaggaacatgtggtttaattcgatgatacgcgaggaaccttacccgggcttgaattgcagaggaattatttagagataaatatgcccttcggggtctctgtgaaggtgctgcatggtt">send to BLAST</a>\n' |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/otutable_without_blast.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/otutable_without_blast.tsv Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,47 @@ +OTU Size Perc Kingdom Phylum Class Order Family Genus +Otu01 89 17.8357% Bacteria Firmicutes Bacilli Lactobacillales Streptococcaceae Streptococcus +Otu02 67 13.4269% Bacteria Firmicutes Bacilli Lactobacillales Carnobacteriaceae Dolosigranulum +Otu03 66 13.2265% Bacteria Firmicutes Bacilli Lactobacillales Aerococcaceae Abiotrophia +Otu04 57 11.4228% Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus +Otu05 42 8.41683% Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Moraxella +Otu06 31 6.21242% Bacteria Actinobacteria Actinobacteria Corynebacteriales Corynebacteriaceae Corynebacterium_1 +Otu07 29 5.81162% Bacteria Actinobacteria Actinobacteria Corynebacteriales Corynebacteriaceae Corynebacterium_1 +Otu08 28 5.61122% Bacteria Firmicutes Negativicutes Selenomonadales Veillonellaceae Veillonella +Otu09 14 2.80561% Bacteria Actinobacteria Actinobacteria Corynebacteriales Corynebacteriaceae Corynebacterium_1 +Otu10 11 2.20441% Bacteria Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Prevotella_7 +Otu11 5 1.002% Bacteria Proteobacteria Betaproteobacteria Neisseriales Neisseriaceae unclassified +Otu12 5 1.002% Bacteria Actinobacteria Actinobacteria Corynebacteriales Corynebacteriaceae Corynebacterium_1 +Otu13 5 1.002% Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Stomatobaculum +Otu14 5 1.002% Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia-Shigella +Otu15 4 0.801603% Bacteria Actinobacteria Actinobacteria unclassified unclassified unclassified +Otu16 4 0.801603% Bacteria Proteobacteria Betaproteobacteria Neisseriales Neisseriaceae Neisseria +Otu17 3 0.601202% Bacteria Proteobacteria Betaproteobacteria Neisseriales Neisseriaceae unclassified +Otu18 2 0.400802% Bacteria Proteobacteria Gammaproteobacteria unclassified unclassified unclassified +Otu19 2 0.400802% Bacteria Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae Tepidimonas +Otu20 2 0.400802% Bacteria Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae Aquabacterium +Otu21 2 0.400802% Bacteria Firmicutes Negativicutes Selenomonadales Veillonellaceae Selenomonas +Otu22 2 0.400802% Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnoanaerobaculum +Otu23 1 0.200401% Bacteria Actinobacteria Actinobacteria Bifidobacteriales Bifidobacteriaceae Scardovia +Otu24 1 0.200401% Bacteria Deinococcus-Thermus Deinococci Deinococcales Deinococcaceae Deinococcus +Otu25 1 0.200401% Bacteria Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Prevotella +Otu26 1 0.200401% Bacteria Actinobacteria Coriobacteriia Coriobacteriales Coriobacteriaceae Atopobium +Otu27 1 0.200401% Bacteria Actinobacteria Actinobacteria Corynebacteriales Corynebacteriaceae Corynebacterium_1 +Otu28 1 0.200401% Bacteria Firmicutes Bacilli Bacillales Listeriaceae Listeria +Otu29 1 0.200401% Bacteria Actinobacteria Coriobacteriia Coriobacteriales Coriobacteriaceae Olsenella +Otu30 1 0.200401% Bacteria Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Prevotella_7 +Otu31 1 0.200401% Bacteria Firmicutes Clostridia Clostridiales Family_XIII Mogibacterium +Otu32 1 0.200401% Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Oribacterium +Otu33 1 0.200401% Bacteria Firmicutes Clostridia Clostridiales Family_XI Anaerococcus +Otu34 1 0.200401% Bacteria Firmicutes Bacilli Lactobacillales Streptococcaceae Streptococcus +Otu35 1 0.200401% Bacteria Firmicutes Clostridia Clostridiales Family_XI Peptoniphilus +Otu36 1 0.200401% Bacteria Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Prevotella_6 +Otu37 1 0.200401% Bacteria Actinobacteria Actinobacteria Micrococcales Micrococcaceae Kocuria +Otu38 1 0.200401% Bacteria Firmicutes Bacilli Lactobacillales Carnobacteriaceae Granulicatella +Otu39 1 0.200401% Bacteria Actinobacteria Actinobacteria Micrococcales Micrococcaceae Rothia +Otu40 1 0.200401% Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Moraxella +Otu41 1 0.200401% Bacteria Cyanobacteria unclassified unclassified unclassified unclassified +Otu42 1 0.200401% Bacteria Firmicutes Negativicutes Selenomonadales Veillonellaceae Dialister +Otu43 1 0.200401% Bacteria Firmicutes Bacilli Lactobacillales Streptococcaceae Streptococcus +Otu44 1 0.200401% Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae unclassified +Otu45 1 0.200401% Bacteria Proteobacteria Betaproteobacteria Neisseriales Neisseriaceae Eikenella +Otu46 1 0.200401% Bacteria Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Prevotella |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/recovered.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/recovered.fasta Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,16 @@ +>read1 +ACTG +>read2 +ACTG +>read3 +ACTG +>read6 +ACTG +>read7 +ACTG +>read8 +ACTG +>read9 +ACTG +>read10 +ACTG |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/recovered.groups --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/recovered.groups Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,8 @@ +read1 group1 +read2 group1 +read3 group1 +read6 group2 +read7 group2 +read8 group2 +read9 group3 +read10 group3 |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/shared_dereplicated.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shared_dereplicated.tsv Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,7 @@ +label Group numOtus Otu0001 Otu0002 Otu0003 Otu0004 Otu0005 +unique sample1 5 10 5 8 0 7 +unique sample2 5 12 0 6 2 0 +unique negative-control 1 0 2 1 0 1 +0.03 sample1 4 19 17 21 6 +0.03 sample2 4 32 15 15 0 +0.03 negative-control 1 0 2 0 2 |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/shared_mock.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shared_mock.tsv Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,19 @@ +label Group numOtus Otu0001 Otu0002 Otu0003 Otu0004 Otu0005 +unique sample1_replicate1 5 15 4 9 2 1 +unique sample1_replicate2 5 11 8 12 0 7 +unique sample1_replicate3 5 5 4 3 3 13 +unique sample2_replicate1 5 21 0 13 2 1 +unique sample2_replicate2 5 5 4 3 2 0 +unique sample2_replicate3 5 10 4 3 2 0 +unique negative-control_replicate1 1 0 1 2 5 1 +unique negative-control_replicate2 2 1 4 1 0 1 +unique negative-control_replicate3 1 3 2 1 2 1 +0.03 sample1_replicate1 4 14 20 25 3 +0.03 sample1_replicate2 4 24 22 13 9 +0.03 sample1_replicate3 4 18 9 24 7 +0.03 sample2_replicate1 4 27 17 17 0 +0.03 sample2_replicate2 4 26 13 18 1 +0.03 sample2_replicate3 4 44 15 10 9 +0.03 negative-control_replicate1 1 0 2 2 1 +0.03 negative-control_replicate2 4 0 1 1 3 +0.03 negative-control_replicate3 2 2 3 0 1 |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/shared_tocorrect.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shared_tocorrect.tsv Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,19 @@ +label Group numOtus Otu0001 Otu0002 Otu0003 Otu0004 Otu0005 Otu0006 Otu0007 Otu0008 Otu0009 Otu0010 +0.03 DX01_replicate1 10 1025 7700 1333 1335 946 897 33 833 715 443 +0.03 DX01_replicate2 10 930 5150 1123 853 761 614 10 459 454 409 +0.03 DX01_replicate3 10 1769 11678 2015 1941 1909 1397 40 1020 1121 671 +0.03 DX02_replicate1 10 1025 7700 1333 1335 946 897 33 833 715 443 +0.03 DX02_replicate2 10 930 5150 1123 853 761 614 10 459 454 409 +0.03 DX02_replicate3 10 1769 11678 2015 1941 1909 1397 40 1020 1121 671 +0.03 NC_replicate1 10 3098 2 0 0 0 0 156 0 0 0 +0.03 NC_replicate2 10 11487 0 0 0 0 0 1205 0 0 0 +0.03 NC_replicate3 10 7509 1 0 0 0 0 874 0 0 398 +0.02 DX01_replicate1 9 1025 7700 1333 1335 946 897 23 833 715 +0.02 DX01_replicate2 9 930 5150 1123 853 761 614 10 459 454 +0.02 DX01_replicate3 9 1769 11678 2015 1941 1909 1397 30 1020 1121 +0.02 DX02_replicate1 9 1025 7700 1333 1335 946 897 23 833 715 +0.02 DX02_replicate2 9 930 5150 1123 853 761 614 10 459 454 +0.02 DX02_replicate3 9 1769 11678 2015 1941 1909 1397 30 1020 1121 +0.02 NC_replicate1 9 3098 2 0 0 0 0 156 0 0 +0.02 NC_replicate2 9 11487 0 0 0 0 0 1205 0 0 +0.02 NC_replicate3 9 7509 1 0 0 0 0 874 0 0 |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/shared_with_taxonomy.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shared_with_taxonomy.tsv Wed Dec 13 10:09:50 2017 -0500 |
| b |
| b'@@ -0,0 +1,335 @@\n+OTU\tF3D0\tF3D141\tF3D142\tF3D143\tF3D144\tF3D145\tF3D146\tF3D147\tF3D148\tKingdom\tPhylum\tClass\tOrder\tFamily\tGenus\n+Otu0001\t669\t481\t274\t345\t533\t742\t452\t1815\t1364\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0002\t526\t435\t269\t205\t401\t642\t300\t1513\t854\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0003\t430\t515\t163\t229\t352\t574\t406\t1212\t934\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0004\t380\t316\t217\t201\t319\t530\t291\t1215\t814\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0005\t327\t359\t284\t165\t268\t478\t226\t1218\t735\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0006\t421\t332\t160\t208\t298\t514\t246\t940\t591\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0007\t169\t210\t210\t120\t139\t367\t195\t565\t514\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tBacteroidaceae\tBacteroides\n+Otu0008\t19\t181\t49\t85\t276\t345\t202\t551\t444\tBacteria\tFirmicutes\tBacilli\tLactobacillales\tLactobacillaceae\tLactobacillus\n+Otu0009\t119\t112\t94\t47\t97\t212\t86\t533\t281\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0010\t166\t343\t83\t95\t38\t130\t66\t90\t561\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tRikenellaceae\tAlistipes\n+Otu0011\t28\t118\t58\t78\t110\t143\t89\t604\t311\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0012\t144\t134\t78\t78\t164\t242\t92\t271\t213\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0013\t79\t99\t51\t38\t106\t112\t35\t304\t268\tBacteria\tFirmicutes\tErysipelotrichia\tErysipelotrichales\tErysipelotrichaceae\tTuricibacter\n+Otu0014\t36\t66\t27\t28\t45\t93\t61\t409\t215\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0015\t300\t75\t12\t19\t28\t20\t32\t103\t43\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tBlautia\n+Otu0016\t62\t38\t24\t15\t43\t93\t32\t133\t113\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0017\t40\t46\t6\t11\t43\t35\t18\t160\t111\tBacteria\tFirmicutes\tBacilli\tLactobacillales\tLactobacillaceae\tLactobacillus\n+Otu0018\t35\t80\t28\t58\t13\t12\t73\t72\t91\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tunclassified\n+Otu0019\t52\t9\t107\t37\t14\t27\t4\t146\t18\tBacteria\tFirmicutes\tBacilli\tLactobacillales\tLactobacillaceae\tLactobacillus\n+Otu0020\t25\t51\t11\t2\t11\t15\t14\t102\t164\tBacteria\tunclassified\tunclassified\tunclassified\tunclassified\tunclassified\n+Otu0021\t2\t58\t11\t38\t33\t41\t98\t39\t10\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tunclassified\n+Otu0022\t149\t41\t8\t13\t22\t11\t22\t24\t26\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tBlautia\n+Otu0023\t61\t11\t20\t18\t18\t18\t25\t49\t88\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tBlautia\n+Otu0024\t90\t30\t9\t7\t10\t14\t26\t73\t45\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tBlautia\n+Otu0025\t0\t31\t25\t24\t16\t17\t5\t54\t87\tBacteria\tTenericutes\tMollicutes\tRF9\tunclassified\tunclassified\n+Otu0026\t107\t15\t6\t2\t7\t7\t43\t22\t50\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tunclassified\n+Otu0027\t24\t56\t10\t24\t9\t18\t23\t49\t44\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tunclassified\n+Otu0028\t0\t16\t8\t3\t18\t11\t35\t80\t58\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tBlautia\n+Otu0029\t29\t42\t4\t33\t2\t12\t29\t20\t51\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tunclassified\n+Otu0030\t50\t3\t14\t13\t13\t10\t43\t53\t21\tBacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\tunclassified\n+Otu0031\t23\t16\t27\t11\t21\t5\t3\t30\t69\tBacteria\tActinobacteria\tActinobacteria\tBifidobacteriales\tBifidobacteriaceae\tBifidobacterium\n+Otu0032\t121\t4\t3\t2\t6\t14\t1\t22\t30\tBacteria\tFirmicutes\tClostridia\tClostridiales\tClostridiaceae_1\tClostridium_sensu_stricto_1\n+Otu0033\t27\t23\t11\t15\t5\t5\t30\t41\t46\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tunclassified\n+Otu0034\t74\t21\t6\t11\t15\t12\t21\t11\t9\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tunclassified\n+Otu0035\t60\t4\t5\t2\t5\t5\t4\t40\t52\tBacteria\tTenericutes\tMollicutes\tRF9\tunclassified\tunclassified\n+Otu0036\t58'..b'a\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0295\t1\t0\t0\t0\t0\t0\t0\t0\t0\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tBlautia\n+Otu0296\t1\t0\t0\t0\t0\t0\t0\t0\t0\tBacteria\tProteobacteria\tAlphaproteobacteria\tRickettsiales\tmitochondria\tunclassified\n+Otu0297\t1\t0\t0\t0\t0\t0\t0\t0\t0\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tunclassified\n+Otu0298\t0\t0\t0\t0\t0\t0\t0\t0\t1\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tunclassified\n+Otu0299\t0\t1\t0\t0\t0\t0\t0\t0\t0\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0300\t0\t0\t0\t0\t0\t0\t0\t1\t0\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0301\t0\t0\t0\t0\t0\t0\t1\t0\t0\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0302\t0\t0\t0\t0\t0\t0\t1\t0\t0\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0303\t0\t0\t0\t0\t0\t0\t1\t0\t0\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tunclassified\n+Otu0304\t0\t0\t0\t0\t0\t0\t1\t0\t0\tBacteria\tFirmicutes\tunclassified\tunclassified\tunclassified\tunclassified\n+Otu0305\t0\t0\t0\t0\t0\t0\t1\t0\t0\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tunclassified\n+Otu0306\t0\t0\t0\t0\t0\t0\t0\t1\t0\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0307\t0\t0\t0\t0\t0\t0\t0\t1\t0\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0308\t0\t0\t0\t0\t0\t0\t0\t1\t0\tBacteria\tFirmicutes\tBacilli\tLactobacillales\tLactobacillaceae\tunclassified\n+Otu0309\t0\t0\t0\t0\t0\t0\t1\t0\t0\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tunclassified\n+Otu0310\t0\t0\t0\t0\t0\t0\t0\t1\t0\tBacteria\tunclassified\tunclassified\tunclassified\tunclassified\tunclassified\n+Otu0311\t0\t0\t0\t0\t0\t0\t0\t1\t0\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0312\t0\t0\t0\t0\t0\t0\t0\t1\t0\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tBlautia\n+Otu0313\t0\t0\t0\t0\t0\t0\t0\t1\t0\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0314\t0\t0\t0\t0\t0\t0\t0\t1\t0\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tunclassified\n+Otu0315\t0\t0\t0\t0\t0\t0\t0\t1\t0\tBacteria\tFirmicutes\tClostridia\tClostridiales\tEubacteriaceae\tAnaerofustis\n+Otu0316\t0\t0\t0\t0\t0\t0\t0\t1\t0\tBacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\tAnaerotruncus\n+Otu0317\t0\t0\t0\t0\t0\t0\t0\t1\t0\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0318\t0\t0\t0\t0\t0\t1\t0\t0\t0\tBacteria\tFirmicutes\tBacilli\tunclassified\tunclassified\tunclassified\n+Otu0319\t0\t0\t0\t0\t1\t0\t0\t0\t0\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tBacteroidaceae\tBacteroides\n+Otu0320\t0\t0\t0\t0\t1\t0\t0\t0\t0\tBacteria\tBacteroidetes\tFlavobacteriia\tFlavobacteriales\tCryomorphaceae\tFluviicola\n+Otu0321\t0\t0\t0\t0\t1\t0\t0\t0\t0\tBacteria\tunclassified\tunclassified\tunclassified\tunclassified\tunclassified\n+Otu0322\t0\t0\t0\t0\t0\t1\t0\t0\t0\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tunclassified\n+Otu0323\t0\t0\t0\t0\t0\t1\t0\t0\t0\tBacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\tOscillibacter\n+Otu0324\t0\t0\t0\t0\t0\t1\t0\t0\t0\tBacteria\tFirmicutes\tBacilli\tunclassified\tunclassified\tunclassified\n+Otu0325\t0\t0\t0\t0\t0\t1\t0\t0\t0\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0326\t0\t0\t0\t0\t0\t1\t0\t0\t0\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tunclassified\n+Otu0327\t0\t0\t0\t0\t0\t0\t0\t1\t0\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tunclassified\n+Otu0328\t0\t0\t0\t0\t0\t1\t0\t0\t0\tBacteria\tunclassified\tunclassified\tunclassified\tunclassified\tunclassified\n+Otu0329\t0\t0\t0\t0\t0\t1\t0\t0\t0\tBacteria\tFirmicutes\tBacilli\tunclassified\tunclassified\tunclassified\n+Otu0330\t0\t0\t0\t0\t0\t1\t0\t0\t0\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0331\t0\t0\t0\t0\t0\t1\t0\t0\t0\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0332\t0\t0\t0\t0\t0\t1\t0\t0\t0\tBacteria\tFirmicutes\tBacilli\tBacillales\tListeriaceae\tListeria\n+Otu0333\t0\t0\t0\t0\t0\t1\t0\t0\t0\tBacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tS24-7\tunclassified\n+Otu0334\t0\t0\t0\t0\t0\t1\t0\t0\t0\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tMarvinbryantia\n' |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/summarylog1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarylog1.txt Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,50 @@ +Linux version + +Using ReadLine + +Running 64Bit Version + +mothur v.1.36.1 +Last updated: 7/27/2015 + +by +Patrick D. Schloss + +Department of Microbiology & Immunology +University of Michigan +pschloss@umich.edu +http://www.mothur.org + +When using, please cite: +Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41. + +Distributed under the GNU General Public License + +Type 'help()' for information on the commands that are available + +Type 'quit()' to exit program +Interactive Mode + + +mothur > summary.seqs(fasta=fasta.dat,processors=1) + +Using 1 processors. + + Start End NBases Ambigs Polymer NumSeqs +Minimum: 1 297 297 0 4 1 +2.5%-tile: 1 299 299 0 4 16 +25%-tile: 1 304 304 0 5 151 +Median: 1 305 305 0 5 301 +75%-tile: 1 305 305 0 5 451 +97.5%-tile: 1 307 307 0 5 586 +Maximum: 1 312 312 0 6 600 +Mean: 1 304.715 304.715 0 4.94833 +# of Seqs: 600 + +Output File Names: +fasta.summary + +It took 0 secs to summarize 600 sequences. +quit + +mothur > quit |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/summarylog2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarylog2.txt Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,50 @@ +Linux version + +Using ReadLine + +Running 64Bit Version + +mothur v.1.36.1 +Last updated: 7/27/2015 + +by +Patrick D. Schloss + +Department of Microbiology & Immunology +University of Michigan +pschloss@umich.edu +http://www.mothur.org + +When using, please cite: +Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41. + +Distributed under the GNU General Public License + +Type 'help()' for information on the commands that are available + +Type 'quit()' to exit program +Interactive Mode + + +mothur > summary.seqs(fasta=fasta.dat,processors=1) + +Using 1 processors. + + Start End NBases Ambigs Polymer NumSeqs +Minimum: 1 249 249 0 4 1 +2.5%-tile: 1 250 250 0 4 14 +25%-tile: 1 255 255 0 5 137 +Median: 1 256 256 0 5 273 +75%-tile: 1 256 256 0 5 409 +97.5%-tile: 1 258 258 0 5 532 +Maximum: 1 263 263 0 6 545 +Mean: 1 255.739 255.739 0 4.94679 +# of Seqs: 545 + +Output File Names: +fasta.summary + +It took 0 secs to summarize 545 sequences. +quit + +mothur > quit |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/summarylog3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarylog3.txt Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,51 @@ +Linux version + +Using ReadLine + +Running 64Bit Version + +mothur v.1.36.1 +Last updated: 7/27/2015 + +by +Patrick D. Schloss + +Department of Microbiology & Immunology +University of Michigan +pschloss@umich.edu +http://www.mothur.org + +When using, please cite: +Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41. + +Distributed under the GNU General Public License + +Type 'help()' for information on the commands that are available + +Type 'quit()' to exit program +Interactive Mode + + +mothur > summary.seqs(fasta=fasta.dat,name=name.dat,processors=1) + +Using 1 processors. + + Start End NBases Ambigs Polymer NumSeqs +Minimum: 2943 11738 249 0 4 1 +2.5%-tile: 2943 11738 250 0 4 14 +25%-tile: 2943 11738 255 0 5 135 +Median: 2943 11738 256 0 5 269 +75%-tile: 2943 11738 256 0 5 403 +97.5%-tile: 2943 11738 258 0 5 524 +Maximum: 2943 11738 260 0 6 537 +Mean: 2943 11738 255.723 0 4.94786 +# of unique seqs: 158 +total # of seqs: 537 + +Output File Names: +fasta.summary + +It took 0 secs to summarize 537 sequences. +quit + +mothur > quit |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/test-out.count_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-out.count_table Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,9 @@ +Representative_Sequence total F3D0 F3D141 F3D142 F3D143 F3D144 F3D145 F3D146 F3D147 F3D148 +M00967_43_000000000-A3JHG_1_1101_18327_1699 6 2 0 0 0 0 0 1 3 0 +M00967_43_000000000-A3JHG_1_1101_14069_1827 3524 370 257 142 176 298 363 229 958 731 +M00967_43_000000000-A3JHG_1_1101_18044_1900 20 1 1 0 0 1 0 0 9 8 +M00967_43_000000000-A3JHG_1_1101_13234_1983 3874 425 340 205 153 294 475 233 1114 635 +M00967_43_000000000-A3JHG_1_1101_16780_2259 69 13 1 7 3 4 3 16 17 5 +M00967_43_000000000-A3JHG_1_1101_17674_2779 3256 265 301 230 136 216 390 178 967 573 +M00967_43_000000000-A3JHG_1_1101_18089_2781 92 44 4 0 1 3 2 12 10 16 +total 10841 1120 904 584 469 816 1233 669 3078 1968 |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/test.count_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.count_table Wed Dec 13 10:09:50 2017 -0500 |
| b |
| @@ -0,0 +1,8 @@ +Representative_Sequence total F3D0 F3D141 F3D142 F3D143 F3D144 F3D145 F3D146 F3D147 F3D148 +M00967_43_000000000-A3JHG_1_1101_18327_1699 6 2 0 0 0 0 0 1 3 0 +M00967_43_000000000-A3JHG_1_1101_14069_1827 3524 370 257 142 176 298 363 229 958 731 +M00967_43_000000000-A3JHG_1_1101_18044_1900 20 1 1 0 0 1 0 0 9 8 +M00967_43_000000000-A3JHG_1_1101_13234_1983 3874 425 340 205 153 294 475 233 1114 635 +M00967_43_000000000-A3JHG_1_1101_16780_2259 69 13 1 7 3 4 3 16 17 5 +M00967_43_000000000-A3JHG_1_1101_17674_2779 3256 265 301 230 136 216 390 178 967 573 +M00967_43_000000000-A3JHG_1_1101_18089_2781 92 44 4 0 1 3 2 12 10 16 |
| b |
| diff -r 000000000000 -r 607c5e7e0a64 test-data/test2.count_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.count_table Wed Dec 13 10:09:50 2017 -0500 |
| b |
| b'@@ -0,0 +1,17404 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