| Previous changeset 1:7332408e1f37 (2017-09-05) Next changeset 3:22cac0572d4c (2018-04-06) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3 |
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modified:
fastq.info.xml macros.xml |
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added:
test-data/Fasting_Example1.scrap.sff test-data/amazon.an.0.03.pearson.otu.corr test-data/amazon.otus.accnos test-data/esophagus.fn.shared test-data/samplebiom.biom1 test-data/stool_small.count_table test-data/stool_small.denovo.vsearch.accnos test-data/stool_small.names test-data/stool_small.unique.fasta test-data/stool_small.vsearch.chimeras |
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| diff -r 7332408e1f37 -r 1aa945e00ef2 fastq.info.xml --- a/fastq.info.xml Tue Sep 05 16:52:35 2017 -0400 +++ b/fastq.info.xml Tue Mar 20 22:01:25 2018 -0400 |
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| b'@@ -7,60 +7,65 @@\n <expand macro="stdio"/>\n <expand macro="version_command"/>\n <command><![CDATA[\n- @SHELL_OPTIONS@\n+@SHELL_OPTIONS@\n \n- ## create symlinks to input datasets\n- ln -s "$fastq" fastq.dat &&\n- #if $oligo.add == "yes":\n- ln -s "$oligo.oligos" oligo.oligos.dat &&\n- #end if\n+## create symlinks to input datasets\n+ln -s \'$fastq\' fastq.dat &&\n+#if $oligo.add == "yes":\n+ ln -s \'$oligo.oligos\' oligo.oligos.dat &&\n+#end if\n \n- echo \'fastq.info(\n- fastq=fastq.dat,\n- pacbio=$pacbio,\n- format=$format\n- #if $oligo.add == "yes":\n- ,oligos=oligo.oligos.dat\n- ,bdiffs=$oligo.bdiffs\n- ,pdiffs=$oligo.pdiffs\n- ,tdiffs=$oligo.tdiffs\n- ,ldiffs=$oligo.ldiffs\n- ,sdiffs=$oligo.sdiffs\n- #end if\n- )\'\n- | sed \'s/ //g\' ## mothur trips over whitespace\n- | mothur\n- | tee mothur.out.log\n- ## rename some outputs\n- #if $oligo.add == "yes":\n- && mv fastq.scrap.fasta scrap.fasta\n- && mv fastq.scrap.qual scrap.qual\n- #end if\n+echo \'fastq.info(\n+ fastq=fastq.dat,\n+ pacbio=$pacbio,\n+ format=$format\n+ #if $oligo.add == "yes":\n+ ,oligos=oligo.oligos.dat\n+ ,bdiffs=$oligo.bdiffs\n+ ,pdiffs=$oligo.pdiffs\n+ ,tdiffs=$oligo.tdiffs\n+ ,ldiffs=$oligo.ldiffs\n+ ,sdiffs=$oligo.sdiffs\n+ #end if\n+)\'\n+| sed \'s/ //g\' ## mothur trips over whitespace\n+| mothur\n+| tee mothur.out.log\n+## rename some outputs\n+#if $oligo.add == "yes":\n+ && mv fastq.scrap.fasta scrap.fasta\n+ && mv fastq.scrap.qual scrap.qual\n+#end if\n ]]></command>\n <inputs>\n- <param name="fastq" type="data" format="fastq" label="fastq - Fastq Sequence file"/>\n- <param name="pacbio" type="boolean" truevalue="true" falsevalue="false" checked="false" label="pacbio - if set to true, quality scores of 0 will results in a corresponding base of N"/>\n- <param name="format" type="select" label="format of sequence">\n+ <param argument="fastq" type="data" format="fastq" label="fastq - Fastq Sequence file"/>\n+ <param argument="pacbio" type="boolean" truevalue="true" falsevalue="false" checked="false"\n+ label="pacbio - if set to true, quality scores of 0 will results in a corresponding base of N"/>\n+ <param argument="format" type="select" label="format of sequence">\n <option value="sanger" selected="true">sanger</option>\n <option value="solexa">solexa</option>\n <option value="illumina">illumina</option>\n <option value="illumina1.8+">illumina1.8+</option>\n </param>\n <conditional name="oligo">\n- <param name="add" type="select" label="Use oligos file?" help="a file that contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words "forward", "reverse", and "barcode" or it can start with a "#" to tell mothur to ignore that line of the oligos file.">\n+ <param name="add" type="select" label="Use oligos file?"\n+ help="a file that contain the sequences of the forward and reverse primers and barcodes and their sample identifier.\n+ Each line of the oligos file can start with the key words "forward", "reverse", and "barcode"\n+ or it can start with a "#" to tell mothur to ignore that line of the oligos file.">\n <option value="no">no</option>\n <option value="yes">yes</option>\n </param>\n <when value="yes">\n- <param name="oligos" type="data" format="mothur.oligos" label="oligos - barcodes and primers"/>\n- <param name="bdiffs" type="integer" value="0" '..b'c01" ftype="qual454"/>\n+ <output name="fasta_out" ftype="fasta">\n+ <assert_contents>\n+ <expand macro="test-fasta-format"/>\n+ </assert_contents>\n+ </output>\n+ <output name="qfile_out" ftype="qual454">\n+ <assert_contents>\n+ <expand macro="test-qfile-format"/>\n+ <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/>\n+ </assert_contents>\n+ </output>\n+ <output name="fastq_scrap_out" ftype="fastq">\n+ <assert_contents>\n+ <expand macro="test-fastq-format"/>\n+ <has_text text="@M00967_43_000000000-A3JHG_1_1101_19936_3208"/>\n+ </assert_contents>\n+ </output>\n+ <output name="fasta_scrap_out" ftype="fasta">\n+ <assert_contents>\n+ <expand macro="test-fasta-format"/>\n+ </assert_contents>\n+ </output>\n+ <output name="qfile_scrap_out" ftype="qual454">\n+ <assert_contents>\n+ <expand macro="test-qfile-format"/>\n+ <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/>\n+ </assert_contents>\n+ </output>\n+ <param name="savelog" value="true"/>\n <expand macro="logfile-test"/>\n </test>\n <test>\n <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/>\n <param name="pacbio" value="false"/>\n <param name="format" value="sanger"/>\n- <param name="add" value="yes"/>\n+ <param name="oligo|add" value="yes"/>\n <param name="oligos" value="HMPv5-v3_1368-1369.oligos"/>\n <param name="bdiffs" value="1"/>\n <param name="pdiffs" value="3"/>\n <param name="tdiffs" value="3"/>\n <param name="ldiffs" value="3"/>\n <param name="sdiffs" value="7"/>\n- <output name="fasta_out" md5="88c573d00181be6dd519a0c9599f8b0c"/>\n- <output name="qfile_out" md5="d382c496c583b1501666459757cabbe3"/>\n- <output name="fastq_scrap_out" md5="37a280b8af54af2a0a52b2eba1e58933"/>\n- <output name="fasta_scrap_out" md5="88c573d00181be6dd519a0c9599f8b0c"/>\n- <output name="qfile_scrap_out" md5="96c2f7ea3cf6336d50bef2c087280c01"/>\n+ <output name="fasta_out">\n+ <assert_contents>\n+ <expand macro="test-fasta-format"/>\n+ </assert_contents>\n+ </output>\n+ <output name="qfile_out">\n+ <assert_contents>\n+ <expand macro="test-qfile-format"/>\n+ <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/>\n+ </assert_contents>\n+ </output>\n+ <output name="fastq_scrap_out">\n+ <assert_contents>\n+ <expand macro="test-fastq-format"/>\n+ <has_text text="@M00967_43_000000000-A3JHG_1_1101_19936_3208"/>\n+ </assert_contents>\n+ </output>\n+ <output name="fasta_scrap_out">\n+ <assert_contents>\n+ <expand macro="test-fasta-format"/>\n+ </assert_contents>\n+ </output>\n+ <output name="qfile_scrap_out">\n+ <assert_contents>\n+ <expand macro="test-qfile-format"/>\n+ <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/>\n+ </assert_contents>\n+ </output>\n+ <param name="savelog" value="true"/>\n <expand macro="logfile-test"/>\n </test>\n </tests>\n- <help>\n-<![CDATA[\n+ <help><![CDATA[\n \n @MOTHUR_OVERVIEW@\n \n@@ -134,7 +197,7 @@\n \n \n .. _fastq.info: https://www.mothur.org/wiki/Fastq.info\n-]]>\n- </help>\n+\n+ ]]></help>\n <expand macro="citations"/>\n </tool>\n' |
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| diff -r 7332408e1f37 -r 1aa945e00ef2 macros.xml --- a/macros.xml Tue Sep 05 16:52:35 2017 -0400 +++ b/macros.xml Tue Mar 20 22:01:25 2018 -0400 |
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| b'@@ -1,11 +1,13 @@\n <macros>\n+ <token name="@WRAPPER_VERSION@">1.39.5</token>\n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="1.36.1">mothur</requirement>\n+ <requirement type="package" version="@WRAPPER_VERSION@">mothur</requirement>\n+ <yield/>\n </requirements>\n </xml>\n <xml name="version_command">\n- <version_command>mothur "#help()" | sed \'7q;d\' | cut -d" " -f2 </version_command>\n+ <version_command><![CDATA[ mothur "#help()" | sed \'7q;d\' | cut -d" " -f2 ]]></version_command>\n </xml>\n <xml name="stdio">\n <stdio>\n@@ -13,20 +15,10 @@\n <exit_code range="1:" level="fatal"/>\n </stdio>\n </xml>\n- <token name="@WRAPPER_VERSION@">1.36.1</token>\n <token name="@SHELL_OPTIONS@">set -o pipefail;</token>\n- <token name="@MOTHUR_OVERVIEW@">\n-<![CDATA[\n-\n-**Mothur Overview**\n \n-Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team\n-in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_.\n \n-.. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page\n-\n-]]>\n- </token>\n+ <!-- Input parameters -->\n <xml name="labeloptions">\n <options>\n <filter type="data_meta" ref="otu" key="labels"/>\n@@ -78,9 +70,70 @@\n <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>\n <yield/>\n </xml>\n+\n+ <!-- CLUSTERING -->\n+ <xml name="param-clustermethods">\n+ <param argument="method" type="select" label="Clustering Method">\n+ <option value="opti" selected="true">Opticlust method</option>\n+ <option value="furthest">Furthest neighbor</option>\n+ <option value="nearest">Nearest neighbor</option>\n+ <option value="average">Average neighbor</option>\n+ <yield/>\n+ </param>\n+ </xml>\n+ <xml name="option-vsearch-clustermethods">\n+ <option value="agc">Abundance-based greedy clustering (agc)(VSEARCH)</option>\n+ <option value="dgc">Distance-based greedy clustering (dgc)(VSEARCH)</option>\n+ </xml>\n+ <xml name="params-opticlust">\n+ <param argument="metric" type="select" label="metric - select the metric in the opticluster method"\n+ help="Options are Matthews correlation coefficient (mcc), sensitivity (sens), specificity (spec), true positives + true negatives (tptn),\n+ false positives + false negatives (fpfn), true positives (tp), true negative (tn), false positive (fp), false negative (fn), f1score (f1score),\n+ accuracy (accuracy), positive predictive value (ppv), negative predictive value (npv), false discovery rate (fdr). Default=mcc.">\n+ <option value="mcc" selected="true">Matthews correlation coefficient (mcc)</option>\n+ <option value="sens">Sensitivity</option>\n+ <option value="spec">specificity</option>\n+ <option value="tptn">true positives + true negatives</option>\n+ <option value="fpfn">false positives + false negatives</option>\n+ <option value="tp">true positives</option>\n+ <option value="tn">true negative</option>\n+ <option value="fp">false positive</option>\n+ <option value="fn">false negative</option>\n+ <option value="f1score">f1score</option>\n+ <option value="accuracy">accuracy</option>\n+ <option value="ppv">positive predictive value</option>\n+ <option value="npv">negative predictive value</option>\n+ <option value="fdr">false discovery rate</option>\n+ </param>\n+ <param argument="initialize" type="select" label="Initial randomization"\n+ help="singleton: each sequence is randomly assigned to its own OTU; oneotu: all sequences are assigned to one'..b'ng expression="^name\\tpound\\tdash\\tplus\\tequal\\tloop\\ttilde\\ttotal\\tnumseqs$"/>\n+ </xml>\n+ <xml name="test-alignreport-format">\n+ <has_line_matching expression="^QueryName\\tQueryLength\\tTemplateName\\tTemplateLength\\tSearchMethod\\tSearchScore\\tAlignmentMethod\\tQueryStart\\tQueryEnd\\tTemplateStart\\tTemplateEnd\\tPairwiseAlignmentLength\\tGapsInQuery\\tGapsInTemplate\\tLongestInsert\\tSimBtwnQuery&Template$"/>\n+ </xml>\n+ <xml name="test-axes-format">\n+ <has_line_matching expression="^group(\\taxis\\d+)+$"/>\n+ </xml>\n+ <xml name="test-chimera-format">\n+ <has_line_matching expression="Score\\tQuery\\tParentA\\tParentB\\tIdQM\\tIdQA\\tIdQB\\tIdAB\\tIdQT\\tLY\\tLN\\tLA\\tRY\\tRN\\tRA\\tDiv\\tYN"/>\n+ </xml>\n+ <xml name="test-column-format">\n+ <has_n_columns n="3"/>\n+ <has_line_matching expression="^[\\w\\d\\-]+\\t[\\w\\d\\-]+\\t[\\d\\.]+$"/>\n+ </xml>\n+ <xml name="test-contigsreport-format">\n+ <has_n_columns n="7"/>\n+ <has_line_matching expression="^Name\\tLength\\tOverlap_Length\\tOverlap_Start\\tOverlap_End\\tMisMatches\\tNum_Ns$"/>\n+ </xml>\n+ <xml name="test-count-format">\n+ <has_line_matching expression="^Representative_Sequence\\ttotal(\\t\\w+)*$"/>\n+ <has_line_matching expression="^\\w+(\\t\\d+)+(\\s)*$"/>\n+ </xml>\n+ <xml name="test-dist-format">\n+ <has_line_matching expression="^[ \\t]*\\d+$"/>\n+ <has_line_matching expression="^[\\w\\d\\-]+(\\t[\\d\\.]+)+\\s?$"/>\n+ </xml>\n+ <xml name="test-fasta-format">\n+ <has_line_matching expression="^>.+$"/>\n+ <has_line_matching expression="^[ACTGN-]+$"/>\n+ </xml>\n+ <xml name="test-fastq-format">\n+ <has_line_matching expression="^@.+$"/>\n+ <has_line_matching expression="^[ACTGN]+$"/>\n+ <has_line_matching expression="^\\+$"/>\n+ </xml>\n+ <xml name="test-group-format">\n+ <has_line_matching expression="^Representative_Sequence\\ttotal(\\t[\\w\\d\\-]+)+$"/>\n+ <has_line_matching expression="^[\\w\\d\\-]+(\\t\\d+)+$"/>\n+ </xml>\n+ <xml name="test-list-format">\n+ <has_line_matching expression="^label\\tnumOtus(\\tOtu\\d+)+$"/>\n+ <has_line_matching expression="^(unique|0\\.\\d+)\\t\\d+(\\t[\\w\\d\\-,]+)+$"/>\n+ </xml>\n+ <xml name="test-names-format">\n+ <has_line_matching expression="^[a-zA-Z0-9]+\\t[a-zA-Z0-9]+$"/>\n+ </xml>\n+ <xml name="test-qfile-format">\n+ <has_line_matching expression="^(\\d+ )+$"/>\n+ <has_line_matching expression="^>.+$"/>\n+ </xml>\n+ <xml name="test-rabund-format">\n+ <has_line_matching expression="^(unique|0\\.\\d+)(\\t\\d+\\.?\\d*)+$"/>\n+ </xml>\n+ <xml name="test-sabund-format">\n+ <has_line_matching expression="^(unique|0\\.\\d+)(\\t\\d+)+$"/>\n+ </xml>\n+ <xml name="test-sensspec-format">\n+ <has_n_columns n="14"/>\n+ <has_line_matching expression="^label\\tcutoff\\ttp\\ttn\\tfp\\tfn\\tsensitivity\\tspecificity\\tppv\\tnpv\\tfdr\\taccuracy\\t\\w+\\tf1score$"/>\n+ </xml>\n+ <xml name="test-shared-format">\n+ <has_line_matching expression="^label\\tGroup\\tnumOtus(\\t(Otu|rareOTUs|.*OTU.*)\\d+)+$"/>\n+ </xml>\n+ <xml name="test-taxonomy-format">\n+ <has_n_columns n="3"/>\n+ <has_line_matching expression="^OTU\\tSize\\tTaxonomy$"/>\n+ </xml>\n+ <xml name="test-taxsummary-format">\n+ <has_line_matching expression="^((taxlevel\\trankID\\ttaxon\\tdaughterlevels\\ttotal(\\t[\\w\\d\\-]+)*)|(taxonomy\\ttotal(\\t[\\w\\d]+)*))$"/>\n+ </xml>\n+ <!-- backmatter -->\n+ <token name="@MOTHUR_OVERVIEW@">\n+<![CDATA[\n+\n+**Mothur Overview**\n+\n+Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team\n+in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_.\n+\n+.. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page\n+\n+]]>\n+ </token>\n <xml name="citations">\n <citations>\n <citation type="doi">10.1128/AEM.01541-09</citation>\n' |
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| diff -r 7332408e1f37 -r 1aa945e00ef2 test-data/Fasting_Example1.scrap.sff |
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| Binary file test-data/Fasting_Example1.scrap.sff has changed |
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| diff -r 7332408e1f37 -r 1aa945e00ef2 test-data/amazon.an.0.03.pearson.otu.corr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.an.0.03.pearson.otu.corr Tue Mar 20 22:01:25 2018 -0400 |
| b |
| b'@@ -0,0 +1,3829 @@\n+OTUA\tOTUB\tpearsonCoef\tSignificance\n+Otu02\tOtu01\t-1.000000\t0.000000\n+Otu03\tOtu01\t1.000000\t0.000000\n+Otu03\tOtu02\t-1.000000\t0.000000\n+Otu04\tOtu01\t-1.000000\t0.000000\n+Otu04\tOtu02\t1.000000\t0.000000\n+Otu04\tOtu03\t-1.000000\t0.000000\n+Otu05\tOtu01\t-nan\t0.000000\n+Otu05\tOtu02\t-nan\t0.000000\n+Otu05\tOtu03\t-nan\t0.000000\n+Otu05\tOtu04\t-nan\t0.000000\n+Otu06\tOtu01\t1.000000\t0.000000\n+Otu06\tOtu02\t-1.000000\t0.000000\n+Otu06\tOtu03\t1.000000\t0.000000\n+Otu06\tOtu04\t-1.000000\t0.000000\n+Otu06\tOtu05\t-nan\t0.000000\n+Otu07\tOtu01\t1.000000\t0.000000\n+Otu07\tOtu02\t-1.000000\t0.000000\n+Otu07\tOtu03\t1.000000\t0.000000\n+Otu07\tOtu04\t-1.000000\t0.000000\n+Otu07\tOtu05\t-nan\t0.000000\n+Otu07\tOtu06\t1.000000\t0.000000\n+Otu08\tOtu01\t1.000000\t0.000000\n+Otu08\tOtu02\t-1.000000\t0.000000\n+Otu08\tOtu03\t1.000000\t0.000000\n+Otu08\tOtu04\t-1.000000\t0.000000\n+Otu08\tOtu05\t-nan\t0.000000\n+Otu08\tOtu06\t1.000000\t0.000000\n+Otu08\tOtu07\t1.000000\t0.000000\n+Otu09\tOtu01\t1.000000\t0.000000\n+Otu09\tOtu02\t-1.000000\t0.000000\n+Otu09\tOtu03\t1.000000\t0.000000\n+Otu09\tOtu04\t-1.000000\t0.000000\n+Otu09\tOtu05\t-nan\t0.000000\n+Otu09\tOtu06\t1.000000\t0.000000\n+Otu09\tOtu07\t1.000000\t0.000000\n+Otu09\tOtu08\t1.000000\t0.000000\n+Otu10\tOtu01\t1.000000\t0.000000\n+Otu10\tOtu02\t-1.000000\t0.000000\n+Otu10\tOtu03\t1.000000\t0.000000\n+Otu10\tOtu04\t-1.000000\t0.000000\n+Otu10\tOtu05\t-nan\t0.000000\n+Otu10\tOtu06\t1.000000\t0.000000\n+Otu10\tOtu07\t1.000000\t0.000000\n+Otu10\tOtu08\t1.000000\t0.000000\n+Otu10\tOtu09\t1.000000\t0.000000\n+Otu11\tOtu01\t1.000000\t0.000000\n+Otu11\tOtu02\t-1.000000\t0.000000\n+Otu11\tOtu03\t1.000000\t0.000000\n+Otu11\tOtu04\t-1.000000\t0.000000\n+Otu11\tOtu05\t-nan\t0.000000\n+Otu11\tOtu06\t1.000000\t0.000000\n+Otu11\tOtu07\t1.000000\t0.000000\n+Otu11\tOtu08\t1.000000\t0.000000\n+Otu11\tOtu09\t1.000000\t0.000000\n+Otu11\tOtu10\t1.000000\t0.000000\n+Otu12\tOtu01\t1.000000\t0.000000\n+Otu12\tOtu02\t-1.000000\t0.000000\n+Otu12\tOtu03\t1.000000\t0.000000\n+Otu12\tOtu04\t-1.000000\t0.000000\n+Otu12\tOtu05\t-nan\t0.000000\n+Otu12\tOtu06\t1.000000\t0.000000\n+Otu12\tOtu07\t1.000000\t0.000000\n+Otu12\tOtu08\t1.000000\t0.000000\n+Otu12\tOtu09\t1.000000\t0.000000\n+Otu12\tOtu10\t1.000000\t0.000000\n+Otu12\tOtu11\t1.000000\t0.000000\n+Otu13\tOtu01\t1.000000\t0.000000\n+Otu13\tOtu02\t-1.000000\t0.000000\n+Otu13\tOtu03\t1.000000\t0.000000\n+Otu13\tOtu04\t-1.000000\t0.000000\n+Otu13\tOtu05\t-nan\t0.000000\n+Otu13\tOtu06\t1.000000\t0.000000\n+Otu13\tOtu07\t1.000000\t0.000000\n+Otu13\tOtu08\t1.000000\t0.000000\n+Otu13\tOtu09\t1.000000\t0.000000\n+Otu13\tOtu10\t1.000000\t0.000000\n+Otu13\tOtu11\t1.000000\t0.000000\n+Otu13\tOtu12\t1.000000\t0.000000\n+Otu14\tOtu01\t1.000000\t0.000000\n+Otu14\tOtu02\t-1.000000\t0.000000\n+Otu14\tOtu03\t1.000000\t0.000000\n+Otu14\tOtu04\t-1.000000\t0.000000\n+Otu14\tOtu05\t-nan\t0.000000\n+Otu14\tOtu06\t1.000000\t0.000000\n+Otu14\tOtu07\t1.000000\t0.000000\n+Otu14\tOtu08\t1.000000\t0.000000\n+Otu14\tOtu09\t1.000000\t0.000000\n+Otu14\tOtu10\t1.000000\t0.000000\n+Otu14\tOtu11\t1.000000\t0.000000\n+Otu14\tOtu12\t1.000000\t0.000000\n+Otu14\tOtu13\t1.000000\t0.000000\n+Otu15\tOtu01\t1.000000\t0.000000\n+Otu15\tOtu02\t-1.000000\t0.000000\n+Otu15\tOtu03\t1.000000\t0.000000\n+Otu15\tOtu04\t-1.000000\t0.000000\n+Otu15\tOtu05\t-nan\t0.000000\n+Otu15\tOtu06\t1.000000\t0.000000\n+Otu15\tOtu07\t1.000000\t0.000000\n+Otu15\tOtu08\t1.000000\t0.000000\n+Otu15\tOtu09\t1.000000\t0.000000\n+Otu15\tOtu10\t1.000000\t0.000000\n+Otu15\tOtu11\t1.000000\t0.000000\n+Otu15\tOtu12\t1.000000\t0.000000\n+Otu15\tOtu13\t1.000000\t0.000000\n+Otu15\tOtu14\t1.000000\t0.000000\n+Otu16\tOtu01\t1.000000\t0.000000\n+Otu16\tOtu02\t-1.000000\t0.000000\n+Otu16\tOtu03\t1.000000\t0.000000\n+Otu16\tOtu04\t-1.000000\t0.000000\n+Otu16\tOtu05\t-nan\t0.000000\n+Otu16\tOtu06\t1.000000\t0.000000\n+Otu16\tOtu07\t1.000000\t0.000000\n+Otu16\tOtu08\t1.000000\t0.000000\n+Otu16\tOtu09\t1.000000\t0.000000\n+Otu16\tOtu10\t1.000000\t0.000000\n+Otu16\tOtu11\t1.000000\t0.000000\n+Otu16\tOtu12\t1.000000\t0.000000\n+Otu16\tOtu13\t1.000000\t0.000000\n+Otu16\tOtu14\t1.000000\t0.000000\n+Otu16\tOtu15\t1.000000\t0.000000\n+Otu17\tOtu01\t1.000000\t0.000000\n+Otu17\tOtu02\t-1.000000\t0.000000\n+Otu17\tOtu03\t1.000000\t0.000000\n+Otu17\tOtu04\t-1.000000\t0.000000\n+Otu17\tOtu05\t-nan\t0.000000\n+Otu17\tOtu06\t1.000000\t0.000000\n+Otu17\tOtu07\t1.000000\t0.000000\n+Otu17\tOtu08\t1.000000\t0.000000\n+Otu17\tOtu09'..b'tu46\t-1.000000\t0.000000\n+Otu87\tOtu47\t1.000000\t0.000000\n+Otu87\tOtu48\t1.000000\t0.000000\n+Otu87\tOtu49\t1.000000\t0.000000\n+Otu87\tOtu50\t1.000000\t0.000000\n+Otu87\tOtu51\t1.000000\t0.000000\n+Otu87\tOtu52\t1.000000\t0.000000\n+Otu87\tOtu53\t1.000000\t0.000000\n+Otu87\tOtu54\t1.000000\t0.000000\n+Otu87\tOtu55\t1.000000\t0.000000\n+Otu87\tOtu56\t1.000000\t0.000000\n+Otu87\tOtu57\t1.000000\t0.000000\n+Otu87\tOtu58\t1.000000\t0.000000\n+Otu87\tOtu59\t1.000000\t0.000000\n+Otu87\tOtu60\t1.000000\t0.000000\n+Otu87\tOtu61\t1.000000\t0.000000\n+Otu87\tOtu62\t1.000000\t0.000000\n+Otu87\tOtu63\t1.000000\t0.000000\n+Otu87\tOtu64\t1.000000\t0.000000\n+Otu87\tOtu65\t1.000000\t0.000000\n+Otu87\tOtu66\t1.000000\t0.000000\n+Otu87\tOtu67\t1.000000\t0.000000\n+Otu87\tOtu68\t1.000000\t0.000000\n+Otu87\tOtu69\t1.000000\t0.000000\n+Otu87\tOtu70\t1.000000\t0.000000\n+Otu87\tOtu71\t1.000000\t0.000000\n+Otu87\tOtu72\t1.000000\t0.000000\n+Otu87\tOtu73\t1.000000\t0.000000\n+Otu87\tOtu74\t1.000000\t0.000000\n+Otu87\tOtu75\t1.000000\t0.000000\n+Otu87\tOtu76\t1.000000\t0.000000\n+Otu87\tOtu77\t1.000000\t0.000000\n+Otu87\tOtu78\t1.000000\t0.000000\n+Otu87\tOtu79\t1.000000\t0.000000\n+Otu87\tOtu80\t1.000000\t0.000000\n+Otu87\tOtu81\t1.000000\t0.000000\n+Otu87\tOtu82\t1.000000\t0.000000\n+Otu87\tOtu83\t1.000000\t0.000000\n+Otu87\tOtu84\t1.000000\t0.000000\n+Otu87\tOtu85\t1.000000\t0.000000\n+Otu87\tOtu86\t1.000000\t0.000000\n+Otu88\tOtu01\t-1.000000\t0.000000\n+Otu88\tOtu02\t1.000000\t0.000000\n+Otu88\tOtu03\t-1.000000\t0.000000\n+Otu88\tOtu04\t1.000000\t0.000000\n+Otu88\tOtu05\t-nan\t0.000000\n+Otu88\tOtu06\t-1.000000\t0.000000\n+Otu88\tOtu07\t-1.000000\t0.000000\n+Otu88\tOtu08\t-1.000000\t0.000000\n+Otu88\tOtu09\t-1.000000\t0.000000\n+Otu88\tOtu10\t-1.000000\t0.000000\n+Otu88\tOtu11\t-1.000000\t0.000000\n+Otu88\tOtu12\t-1.000000\t0.000000\n+Otu88\tOtu13\t-1.000000\t0.000000\n+Otu88\tOtu14\t-1.000000\t0.000000\n+Otu88\tOtu15\t-1.000000\t0.000000\n+Otu88\tOtu16\t-1.000000\t0.000000\n+Otu88\tOtu17\t-1.000000\t0.000000\n+Otu88\tOtu18\t-1.000000\t0.000000\n+Otu88\tOtu19\t-1.000000\t0.000000\n+Otu88\tOtu20\t-1.000000\t0.000000\n+Otu88\tOtu21\t-1.000000\t0.000000\n+Otu88\tOtu22\t-1.000000\t0.000000\n+Otu88\tOtu23\t-1.000000\t0.000000\n+Otu88\tOtu24\t1.000000\t0.000000\n+Otu88\tOtu25\t-1.000000\t0.000000\n+Otu88\tOtu26\t-1.000000\t0.000000\n+Otu88\tOtu27\t-1.000000\t0.000000\n+Otu88\tOtu28\t-1.000000\t0.000000\n+Otu88\tOtu29\t-1.000000\t0.000000\n+Otu88\tOtu30\t-1.000000\t0.000000\n+Otu88\tOtu31\t-1.000000\t0.000000\n+Otu88\tOtu32\t-1.000000\t0.000000\n+Otu88\tOtu33\t-1.000000\t0.000000\n+Otu88\tOtu34\t-1.000000\t0.000000\n+Otu88\tOtu35\t-1.000000\t0.000000\n+Otu88\tOtu36\t-1.000000\t0.000000\n+Otu88\tOtu37\t-1.000000\t0.000000\n+Otu88\tOtu38\t-1.000000\t0.000000\n+Otu88\tOtu39\t-1.000000\t0.000000\n+Otu88\tOtu40\t-1.000000\t0.000000\n+Otu88\tOtu41\t-1.000000\t0.000000\n+Otu88\tOtu42\t-1.000000\t0.000000\n+Otu88\tOtu43\t-1.000000\t0.000000\n+Otu88\tOtu44\t-1.000000\t0.000000\n+Otu88\tOtu45\t-1.000000\t0.000000\n+Otu88\tOtu46\t-1.000000\t0.000000\n+Otu88\tOtu47\t1.000000\t0.000000\n+Otu88\tOtu48\t1.000000\t0.000000\n+Otu88\tOtu49\t1.000000\t0.000000\n+Otu88\tOtu50\t1.000000\t0.000000\n+Otu88\tOtu51\t1.000000\t0.000000\n+Otu88\tOtu52\t1.000000\t0.000000\n+Otu88\tOtu53\t1.000000\t0.000000\n+Otu88\tOtu54\t1.000000\t0.000000\n+Otu88\tOtu55\t1.000000\t0.000000\n+Otu88\tOtu56\t1.000000\t0.000000\n+Otu88\tOtu57\t1.000000\t0.000000\n+Otu88\tOtu58\t1.000000\t0.000000\n+Otu88\tOtu59\t1.000000\t0.000000\n+Otu88\tOtu60\t1.000000\t0.000000\n+Otu88\tOtu61\t1.000000\t0.000000\n+Otu88\tOtu62\t1.000000\t0.000000\n+Otu88\tOtu63\t1.000000\t0.000000\n+Otu88\tOtu64\t1.000000\t0.000000\n+Otu88\tOtu65\t1.000000\t0.000000\n+Otu88\tOtu66\t1.000000\t0.000000\n+Otu88\tOtu67\t1.000000\t0.000000\n+Otu88\tOtu68\t1.000000\t0.000000\n+Otu88\tOtu69\t1.000000\t0.000000\n+Otu88\tOtu70\t1.000000\t0.000000\n+Otu88\tOtu71\t1.000000\t0.000000\n+Otu88\tOtu72\t1.000000\t0.000000\n+Otu88\tOtu73\t1.000000\t0.000000\n+Otu88\tOtu74\t1.000000\t0.000000\n+Otu88\tOtu75\t1.000000\t0.000000\n+Otu88\tOtu76\t1.000000\t0.000000\n+Otu88\tOtu77\t1.000000\t0.000000\n+Otu88\tOtu78\t1.000000\t0.000000\n+Otu88\tOtu79\t1.000000\t0.000000\n+Otu88\tOtu80\t1.000000\t0.000000\n+Otu88\tOtu81\t1.000000\t0.000000\n+Otu88\tOtu82\t1.000000\t0.000000\n+Otu88\tOtu83\t1.000000\t0.000000\n+Otu88\tOtu84\t1.000000\t0.000000\n+Otu88\tOtu85\t1.000000\t0.000000\n+Otu88\tOtu86\t1.000000\t0.000000\n+Otu88\tOtu87\t1.000000\t0.000000\n' |
| b |
| diff -r 7332408e1f37 -r 1aa945e00ef2 test-data/amazon.otus.accnos --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.otus.accnos Tue Mar 20 22:01:25 2018 -0400 |
| b |
| @@ -0,0 +1,3 @@ +Otu01 +Otu17 +Otu42 |
| b |
| diff -r 7332408e1f37 -r 1aa945e00ef2 test-data/esophagus.fn.shared --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/esophagus.fn.shared Tue Mar 20 22:01:25 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ +unique B 593 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 5 1 1 1 3 1 1 1 1 1 1 4 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 4 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +unique C 593 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 5 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +unique D 593 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 30 1 1 8 3 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 5 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +0.03 B 87 12 17 16 14 1 2 39 1 1 18 8 6 1 1 2 5 1 7 3 1 12 3 6 2 1 1 1 3 1 2 1 1 1 2 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0.03 C 87 0 0 19 42 0 0 6 2 10 19 7 1 0 0 2 0 5 0 3 2 0 4 2 0 0 0 1 0 0 0 2 0 2 14 0 0 0 7 0 0 0 0 0 29 14 4 2 2 3 2 11 1 3 3 1 8 6 4 1 1 1 1 4 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0.03 D 87 0 2 3 10 0 2 103 2 0 15 1 0 0 1 5 2 1 5 0 0 1 0 0 0 0 3 6 7 1 1 1 0 1 3 0 0 0 1 0 0 1 0 3 0 0 0 1 0 0 0 0 0 1 0 1 0 4 0 0 0 0 0 0 0 0 2 1 3 2 2 1 3 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1 +0.05 B 74 12 23 34 14 3 47 1 1 8 6 1 1 2 5 1 3 2 12 3 2 1 1 4 1 2 1 1 1 2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0.05 C 74 14 2 38 42 0 12 2 10 7 1 0 0 2 0 5 3 2 3 4 0 0 1 29 0 0 2 0 2 14 0 0 0 7 0 0 0 0 4 2 2 2 11 1 3 3 1 8 4 1 1 1 1 4 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0.05 D 74 0 2 18 10 2 115 2 0 1 3 0 1 5 2 1 0 0 1 0 0 0 6 7 1 1 2 0 1 4 0 0 0 1 0 0 1 3 0 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 2 1 2 2 1 3 1 1 1 1 1 1 1 1 1 1 3 1 1 +0.10 B 58 50 37 14 52 2 1 8 6 1 1 3 5 1 2 3 2 1 1 2 1 1 1 2 1 2 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0.10 C 58 19 41 42 41 2 10 7 1 0 0 2 0 5 13 4 0 0 1 0 6 0 2 14 0 0 7 0 0 4 2 2 2 4 3 1 8 4 1 1 1 1 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0.10 D 58 5 18 10 124 2 0 1 3 0 1 9 2 1 0 0 0 0 6 1 2 0 1 4 0 1 1 0 0 0 1 1 0 1 0 1 0 0 0 0 1 0 0 0 2 1 2 2 3 1 1 1 1 1 1 1 1 3 1 |
| b |
| diff -r 7332408e1f37 -r 1aa945e00ef2 test-data/samplebiom.biom1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samplebiom.biom1 Tue Mar 20 22:01:25 2018 -0400 |
| [ |
| b'@@ -0,0 +1,8668 @@\n+{\n+ "id":"otu.dat-0.03",\n+ "format": "Biological Observation Matrix 0.9.1",\n+ "format_url": "http://biom-format.org",\n+ "type": "OTU table",\n+ "generated_by": "mothur1.36.1",\n+ "date": "Mon Jun 26 15:11:52 2017",\n+ "rows":[\n+ {"id":"Otu00001", "metadata":null},\n+ {"id":"Otu00002", "metadata":null},\n+ {"id":"Otu00003", "metadata":null},\n+ {"id":"Otu00004", "metadata":null},\n+ {"id":"Otu00005", "metadata":null},\n+ {"id":"Otu00006", "metadata":null},\n+ {"id":"Otu00007", "metadata":null},\n+ {"id":"Otu00008", "metadata":null},\n+ {"id":"Otu00009", "metadata":null},\n+ {"id":"Otu00010", "metadata":null},\n+ {"id":"Otu00011", "metadata":null},\n+ {"id":"Otu00012", "metadata":null},\n+ {"id":"Otu00013", "metadata":null},\n+ {"id":"Otu00014", "metadata":null},\n+ {"id":"Otu00015", "metadata":null},\n+ {"id":"Otu00016", "metadata":null},\n+ {"id":"Otu00017", "metadata":null},\n+ {"id":"Otu00018", "metadata":null},\n+ {"id":"Otu00019", "metadata":null},\n+ {"id":"Otu00020", "metadata":null},\n+ {"id":"Otu00021", "metadata":null},\n+ {"id":"Otu00022", "metadata":null},\n+ {"id":"Otu00023", "metadata":null},\n+ {"id":"Otu00024", "metadata":null},\n+ {"id":"Otu00025", "metadata":null},\n+ {"id":"Otu00026", "metadata":null},\n+ {"id":"Otu00027", "metadata":null},\n+ {"id":"Otu00028", "metadata":null},\n+ {"id":"Otu00029", "metadata":null},\n+ {"id":"Otu00030", "metadata":null},\n+ {"id":"Otu00031", "metadata":null},\n+ {"id":"Otu00032", "metadata":null},\n+ {"id":"Otu00033", "metadata":null},\n+ {"id":"Otu00034", "metadata":null},\n+ {"id":"Otu00035", "metadata":null},\n+ {"id":"Otu00036", "metadata":null},\n+ {"id":"Otu00037", "metadata":null},\n+ {"id":"Otu00038", "metadata":null},\n+ {"id":"Otu00039", "metadata":null},\n+ {"id":"Otu00040", "metadata":null},\n+ {"id":"Otu00041", "metadata":null},\n+ {"id":"Otu00042", "metadata":null},\n+ {"id":"Otu00043", "metadata":null},\n+ {"id":"Otu00044", "metadata":null},\n+ {"id":"Otu00045", "metadata":null},\n+ {"id":"Otu00046", "metadata":null},\n+ {"id":"Otu00047", "metadata":null},\n+ {"id":"Otu00048", "metadata":null},\n+ {"id":"Otu00049", "metadata":null},\n+ {"id":"Otu00050", "metadata":null},\n+ {"id":"Otu00051", "metadata":null},\n+ {"id":"Otu00052", "metadata":null},\n+ {"id":"Otu00053", "metadata":null},\n+ {"id":"Otu00054", "metadata":null},\n+ {"id":"Otu00055", "metadata":null},\n+ {"id":"Otu00056", "metadata":null},\n+ {"id":"Otu00057", "metadata":null},\n+ {"id":"Otu00058", "metadata":null},\n+ {"id":"Otu00059", "metadata":null},\n+ {"id":"Otu00060", "metadata":null},\n+ {"id":"Otu00061", "metadata":null},\n+ {"id":"Otu00062", "metadata":null},\n+ {"id":"Otu00063", "metadata":null},\n+ {"id":"Otu00064", "metadata":null},\n+ {"id":"Otu00065", "metadata":null},\n+ {"id":"Otu00066", "metadata":null},\n+ {"id":"Otu00067", "metadata":null},\n+ {"id":"Otu00068", "metadata":null},\n+ {"id":"Otu00069", "metadata":null},\n+ {"id":"Otu00070", "metadata":null},\n+ {"id":"Otu00071", "metadata":null},\n+ {"id":"Otu00072", "metadata":null},\n+ {"id":"Otu00073", "metadata":null},\n+ {"id":"Otu00074", "metadata":null},\n+ {"id":"Otu00075", "metadata":null},\n+ {"id":"Otu00076", "metadata":nul'..b' [3827,0,1],\n+ [3828,1,1],\n+ [3829,0,1],\n+ [3830,0,1],\n+ [3831,0,1],\n+ [3832,0,1],\n+ [3833,0,1],\n+ [3834,1,1],\n+ [3835,1,1],\n+ [3836,0,1],\n+ [3837,0,1],\n+ [3838,0,1],\n+ [3839,0,1],\n+ [3840,1,1],\n+ [3841,0,1],\n+ [3842,0,1],\n+ [3843,0,1],\n+ [3844,1,1],\n+ [3845,0,1],\n+ [3846,0,1],\n+ [3847,0,1],\n+ [3848,0,1],\n+ [3849,0,1],\n+ [3850,0,1],\n+ [3851,0,1],\n+ [3852,0,1],\n+ [3853,0,1],\n+ [3854,0,1],\n+ [3855,0,1],\n+ [3856,0,1],\n+ [3857,0,1],\n+ [3858,0,1],\n+ [3859,0,1],\n+ [3860,0,1],\n+ [3861,0,1],\n+ [3862,0,1],\n+ [3863,0,1],\n+ [3864,0,1],\n+ [3865,0,1],\n+ [3866,0,1],\n+ [3867,0,1],\n+ [3868,0,1],\n+ [3869,0,1],\n+ [3870,0,1],\n+ [3871,0,1],\n+ [3872,0,1],\n+ [3873,0,1],\n+ [3874,0,1],\n+ [3875,0,1],\n+ [3876,0,1],\n+ [3877,0,1],\n+ [3878,0,1],\n+ [3879,0,1],\n+ [3880,0,1],\n+ [3881,0,1],\n+ [3882,0,1],\n+ [3883,0,1],\n+ [3884,0,1],\n+ [3885,0,1],\n+ [3886,0,1],\n+ [3887,0,1],\n+ [3888,0,1],\n+ [3889,0,1],\n+ [3890,0,1],\n+ [3891,0,1],\n+ [3892,0,1],\n+ [3893,0,1],\n+ [3894,0,1],\n+ [3895,0,1],\n+ [3896,0,1],\n+ [3897,0,1],\n+ [3898,0,1],\n+ [3899,0,1],\n+ [3900,0,1],\n+ [3901,0,1],\n+ [3902,0,1],\n+ [3903,1,1],\n+ [3904,1,1],\n+ [3905,0,1],\n+ [3906,1,1],\n+ [3907,1,1],\n+ [3908,0,1],\n+ [3909,0,1],\n+ [3910,1,1],\n+ [3911,0,1],\n+ [3912,0,1],\n+ [3913,1,1],\n+ [3914,0,1],\n+ [3915,0,1],\n+ [3916,0,1],\n+ [3917,1,1],\n+ [3918,1,1],\n+ [3919,1,1],\n+ [3920,0,1],\n+ [3921,1,1],\n+ [3922,1,1],\n+ [3923,0,1],\n+ [3924,0,1],\n+ [3925,1,1],\n+ [3926,0,1],\n+ [3927,0,1],\n+ [3928,0,1],\n+ [3929,1,1],\n+ [3930,0,1],\n+ [3931,1,1],\n+ [3932,0,1],\n+ [3933,0,1],\n+ [3934,0,1],\n+ [3935,0,1],\n+ [3936,0,1],\n+ [3937,0,1],\n+ [3938,0,1],\n+ [3939,0,1],\n+ [3940,0,1],\n+ [3941,1,1],\n+ [3942,0,1],\n+ [3943,0,1],\n+ [3944,0,1],\n+ [3945,0,1],\n+ [3946,0,1],\n+ [3947,0,1],\n+ [3948,1,1],\n+ [3949,0,1],\n+ [3950,1,1],\n+ [3951,0,1],\n+ [3952,1,1],\n+ [3953,0,1],\n+ [3954,0,1],\n+ [3955,0,1],\n+ [3956,0,1],\n+ [3957,1,1],\n+ [3958,0,1],\n+ [3959,0,1],\n+ [3960,0,1],\n+ [3961,1,1],\n+ [3962,1,1],\n+ [3963,0,1],\n+ [3964,0,1],\n+ [3965,0,1],\n+ [3966,0,1],\n+ [3967,0,1],\n+ [3968,1,1],\n+ [3969,0,1],\n+ [3970,0,1],\n+ [3971,0,1],\n+ [3972,0,1],\n+ [3973,0,1],\n+ [3974,0,1],\n+ [3975,0,1],\n+ [3976,1,1],\n+ [3977,1,1],\n+ [3978,0,1],\n+ [3979,0,1],\n+ [3980,0,1],\n+ [3981,1,1],\n+ [3982,0,1],\n+ [3983,1,1],\n+ [3984,0,1],\n+ [3985,0,1],\n+ [3986,0,1]]\n+}\n' |
| b |
| diff -r 7332408e1f37 -r 1aa945e00ef2 test-data/stool_small.count_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.count_table Tue Mar 20 22:01:25 2018 -0400 |
| b |
| @@ -0,0 +1,47 @@ +Representative_Sequence total +F11Fcsw_12747 1 +F11Fcsw_13125 1 +F11Fcsw_13572 2 +F11Fcsw_13584 1 +F11Fcsw_13612 2 +F11Fcsw_13784 2 +F11Fcsw_14513 1 +F11Fcsw_14920 1 +F11Fcsw_14954 1 +F11Fcsw_14980 1 +F11Fcsw_15042 1 +F11Fcsw_15664 1 +F11Fcsw_17394 1 +F11Fcsw_17898 1 +F11Fcsw_18564 1 +F11Fcsw_19115 1 +F11Fcsw_19402 1 +F11Fcsw_19500 1 +F11Fcsw_20028 1 +F11Fcsw_20361 1 +F11Fcsw_20429 1 +F11Fcsw_20462 1 +F11Fcsw_20686 1 +F11Fcsw_21035 1 +F11Fcsw_21196 1 +F11Fcsw_21505 1 +F11Fcsw_21636 1 +F11Fcsw_21645 1 +F11Fcsw_21954 1 +F11Fcsw_22687 1 +F11Fcsw_22831 1 +F11Fcsw_22880 1 +F11Fcsw_22900 1 +F11Fcsw_23043 1 +F11Fcsw_23322 1 +F11Fcsw_23608 1 +F11Fcsw_23684 1 +F11Fcsw_24087 1 +F11Fcsw_24273 1 +F11Fcsw_24701 2 +F11Fcsw_24967 1 +F11Fcsw_25501 1 +F11Fcsw_25574 1 +F11Fcsw_26078 1 +F11Fcsw_26175 1 +F11Fcsw_26418 1 |
| b |
| diff -r 7332408e1f37 -r 1aa945e00ef2 test-data/stool_small.denovo.vsearch.accnos --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.denovo.vsearch.accnos Tue Mar 20 22:01:25 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +F11Fcsw_21505 +F11Fcsw_23322 |
| b |
| diff -r 7332408e1f37 -r 1aa945e00ef2 test-data/stool_small.names --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.names Tue Mar 20 22:01:25 2018 -0400 |
| b |
| @@ -0,0 +1,46 @@ +F11Fcsw_12747 F11Fcsw_12747 +F11Fcsw_13125 F11Fcsw_13125 +F11Fcsw_13572 F11Fcsw_13572,F11Fcsw_14202 +F11Fcsw_13584 F11Fcsw_13584 +F11Fcsw_13612 F11Fcsw_13612,F11Fcsw_23132 +F11Fcsw_13784 F11Fcsw_13784,F11Fcsw_21715 +F11Fcsw_14513 F11Fcsw_14513 +F11Fcsw_14920 F11Fcsw_14920 +F11Fcsw_14954 F11Fcsw_14954 +F11Fcsw_14980 F11Fcsw_14980 +F11Fcsw_15042 F11Fcsw_15042 +F11Fcsw_15664 F11Fcsw_15664 +F11Fcsw_17394 F11Fcsw_17394 +F11Fcsw_17898 F11Fcsw_17898 +F11Fcsw_18564 F11Fcsw_18564 +F11Fcsw_19115 F11Fcsw_19115 +F11Fcsw_19402 F11Fcsw_19402 +F11Fcsw_19500 F11Fcsw_19500 +F11Fcsw_20028 F11Fcsw_20028 +F11Fcsw_20361 F11Fcsw_20361 +F11Fcsw_20429 F11Fcsw_20429 +F11Fcsw_20462 F11Fcsw_20462 +F11Fcsw_20686 F11Fcsw_20686 +F11Fcsw_21035 F11Fcsw_21035 +F11Fcsw_21196 F11Fcsw_21196 +F11Fcsw_21505 F11Fcsw_21505 +F11Fcsw_21636 F11Fcsw_21636 +F11Fcsw_21645 F11Fcsw_21645 +F11Fcsw_21954 F11Fcsw_21954 +F11Fcsw_22687 F11Fcsw_22687 +F11Fcsw_22831 F11Fcsw_22831 +F11Fcsw_22880 F11Fcsw_22880 +F11Fcsw_22900 F11Fcsw_22900 +F11Fcsw_23043 F11Fcsw_23043 +F11Fcsw_23322 F11Fcsw_23322 +F11Fcsw_23608 F11Fcsw_23608 +F11Fcsw_23684 F11Fcsw_23684 +F11Fcsw_24087 F11Fcsw_24087 +F11Fcsw_24273 F11Fcsw_24273 +F11Fcsw_24701 F11Fcsw_24701,F11Fcsw_24794 +F11Fcsw_24967 F11Fcsw_24967 +F11Fcsw_25501 F11Fcsw_25501 +F11Fcsw_25574 F11Fcsw_25574 +F11Fcsw_26078 F11Fcsw_26078 +F11Fcsw_26175 F11Fcsw_26175 +F11Fcsw_26418 F11Fcsw_26418 |
| b |
| diff -r 7332408e1f37 -r 1aa945e00ef2 test-data/stool_small.unique.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.unique.fasta Tue Mar 20 22:01:25 2018 -0400 |
| b |
| b'@@ -0,0 +1,92 @@\n+>F11Fcsw_12747\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGCAGCCTTGGTGAGCCGTTACCTCACCAACTAGCTAATCAGATATGAGCCCATCTTTCAGCGGATTGCTCCTTTGGTATCCCAGAGATGCCTCCAAAATACATTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGG\n+>F11Fcsw_13125\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAATGTGGCCGTTCATCCTCTCAGACCGGCTACTGATCGTCGCCTTGGTAGGCCGTTACCCCACCAACTAGCTAATCAGACGCAGACCCATCGTAAAGCGATAGCTTACAAGTAGAGGCCATCTTTAGTCGAGCTTCCATGCGGAAGTTCGACAACATTCGGTATTAGCAGTCCTTTCGAACTGTTGTCCCCATCTTTACGG\n+>F11Fcsw_13572\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACCCATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATGGGACGCATCCCCATCCTTTACCAATTAATCTTTATTTGTCGCTCCCATGCGGAAAGACAAACACATCCGGTATTAAACTCCCTTTCAGGAGACTATCCCGGAGTAAAGGGCAGGTTGGATACGCGTTACTCACCCGTGCGCCGGTCGCCATCAAAA\n+>F11Fcsw_13584\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGATGTCTTGGTGGGCCGTTACCCCGCCAACAAACTAATGGAACGCATCCCCATCGGTTATCGAAATTCTTTAATAACAAGAAGATGCCTTCTCGTTATACTATCCGGTATTAATCTTTCTTTCGAAAGGCTATCCCGGAATAACCGGTAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCATCAACCTA\n+>F11Fcsw_13612\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGTCCGTGTCTCAGTACCAATGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTTGGTGGGCCGTTACCCCCCAACTAGCTAATGCGCCGCATGCCCATCCCTGTCCGGATTACTCCTTTGGCGCTCGCAGGATGCCCCGCAAACGCTTTATGCGATATTAGACCGGATTTCTCCGGATTATCCCTCTGACAGGGGCAGGTTGCATACGTGTTACTCACCCG\n+>F11Fcsw_13784\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACCGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCGGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGATCACTGTATCATGCGGTACTGTAATCTTATGCGGTATTAGCATCTGTTTCCAAATGTTATCCCCCTCTGAAAGGCAGGTTG\n+>F11Fcsw_14513\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTATCTCAGTTCCAATGTGGCCGATCACCCTCTCAGGTCGGCTAACCATCGTCGACTTGGTAGTCCGTTACACTACCAACTATCTAATGGTACGCGAGCCCATCCACATCCGATAAATCTTTTACCCCTGAGAGATGCCTCTCTGTGGTCTTATGCGGTATTAGCACACATTTCTATGTGTTATTCCCCAGATGTGGGCAGGTTG\n+>F11Fcsw_14920\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCATCCTCTCAGACCGGCTACTGATCGTCGCCTTGGTGAGCCATTACCTCTCCAACTAGCTAATCAGACGCGGGCCCATCCTATACCACCTGAGTTTTTCCTACCGTATCATGCGGTACTGTAGGCTTATGCGGTTTTAGCACAGATTTCTCTGTGTTATCCCCTGTATAGGGCAGGTTACCCACGCGTTT\n+>F11Fcsw_14954\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGGCCAACCTCTCAGTCCGGCTACCGATCGTCGACTTGGTGGGCCGTTACCCCGCCAACTATCTAATCGGACGCGAGGCCATCTTTCAGCGATAAATCTTTGGCATGTCCGGGATGCCCCGGTCATGCGTCATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTCCTCACGCGTTACT\n+>F11Fcsw_14980\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTTTCTCAGTTCCAATGTGGCCGTTCATCCTCTCAGATCGGCTACCCATCGTCGCCTTGGTGAGCCGTTACCTCTCCAACTAGCTAATGGGCCGCGAGCCCCTCCTATACCGCCTCAGCTTTTACCCCTCTCCGATGCCGGAGTGTGGTCTTATACCGTATTAGCACAAATTTCTCTGTGTTATCCCGTTGTATAGGATAGGTTGCTCACGTGTTACTCACCCG\n+>F11Fcsw_15042\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCGCCCTCTCAGGCCGGCTACTGATCGTCGGTTTGGTGGGCCGTTACCCCGCCAACTGCCTAATCAGACGCGGGCCCATCCCATACCACCGGAGTTTTTCACACTGAGCCATGCAGCTCTGTGCGCTTATGCGGTATTAGCAGCCGTTTCCAGCTGTTATCCCCCGGTATGGGGCAGGTCACCCACGCGTTACT\n+>F11Fcsw_15664\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCAGTACAAGGCAGGTTACCCACGCGTTACT\n+>F11Fcsw_17394\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTTGCCTTGGTAGGCCGTTACCCCGCCAACAAGCTAATCAGACGCGGGTCCATCTCACACCACCGGAGTTTTTCACACTGTACCATGCGGTACTGTGCGCTTATGCGGTATTATCAGCCGTTTCCAACTGCTATCCCCCTGTGTGAGGCAGGTTACCCACGCGTTA\n+>F11Fcsw_17898\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACTGTATCATGCGATACCGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTATCCCCCTGTATAAGGCAGGTTACCCACGCGTTACTCACCCG\n+>F11Fcsw_18564\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAACCTCTCA'..b'GCAGCTCTGTGCGCTTATGCGGTATTAGCAGTCATTTCTGACTGTTATCCCCCTGTATAAGGCAGGTTACCCACGCG\n+>F11Fcsw_22900\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTTGGCTTGGTGGGCCGTTACCCCTCCAACTACCTAATGGGACGCGAACCCCTCTCAAAGCGATAAATCTTTGACCCCTTCATCATGCGGTGTTGTGGTCTCATGCGGTATTAGCAACAGTTTCCCGTTGTTATCCCCCTCTTTGAGTCAGGTTATTCACGCGTTACTCACCCG\n+>F11Fcsw_23043\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGGTCAACCTCTCAGTCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCAGTACAAGGCAGGTTACCCACGCGTTA\n+>F11Fcsw_23322\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCCGTTACCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCACCCGTGCGCCAA\n+>F11Fcsw_23608\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTAGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCTCTTTCAGATGTCTTCTAGAGATATCATTGGGTATTAGTCTTACTTTGCAAGGTTATCCCAAGTGATGGGCAGGTTGGATACGCGTTACTCACCCG\n+>F11Fcsw_23684\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCCCTTTCAGATGTCTTCTAGAGACGTCATTGGGTATTAGTCTTACTTTCGCAAGGTTATCCCAAGTGATGGGCAGGTTGGATACGCGTTACTCACCCGTGCG\n+>F11Fcsw_24087\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTATGGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACAAGCTAATCCAACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACTGAGCCATGCAGCTCTGTGCGCTTATGCGGTATTAGCAGCCATTTCTGACTGTTATCCCCCTGTATAAGGCAGGTTACCCACG\n+>F11Fcsw_24273\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTAGGCCGTTACCCCACCAACTATCTAATCAGACGCGAGCCCATCTATCAGCGGATTACTCCTTTCCCACTTTCATCATGTGATATTTATTGGCATATGCGGTATTAGCAATGATTTCTCACTGTTATTCCCCTCCTGATAGGCG\n+>F11Fcsw_24701\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCTGTTACCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCACCCGTGCG\n+>F11Fcsw_24967\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACT\n+>F11Fcsw_25501\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGGGCCGTTACCCCGCCAACTATCTAATCAGACGCGAGGCCATCTTTCAGCGATAAATCTTTGGCATTTCGACCATGCGATCAAAATGCGTCATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTCCTCACG\n+>F11Fcsw_25574\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCTCACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAAATCTTTTACCTCAGAACCATGTGATCCCGTGGTCTTATGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCCTGTCTGGAAAAGGTTGCTCACGCGTTACTCACCCGTCCGCCGCTAAAACAG\n+>F11Fcsw_26078\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCTGTTATCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCA\n+>F11Fcsw_26175\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCTCACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAAATCTTTTACCCCAGAACCATGTGATCCCGTGGTCTTATGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCCTGTCTGGGAAAGGTTGCTCACGCGTTACTCACCCGTCCGCCGCTAAAACAG\n+>F11Fcsw_26418\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACCAGCTAATCAGACGCGGGTCCATCCTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTGTACAGGGCAGGTTACCCACGCGTTACT\n' |
| b |
| diff -r 7332408e1f37 -r 1aa945e00ef2 test-data/stool_small.vsearch.chimeras --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.vsearch.chimeras Tue Mar 20 22:01:25 2018 -0400 |
| b |
| @@ -0,0 +1,47 @@ +Score Query ParentA ParentB IdQM IdQA IdQB IdAB IdQT LY LN LA RY RN RA Div YN +0.0000 F11Fcsw_13572;size=2; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_13612;size=2; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_13784;size=2; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_24701;size=2; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_12747;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0514 F11Fcsw_13125;size=1; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; F11Fcsw_13784;size=2; 80.5 77.1 80.1 72.7 80.1 21 20 19 8 0 6 0.4 N +0.1560 F11Fcsw_13584;size=1; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; 82.5 80.4 72.9 73.3 80.4 23 0 8 15 10 24 2.1 N +0.0259 F11Fcsw_14513;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 82.7 79.3 81.4 81.9 81.4 11 8 11 11 3 19 1.3 N +0.0550 F11Fcsw_14920;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_13784;size=2; 84.7 83.5 76.3 80.9 83.5 23 3 21 5 2 10 1.3 N +0.0000 F11Fcsw_14954;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0216 F11Fcsw_14980;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 82.0 79.1 80.8 82.4 80.8 7 4 6 12 5 28 1.3 N +0.0400 F11Fcsw_15042;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_13784;size=2; 84.6 82.9 79.1 79.9 82.9 21 8 18 5 1 9 1.7 N +0.0524 F11Fcsw_15664;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 84.6 83.8 71.7 72.9 83.8 41 10 25 3 1 1 0.8 N +0.0000 F11Fcsw_17394;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0428 F11Fcsw_17898;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 86.7 86.2 71.7 72.5 86.2 45 9 21 2 1 1 0.4 N +0.0000 F11Fcsw_18564;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_19115;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_19402;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_19500;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0158 F11Fcsw_20028;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 77.8 77.4 70.4 73.0 77.4 32 15 35 1 0 1 0.4 N +0.0161 F11Fcsw_20361;size=1; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; F11Fcsw_13784;size=2; 77.5 71.4 77.1 73.1 77.1 2 1 3 28 14 33 0.4 N +0.1919 F11Fcsw_20429;size=1; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; 84.6 82.1 75.4 73.3 82.1 22 0 5 16 10 22 2.5 N +0.0158 F11Fcsw_20462;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 77.8 77.4 70.4 73.0 77.4 32 15 35 1 0 1 0.4 N +0.0000 F11Fcsw_20686;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0422 F11Fcsw_21035;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_13784;size=2; 86.3 84.6 81.3 82.2 84.6 16 4 4 8 4 21 1.7 N +0.0000 F11Fcsw_21196;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.5878 F11Fcsw_21505;size=1; F11Fcsw_13572;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 92.4 76.7 88.2 72.1 88.2 11 0 0 48 7 13 4.2 Y +0.0000 F11Fcsw_21636;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_21645;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_21954;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_22687;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_22831;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0322 F11Fcsw_22880;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 83.3 82.9 70.8 72.5 82.9 41 11 27 2 1 1 0.4 N +0.0000 F11Fcsw_22900;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_23043;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.5123 F11Fcsw_23322;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 99.2 83.0 97.9 81.7 97.9 3 0 1 40 1 0 1.2 Y +0.0000 F11Fcsw_23608;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_23684;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0324 F11Fcsw_24087;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 83.8 83.3 71.2 72.5 83.3 41 11 26 2 1 1 0.4 N +0.0000 F11Fcsw_24273;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_24967;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_25501;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0461 F11Fcsw_25574;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 84.9 80.8 82.0 82.4 82.0 12 5 3 14 4 24 2.9 N +0.0000 F11Fcsw_26078;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0509 F11Fcsw_26175;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 85.8 81.2 82.8 82.4 82.8 12 5 3 15 4 22 2.9 N +0.0696 F11Fcsw_26418;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 83.3 82.1 72.5 72.9 82.1 38 12 27 3 0 1 1.2 N |