| Next changeset 1:bf20a30c263a (2017-09-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d |
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added:
README filter.seqs.xml macros.xml test-data/98_sq_phylip_amazon.dist test-data/Fasting_Example1.fasta test-data/Fasting_Example1.qual test-data/Fasting_Example1.sff test-data/Fasting_Example2.sff test-data/GQY1XT001.oligos test-data/HMP_MOCK.v35.align test-data/HMP_MOCK.v35.align.names test-data/HMP_MOCK.v35.fasta test-data/HMP_MOCK.v35.pintail.quan test-data/HMP_MOCK.v35.slayer.chimeras test-data/HMPv5-v3_1368-1369.oligos test-data/LookUp_Titanium.pat test-data/M00967_43_000000000-A3JHG_1_1101_14010_4122.chimeracheck.svg test-data/Mock_S280_L001_R1_001_small.contigs.report test-data/Mock_S280_L001_R1_001_small.fastq test-data/Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos test-data/Mock_S280_L001_R1_001_small.trim.contigs.fasta test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align.report test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head.names test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.bellerophon.accnos test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.chop.fasta test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.denovo.uchime.chimeras test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.error.summary test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.fasta test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.names test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ng.fasta test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.pintail.accnos test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.accnos test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.alns test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.slayer.chimeras test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.unique.align_head test-data/Mock_S280_L001_R1_001_small.trim.contigs.qual test-data/Mock_S280_L001_R1_001_small.trim.contigs.summary test-data/Mock_S280_L001_R2_001_small.fastq test-data/abrecovery.fasta test-data/abrecovery.groups test-data/abrecovery.names test-data/abrecovery.pds.wang.taxonomy test-data/abrecovery.pds.wang.tree.sum test-data/abrecovery.tre test-data/amazon.accnos.otulabels test-data/amazon.align_head test-data/amazon.align_head.count_table test-data/amazon.align_head.list test-data/amazon.align_head.names test-data/amazon.align_head.wang.taxonomy test-data/amazon.align_head_short test-data/amazon.an.0.03.-.0.05.otu.hierarchy test-data/amazon.an.jclass.unique.tre test-data/amazon.an.list test-data/amazon.an.rabund test-data/amazon.an.rabund2 test-data/amazon.an.relabund test-data/amazon.an.sabund test-data/amazon.an.sabund2 test-data/amazon.an.sabund3 test-data/amazon.an.shared test-data/amazon.bad.accnos test-data/amazon.count_table test-data/amazon.design test-data/amazon.dist test-data/amazon.fasta test-data/amazon.fasta_head test-data/amazon.fragclust.fasta test-data/amazon.fragclust.names test-data/amazon.groupaccnos test-data/amazon.groups test-data/amazon.head.names test-data/amazon.metadata test-data/amazon.mothur.shared test-data/amazon.names test-data/amazon.pair.dist test-data/amazon.pcoa.axes test-data/amazon.pcoa.loadings test-data/amazon.silva.wang.tax.summary test-data/amazon.square.pcoa.axes test-data/amazon.unique.fasta test-data/amazon.unique.names test-data/amazon.wang.knn.tax.summary test-data/amazon.wang.wang.taxonomy test-data/amazon1.count_table test-data/amazon1.names test-data/amazon_withgroups.count_table test-data/amazon_withgroups.redundant.groups test-data/amazon_withgroups_pasture.count_table test-data/biosample.source test-data/biosample.tsv test-data/biosample.xml test-data/cd-test.constaxonomy test-data/cd-test.count_table test-data/cd-test.database test-data/cd-test.list test-data/cd-test.repfasta test-data/cd-test.repname test-data/env.dist test-data/example.biom test-data/example.constaxonomy test-data/final.tx.1.cons.taxonomy test-data/final.tx.1.subsample.1.pick.shared test-data/makesra.project test-data/metadata test-data/mock.flow test-data/mouse.design test-data/output.fa test-data/sample1.fa test-data/sample2.fa test-data/sample3.fa test-data/silva.ss.map.head test-data/testflow.flow test-data/toymothur.design test-data/toymothur.design2 test-data/treetest.deunique.tre test-data/treetest.groups test-data/treetest.names test-data/treetest.tre test-data/veg.dist tool-data/mothur_aligndb.loc.sample tool-data/mothur_lookup.loc.sample tool-data/mothur_map.loc.sample tool-data/mothur_taxonomy.loc.sample tool_data_table_conf.xml.sample tools.yaml |
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| diff -r 000000000000 -r 870f2a438139 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Fri May 19 05:26:45 2017 -0400 |
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| @@ -0,0 +1,57 @@ +Galaxy wrappers for the Mothur metagenomics tools (http://www.mothur.org/wiki/Main_Page) + +The Mothur Tool Suite repository: + - Provides Mothur wrappers for the Mothur tools + - Downloads and builds Mothur and all its dependencies on the Linux or Mac operating system + +Installing Tools via the API: +This is a rather large tool suite, if you are having problems installing via the toolshed, try using the API instead + - Install ephemeris: pip install ephemeris -U + - Use ephemeris to install tools: shed_install -a <your admin API key> -t tools.yaml + - (You can find a tools.yaml you can use in this repo as well) + +Installing reference data from silva and greengenes: + - There is a Galaxy datamanager for available for Mothur + + RDP reference file (modified for mothur): + http://www.mothur.org/wiki/RDP_reference_files + - 16S rRNA reference (RDP): A collection of 9,662 bacterial and 384 archaeal 16S rRNA gene sequences with an improved taxonomy compared to version 6. + http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip + - 16S rRNA reference (PDS): The RDP reference with three sequences reversed and 119 mitochondrial 16S rRNA gene sequences added as members of the Rickettsiales + http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip + - 28S rRNA reference (RDP): A collection of 8506 reference 28S rRNA gene sequences from the Fungi that were curated by the Kuske lab + http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip + Silva reference: + http://www.mothur.org/wiki/Silva_reference_files + - Bacterial references (14,956 sequences) + http://www.mothur.org/w/images/9/98/Silva.bacteria.zip + - Archaeal references (2,297 sequences) + http://www.mothur.org/w/images/3/3c/Silva.archaea.zip + - Eukaryotic references (1,238 sequences) + http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip + - Silva-based alignment of template file for chimera.slayer (5,181 sequences) + http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip + Alignment database rRNA gene sequences: + http://www.mothur.org/wiki/Alignment_database + - greengenes reference alignment + http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip + - SILVA (Silva reference) + http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip + Secondary structure mapping files: + http://www.mothur.org/wiki/Secondary_structure_map + http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip + http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip + Lane masks: + http://www.mothur.org/wiki/Lane_mask + greengenes-compatible mask: + - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database + http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter + - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database + http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter + - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper + http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter + SILVA-compatible mask: + - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper + http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter + Lookup Files for sff flow analysis using shhh.flows: + http://www.mothur.org/wiki/Alignment_database |
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| diff -r 000000000000 -r 870f2a438139 filter.seqs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter.seqs.xml Fri May 19 05:26:45 2017 -0400 |
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| @@ -0,0 +1,102 @@ +<tool profile="16.07" id="mothur_filter_seqs" name="Filter.seqs" version="@WRAPPER_VERSION@.0"> + <description>removes columns from alignments</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + <command><![CDATA[ + @SHELL_OPTIONS@ + + ## create symlinks to input datasets + ln -s "$fasta" fasta.dat && + #for $i in $inputs: + ln -s "$i.fasta" fasta${inputs.index($i)}.dat && + #end for + ln -s "$hard" hard.dat && + + echo 'filter.seqs( + fasta=fasta.dat#for $i in $inputs#-fasta${inputs.index($i)}.dat#end for#, + vertical=$vertical, + #if $trump: + trump=$trump, + #end if + soft=$soft, + #if $hard: + hard=hard.dat, + #end if + processors='\${GALAXY_SLOTS:-8}' + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log && + + ## rename collection files for more transparent element naming + mv fasta.filter.fasta "${fasta.element_identifier}".filter.fasta + #for i in $inputs: + && mv fasta${inputs.index($i)}.filter.fasta "${i.fasta.element_identifier}".filter.fasta + #end for + ]]></command> + <inputs> + <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/> + <repeat name="inputs" title="Additional Alignment File"> + <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/> + </repeat> + <param name="vertical" type="boolean" checked="true" truevalue="true" falsevalue="false" label="vertical - Vertical column" help="Ignore any column that only contains gap characters (i.e. '-' or '.')"/> + <param name="trump" type="select" label="trump - Trump character" help="Remove a column if the trump character is found at that position in any sequence of the alignment"> + <option value="">Off</option> + <option value=".">.</option> + <option value="-">-</option> + <option value="N">N</option> + </param> + <param name="soft" type="integer" value="0" min="0" max="100" label="soft - percentage required to retain column. (0-100)" help="Removes any column where the dominant base (i.e. A, T, G, C, or U) does not occur in at least a designated percentage of sequences"/> + <param name="hard" type="data" format="mothur.filter" optional="True" label="hard - Hard Column Filter" help="A file should only contain one line consisting of 0's and 1's"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="out_filter" format="mothur.filter" from_work_dir="fasta*.filter" label="${tool.name} on ${on_string}: filter"/> + <collection name="filteredfastas" type="list" label="${tool.name} on ${on_string}: filtered fastas"> + <discover_datasets pattern="(?P<designation>.*)\.filter\.fasta" format="fasta"/> + <filter>inputs</filter> <!-- only output collection if multiple outputs--> + </collection> + <data name="filteredfasta" format="fasta" from_work_dir="*.filter.fasta" label="${tool.name} on ${on_string}: filtered fasta"> + <filter>not inputs</filter> + </data> + </outputs> + <tests> + <test><!-- test with multiple inputs and collection output --> + <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/> + <repeat name="inputs"> + <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/> + </repeat> + <output name="out_filter" md5="3e6c2cfef46baf35d2a8b5cafe53e3a4"/> + <output_collection name="filteredfastas" count="2"> + <element name="HMP_MOCK.v35.align" md5="ef4c6c2d9a882f7a22e5fa3c814af7cc" ftype="fasta"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <test><!-- test with single input and non-collection output --> + <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/> + <output name="out_filter" md5="3e6c2cfef46baf35d2a8b5cafe53e3a4"/> + <output name="filteredfasta" md5="ef4c6c2d9a882f7a22e5fa3c814af7cc"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The filter.seqs_ command removes columns from alignments based on a criteria defined by the user. For example, alignments generated against reference alignments (e.g. from RDP, SILVA, or greengenes) often have columns where every character is either a '.' or a '-'. These columns are not included in calculating distances because they have no information in them. By removing these columns, the calculation of a large number of distances is accelerated. Also, people also like to mask their sequences to remove variable regions using a soft or hard mask (e.g. Lane's mask). This type of masking is only encouraged for deep-level phylogenetic analysis, not fine level analysis such as that needed with calculating OTUs. + +.. _filter.seqs: https://www.mothur.org/wiki/Filter.seqs + +v.1.20.0: Updated to Mothur 1.33 + +]]> + </help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 870f2a438139 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri May 19 05:26:45 2017 -0400 |
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| @@ -0,0 +1,98 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.36.1">mothur</requirement> + </requirements> + </xml> + <xml name="version_command"> + <version_command>mothur "#help()" | sed '7q;d' | cut -d" " -f2 </version_command> + </xml> + <xml name="stdio"> + <stdio> + <regex match="\[ERROR\]" source="stdout" level="fatal"/> + <exit_code range="1:" level="fatal"/> + </stdio> + </xml> + <token name="@WRAPPER_VERSION@">1.36.1</token> + <token name="@SHELL_OPTIONS@">set -o pipefail;</token> + <token name="@MOTHUR_OVERVIEW@"> +<![CDATA[ + +**Mothur Overview** + +Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_. + +.. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page + +]]> + </token> + <xml name="labeloptions"> + <options> + <filter type="data_meta" ref="otu" key="labels"/> + </options> + </xml> + <xml name="calc-common"> + <!-- you can set defaults in tool xml by repeating those options again after macro expand, overriding first --> + <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option> + <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option> + <option value="canberra">canberra - Community Structure Similarity</option> + <option value="gower">gower - Community Structure Similarity</option> + <option value="hamming">hamming - Community Membership Similarity</option> + <option value="hellinger">hellinger - Community Structure Similarity</option> + <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option> + <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> + <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option> + <option value="jsd">jsd</option> + <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option> + <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option> + <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option> + <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option> + <option value="manhattan">manhattan - Community Structure Similarity</option> + <option value="memchi2">memchi2 - Community Membership Similarity</option> + <option value="memchord">memchord - Community Membership Similarity</option> + <option value="memeuclidean">memeuclidean - Community Membership Similarity</option> + <option value="mempearson">mempearson - Community Membership Similarity</option> + <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option> + <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option> + <option value="odum">odum - Community Structure Similarity</option> + <option value="rjsd">rjsd</option> + <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option> + <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option> + <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option> + <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> + <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option> + <option value="soergel">soergel - Community Structure Similarity</option> + <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option> + <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option> + <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option> + <option value="spearman">spearman - Community Structure Similarity</option> + <option value="speciesprofile">speciesprofile - Community Structure Similarity</option> + <option value="structchi2">structchi2 - Community Structure Similarity</option> + <option value="structchord">structchord - Community Structure Similarity</option> + <option value="structeuclidean">structeuclidean - Community Structure Similarity</option> + <option value="structkulczynski">structkulczynski - Community Structure Similarity</option> + <option value="structpearson">structpearson - Community Structure Similarity</option> + <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option> + <option value="thetayc">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option> + <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option> + <yield/> + </xml> + <xml name="logfile-output"> + <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"/> + </xml> + <xml name="logfile-test"> + <output name="logfile" ftype="txt"> + <assert_contents> + <has_text text="mothur"/> + <has_text text="@WRAPPER_VERSION@"/> + </assert_contents> + </output> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1128/AEM.01541-09</citation> + <yield/> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 870f2a438139 test-data/98_sq_phylip_amazon.dist --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/98_sq_phylip_amazon.dist Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,99 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|
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Fasting_Example1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Fasting_Example1.fasta Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,20 @@ +>FLP3FBN01ELBSX xy=1766_111 +ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTTACCCTCTCAGGCCGGCTACGCATCATCGCCTTGGTGGGCCGTTACCTCACCAACTAGCTAATGCGCCGCAGGTCCATCCATGTTCACGCCTTGATGGGCGCTTTAATATACTGAGCATGCGCTCTGTATACCTATCCGGTTTTAGCTACCGTTTCCAGCAGTTATCCCGGACACATGGGCTAGg +>FLP3FBN01EG8AX xy=1719_1463 +ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGCCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACAACCTAATGGAACGCATCCCCATCGATGACCGAAGTTCTTTAATAGTTCTACCATGCGGAAGAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCa +>FLP3FBN01EEWKD xy=1692_3531 +AGCACGAGCCTACATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTTAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCTTACCAACTAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGACATGCGTCTAGTGTTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCTTGGg +>FLP3FBN01DEHK3 xy=1278_245 +ACCAGCGACTAGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCAGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGGTATTCCGGCGATGCCGCCAAAATCATTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTGCTCACg +>FLP3FBN01DGFYQ xy=1300_1344 +ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTAGGCCGTTACCCTGCCAACTGGCTAATCAGACGCGGGTCCATCTCACACCGATTAATCTTTTTCCAACCAGAGCATGCGCCCCTGTTGGCTTATGCGGTATTAGCGGTCGTTTCCAACTGTTATCCCCCTGTGTGAGGCAGGTTACCCACGCGTTACTCACCCGTCCg +>FLP3FBN01A55WZ xy=363_481 +ACGGTGAGTGTCCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCTTATACCGGTAAACCTTTAATCATGAGAAAATGCTCACTCATGATACCATCTTGTATTAATCTCCCTTTCAGAAGGCTATCCAAGAGTATAAGGCAGGTTGGATACGCGTTACTCACCCGTGCGCCGg +>FLP3FBN01D7O1S xy=1610_3070 +ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGATAACCGAAATTCTTTAATAGTGAAACCATGCGGAAATACTATACTATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTTATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCATc +>FLP3FBN01CV5ZU xy=1069_1480 +ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGTCCGTGTCTCAGTACCAATGTGGGGGGTTAACCTCTCAGTCCCCCTATGTATCGTCGCCTTGGTAAGCCGTTACCTTACCAACCAGCTAATACAACGCATGCCCATCTGTAACCGCCGAAACTTTCAACCACAAGAGATGCCTCTCATAGTGTTATGCGGTATTAGTACCGATTTCTCAGTGTTATCCCCCTGTTACAGGTAGGTTGCATACGCGTTACGCACCCGTGCGCCGGTCg +>FLP3FBN01DQ783 xy=1423_757 +ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCCg +>FLP3FBN01DDPFF xy=1269_617 +ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTCCCTTTCAGAAGGCTATCCAAGAGTATAAGGCAGGTTGGGTACGCGTTACTc |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Fasting_Example1.qual --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Fasting_Example1.qual Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,20 @@\n+>FLP3FBN01ELBSX xy=1766_111 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xy=1269_617 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|
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Fasting_Example1.sff |
| b |
| Binary file test-data/Fasting_Example1.sff has changed |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Fasting_Example2.sff |
| b |
| Binary file test-data/Fasting_Example2.sff has changed |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/GQY1XT001.oligos --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GQY1XT001.oligos Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,12 @@ +forward CCGTCAATTCMTTTRAGT +barcode AATGGTAC F003D000 +barcode AACCTGGC F003D002 +barcode TTCGTGGC F003D004 +barcode TTCTTGAC F003D006 +barcode TTCGCGAC F003D008 +barcode TCCAGAAC F003D142 +barcode AAGGCCTC F003D144 +barcode TGACCGTC F003D146 +barcode AGGTTGTC F003D148 +barcode TGGTGAAC F003D150 +barcode AACCGTGTC MOCK.GQY1XT001 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/HMP_MOCK.v35.align --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HMP_MOCK.v35.align Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,64 @@\n+>A.baumannii.1\n+.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................'..b'..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/HMP_MOCK.v35.align.names --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HMP_MOCK.v35.align.names Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,32 @@ +A.baumannii.1 A.baumannii.1 +A.odontolyticus.1 A.odontolyticus.1 +B.cereus.1 B.cereus.1 +B.vulgatus.1 B.vulgatus.1 +B.vulgatus.2 B.vulgatus.2 +B.vulgatus.4 B.vulgatus.4 +B.vulgatus.5 B.vulgatus.5 +B.vulgatus.7 B.vulgatus.7 +C.beijerinckii.1 C.beijerinckii.1 +C.beijerinckii.3 C.beijerinckii.3 +C.beijerinckii.4 C.beijerinckii.4 +D.radiodurans.1 D.radiodurans.1 +E.faecalis.1 E.faecalis.1 +E.faecalis.2 E.faecalis.2 +E.coli.1 E.coli.1 +H.pylori.1 H.pylori.1 +L.gasseri.1 L.gasseri.1 +L.monocytogenes.1 L.monocytogenes.1 +N.meningitidis.1 N.meningitidis.1 +P.acnes.1 P.acnes.1 +P.aeruginosa.1 P.aeruginosa.1 +P.aeruginosa.2 P.aeruginosa.2 +P.gingivalis.1 P.gingivalis.1 +R.sphaeroides.1 R.sphaeroides.1 +S.aureus.1 S.aureus.1 +S.aureus.5 S.aureus.5 +S.epidermidis.1 S.epidermidis.1 +S.epidermidis.2 S.epidermidis.2 +S.epidermidis.5 S.epidermidis.5 +S.agalactiae.1 S.agalactiae.1 +S.mutans.1 S.mutans.1 +S.pneumoniae.1 S.pneumoniae.1 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/HMP_MOCK.v35.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HMP_MOCK.v35.fasta Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,64 @@\n+>A.baumannii.1\n+TGGGGAATATTGGACAATGGGGGGAACCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGCCTTATGGTTGTAAAGCACTTTAAGCGAGGAGGAGGCTACTTTAGTTAATACCTAGAGATAGTGGACGTTACTCGCAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCGAGCGTTAATCGGATTTACTGGGCGTAAAGCGTGCGTAGGCGGCTTATTAAGTCGGATGTGAAATCCCCGAGCTTAACTTGGGAATTGCATTCGATACTGGTGAGCTAGAGTATGGGAGAGGATGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGATGGCGAAGGCAGCCATCTGGCCTAATACTGACGCTGAGGTACGAAAGCATGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCATGCCGTAAACGATGTCTACTAGCCGTTGGGGCCTTTGAGGCTTTAGTGGCGCAGCTAACGCGATAAGTAGACCGCCTGGGGAGTACGGTC\n+>A.odontolyticus.1\n+TGGGGAATATTGCACAATGGGCGAAAGCCTGATGCAGCGACGCCGCGTGAGGGATGGAGGCCTTCGGGTTGTAAACCTCTTTCGCTCATGGTCAAGCCGCAACTCAAGGTTGTGGTGAGGGTAGTGGGTAAAGAAGCGCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGTTGGGCACTAGGTGTGGGGGCCACCCGTGGTTTCTGCGCCGTAGCTAACGCTTTAAGTGCCCCGCCTGGGGAGTACGGCC\n+>B.cereus.1\n+TAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGTAAAACTCTGTTGTTAGGGAAGAACAAGTGCTAGTTGAATAAGCTGGCACCTTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGAGGGTTTCCGCCCTTTAGTGCTGAAGTTAACGCATTAAGCACTCCGCCTGGGGAGTACGGCC\n+>B.vulgatus.1\n+TGAGGAATATTGGTCAATGGGCGCAGGCCTGAACCAGCCAAGTAGCGTGAAGGATGACTGCCCTATGGGTTGTAAACTTCTTTTATAAAGGAATAAAGTCGGGTATGGATACCCGTTTGCATGTACTTTATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGGATTAGATACCCTGGTAGTCCACACGGTAAACGATGAATACTCGCTGTTTGCGATATACGGCAAGCGGCCAAGCGAAAGCGTTAAGTATTCCACCTGGGGAGTACGCCG\n+>B.vulgatus.2\n+TGAGGAATATTGGTCAATGGGCGAGAGCCTGAACCAGCCAAGTAGCGTGAAGGATGACTGCCCTATGGGTTGTAAACTTCTTTTATAAAGGAATAAAGTCGGGTATGGATACCCGTTTGCATGTACTTTATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGGATTAGATACCCTGGTAGTCCACACGGTAAACGATGAATACTCGCTGTTTGCGATATACGGCAAGCGGCCAAGCGAAAGCGTTAAGTATTCCACCTGGGGAGTACGCCG\n+>B.vulgatus.4\n+TGAGGAATATTGGTCAATGGGCGAGAGCCTGAACCAGCCAAGTAGCGTGAAGGATGACTGCCCTATGGGTTGTAAACTTCTTTTATAAAGGAATAAAGTCGGGTATGGATACCCGTTTGCATGTACTTTATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATATTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGGATTAGATACCCTGGTAGTCCACACGGTAAACGATGAATACTCGCTGTTTGCGATATACTGCAAGCGGCCAAGCGAAAGCGTTAAGTATTCCACCTGGGGAGTACGCCG\n+>B.vulgatus.5\n+TGAGGAATATTGGTCAATGGGCGAGAGCCTGAACCAGCCAAGTAGCGTGAAGGATGACTGCCCTATGGGTTGTAAACTTCTTTTATAAAGGAATAAAGTCGGGTATGGATACCCGTTTGCATGTACTTTATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGGATTAGATACCCTGGTAGTCCACACGGTAAACGATGAATACTCGCTGTTTGCGATATACTGCAAGCGGCCAAGCGAAAGCGTTAAGTATTCCACCTGGGGAGTACGCCG\n+>B.vulgatus.7\n+TGAGGAATATTGGTCAATGGGCGAGAGCCTGAACCAGCCAAGTAGCGTGAAGGATGACTGCCCTATGGGTTGTAAACTTCTTTTATAAAGGAATAAAG'..b'ACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACC\n+>S.aureus.5\n+TAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGTAAGTAACTGTGCACATCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTTATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACC\n+>S.epidermidis.1\n+TAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACAAATGTGTAAGTAACTATGCACGTCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACC\n+>S.epidermidis.2\n+TAGGGAATCTTCCGCAATGGGCGAAAGCTTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACAAATGTGTAAGTAACTATGCACGTCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACC\n+>S.epidermidis.5\n+TAGGGAATCTTCCGCAATGGGCGAAAGCTTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACAAATGTCTAAGTAACTATGCACGTCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATCATTGGGCGTAAAGCGCGCGTAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAGGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACC\n+>S.agalactiae.1\n+TAGGGAATCTTCGGCAATGGACGGAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGAGAAGAACGTTGGTAGGAGTGGAAAATCTACCAAGTGACGGTAACTAACCAGAAAGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAACCATTGTACGCTTTGGAAACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAGGTGTTAGGCCCTTTCCGGGGCTTAGTGCCGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACC\n+>S.mutans.1\n+TAGGGAATCTTCGGCAATGGACGAAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAGCTCTGTTGTAAGTCAAGAACGTGTGTGAGAGTGGAAAGTTCACACAGTGACGGTAGCTTACCAGAAAGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAGCGCAGGCGGTCAGGAAAGTCTGGAGTAAAAGGCTATGGCTCAACCATAGTGTGCTCTGGAAACTGTCTGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTCACTGACGCTGAGGCTCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAGGTGTTAGGCCCTTTCCGGGGCTTAGTGCCGGAGCTAACGCAATAAGCACTCCGCCTGGGGAGTACGACC\n+>S.pneumoniae.1\n+TAGGGAATCTTCGGCAATGGACGGAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAGCTCTGTTGTAAGAGAAGAACGAGTGTGAGAGTGGAAAGTTCACACTGTGACGGTATCTTACCAGAAAGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTAGATAAGTCTGAAGTTAAAGGCTGTGGCTTAACCATAGTAGGCTTTGGAAACTGTTTAACTTGAGTGCAAGAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGCTTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGATGAGTGCTAGGTGTTAGACCCTTTCCGGGGTTTAGTGCCGTAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACC\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/HMP_MOCK.v35.pintail.quan --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HMP_MOCK.v35.pintail.quan Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,101 @@ +#1.36.1 +1 0 0 0 0 0 0 +2 0.0401289 0.0401329 0.0686107 0.0957638 0.131891 0.131891 +3 0.129874 0.129874 0.129874 0.129874 0.129874 0.129874 +4 0 0 0 0 0 0 +5 0 0 0 0 0 0 +6 0 0 0 0 0 0 +7 0 0 0 0 0 0 +8 0 0 0 0 0 0 +9 0.570673 0.574425 0.597189 0.598318 0.598318 0.598318 +10 0.58334 0.58334 0.616837 0.617589 0.621807 0.621807 +11 0.624381 0.624381 0.629133 0.629753 0.629753 0.629753 +12 0 0 0 0 0 0 +13 0 0 0 0 0 0 +14 0.85247 0.85247 0.857164 0.857164 0.857164 0.857164 +15 0.848826 0.848826 0.848826 0.848826 0.848826 0.848826 +16 0.825389 0.831909 0.850142 0.872023 0.901994 0.901994 +17 0.844032 0.867226 0.874392 0.915192 0.960654 0.960654 +18 0.916939 0.916939 0.932322 0.938464 0.938464 0.938464 +19 0 0 0 0 0 0 +20 0 0 0 0 0 0 +21 0 0 0 0 0 0 +22 1.14494 1.14965 1.15471 1.16133 1.16828 1.16828 +23 0.997234 1.01547 1.21699 1.22643 1.24343 1.24343 +24 0.965161 1.03942 1.05406 1.21764 1.23287 1.23287 +25 1.29418 1.29515 1.29922 1.30707 1.31744 1.31744 +26 1.25809 1.26771 1.30164 1.34484 1.35981 1.35981 +27 1.22549 1.28661 1.32407 1.35436 1.39091 1.3986 +28 1.2438 1.31499 1.39699 1.42888 1.45945 1.46939 +29 1.37043 1.39346 1.45174 1.49716 1.55458 1.55551 +30 1.40454 1.42884 1.46383 1.51374 1.54414 1.56418 +31 1.44839 1.46554 1.46665 1.47655 1.49737 1.49737 +32 1.47282 1.49415 1.50836 1.52294 1.54801 1.5841 +33 1.5124 1.5231 1.53378 1.56165 1.59736 1.60412 +34 1.54717 1.563 1.59252 1.60734 1.63868 1.63868 +35 0 0 0 0 0 0 +36 0 0 0 0 0 0 +37 0 0 0 0 0 0 +38 0 0 0 0 0 0 +39 0 0 0 0 0 0 +40 0 0 0 0 0 0 +41 0 0 0 0 0 0 +42 0 0 0 0 0 0 +43 0 0 0 0 0 0 +44 0 0 0 0 0 0 +45 0 0 0 0 0 0 +46 0 0 0 0 0 0 +47 0 0 0 0 0 0 +48 0 0 0 0 0 0 +49 0 0 0 0 0 0 +50 0 0 0 0 0 0 +51 0 0 0 0 0 0 +52 0 0 0 0 0 0 +53 0 0 0 0 0 0 +54 0 0 0 0 0 0 +55 0 0 0 0 0 0 +56 0 0 0 0 0 0 +57 0 0 0 0 0 0 +58 0 0 0 0 0 0 +59 0 0 0 0 0 0 +60 0 0 0 0 0 0 +61 0 0 0 0 0 0 +62 0 0 0 0 0 0 +63 0 0 0 0 0 0 +64 0 0 0 0 0 0 +65 0 0 0 0 0 0 +66 0 0 0 0 0 0 +67 0 0 0 0 0 0 +68 0 0 0 0 0 0 +69 0 0 0 0 0 0 +70 0 0 0 0 0 0 +71 0 0 0 0 0 0 +72 0 0 0 0 0 0 +73 0 0 0 0 0 0 +74 0 0 0 0 0 0 +75 0 0 0 0 0 0 +76 0 0 0 0 0 0 +77 0 0 0 0 0 0 +78 0 0 0 0 0 0 +79 0 0 0 0 0 0 +80 0 0 0 0 0 0 +81 0 0 0 0 0 0 +82 0 0 0 0 0 0 +83 0 0 0 0 0 0 +84 0 0 0 0 0 0 +85 0 0 0 0 0 0 +86 0 0 0 0 0 0 +87 0 0 0 0 0 0 +88 0 0 0 0 0 0 +89 0 0 0 0 0 0 +90 0 0 0 0 0 0 +91 0 0 0 0 0 0 +92 0 0 0 0 0 0 +93 0 0 0 0 0 0 +94 0 0 0 0 0 0 +95 0 0 0 0 0 0 +96 0 0 0 0 0 0 +97 0 0 0 0 0 0 +98 0 0 0 0 0 0 +99 0 0 0 0 0 0 +100 0 0 0 0 0 0 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/HMP_MOCK.v35.slayer.chimeras --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HMP_MOCK.v35.slayer.chimeras Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,33 @@ +Name LeftParent RightParent DivQLAQRB PerIDQLAQRB BootStrapA DivQLBQRA PerIDQLBQRA BootStrapB Flag LeftWindow RightWindow +D.radiodurans.1 no +N.meningitidis.1 no +R.sphaeroides.1 no +A.baumannii.1 no +P.aeruginosa.1 no +P.aeruginosa.2 no +C.beijerinckii.4 no +C.beijerinckii.3 no +C.beijerinckii.1 no +P.acnes.1 no +E.coli.1 no +A.odontolyticus.1 no +B.vulgatus.1 no +P.gingivalis.1 no +B.vulgatus.5 no +B.vulgatus.2 no +B.vulgatus.4 no +B.vulgatus.7 no +S.agalactiae.1 no +S.pneumoniae.1 no +S.mutans.1 no +E.faecalis.2 no +E.faecalis.1 no +S.epidermidis.2 no +S.epidermidis.5 no +S.aureus.5 no +S.aureus.1 no +S.epidermidis.1 no +L.monocytogenes.1 no +B.cereus.1 no +L.gasseri.1 no +H.pylori.1 no |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/HMPv5-v3_1368-1369.oligos --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HMPv5-v3_1368-1369.oligos Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +forward GACACTATAGCCGTCAATTCMTTTRAGT +#reverse CACTATAGGGCCTACGGGAGGCAGCAG |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/LookUp_Titanium.pat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LookUp_Titanium.pat Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,10 @@\n+0.706683845240594 1.9844897129 3.1975398420 3.0681448725 2.9432754704 2.8288655827 2.7517923976 2.7065126886 2.6885289802 2.6793079355 2.6991312381 2.7515375718 2.8646417811 3.0552699867 3.3348118518 3.6715935847 4.0062062272 4.2928960392 4.4992469356 4.7042297671 4.8567523503 5.0245620073 5.1947130285 5.3437718821 5.5302245016 5.7318957861 5.8978480121 6.0885309045 6.2651340755 6.5005887845 6.6759592107 6.8738073477 7.0673708989 7.2417747579 7.4330956783 7.6097799839 7.7717092434 8.0075265520 8.0763256063 8.2803935387 8.4321703302 8.5347684131 8.6037612846 8.8832666966 8.9299418352 9.0846615051 9.4171575933 9.1984683924 9.6196818574 9.7738325373 9.6756405111 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 16.2195523567 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 19.3330676659 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19.3330676659 19.333067'..b'135170 18.9474329055 18.8040691129 18.6614221394 18.5194919848 18.3782786491 18.2377821324 18.0980024347 17.9589395560 17.8205934962 17.6829642553 17.5460518335 17.4098562306 17.2743774466 17.1396154816 17.0055703356 16.8722420086 16.7396305005 16.6077358113 16.4765579412 16.3460968900 16.2163526577 16.0873252445 15.9590146501 15.8314208748 15.7045439184 15.5783837810 15.4529404625 15.3282139630 15.2042042825 15.0809114209 14.9583353783 14.8364761546 14.7153337499 14.5949081642 14.4751993974 14.3562074496 14.2379323208 14.1203740109 14.0035325200 13.8874078481 13.7719999951 13.6573089610 13.5433347460 13.4300773499 13.3175367727 13.2057130146 13.0946060754 12.9842159551 12.8745426538 12.7655861715 12.6573465081 12.5498236637 12.4430176383 12.3369284318 12.2315560443 12.1269004758 12.0229617262 11.9197397956 11.8172346839 11.7154463912 11.6143749175 11.5140202627 11.4143824269 11.3154614100 11.2172572122 11.1197698332 11.0229992733 10.9269455323 10.8316086102 10.7369885072 10.6430852231 10.5498987579 10.4574291117 10.3656762845 10.2746402763 10.1843210870 10.0947187166 10.0058331653 9.9176644329 9.8302125194 9.7434774249 9.6574591494 9.5721576929 9.4875730553 9.4037052366 9.3205542370 9.2381200563 9.1564026945 9.0754021517 8.9951184279 8.9155515231 8.8367014372 8.7585681702 8.6811517223 8.6044520933 8.5284692832 8.4532032921 8.3786541200 8.3048217669 8.2317062327 8.1593075175 8.0876256212 8.0166605439 7.9464122855 7.8768808462 7.8080662258 7.7399684243 7.6725874418 7.6059232783 7.5399759337 7.4747454081 7.4102317015 7.3464348138 7.2833547451 7.2209914953 7.1593450645 7.0984154527 7.0382026599 6.9787066860 6.9199275310 6.8618651950 6.8045196780 6.7478909800 6.6919791009 6.6367840408 6.5823057996 6.5285443774 6.4754997742 6.4231719899 6.3715610246 6.3206668782 6.2704895508 6.2210290424 6.1722853530 6.1242584825 6.0769484309 6.0303551984 5.9844787847 5.9393191901 5.8948764144 5.8511504577 5.8081413199 5.7658490011 5.7242735013 5.6834148204 5.6432729585 5.6038479156 5.5651396916 5.5271482866 5.4898737005 5.4533159334 5.4174749853 5.3823508561 5.3479435459 5.3142530547 5.2812793824 5.2490225291 5.2174824947 5.1866592793 5.1565528829 5.1271633054 5.0984905469 5.0705346074 5.0432954868 5.0167731852 4.9909677025 4.9658790388 4.9415071941 4.9178521683 4.8949139615 4.8726925737 4.8511880048 4.8304002549 4.8103293239 4.7909752119 4.7723379189 4.7544174448 4.7372137897 4.7207269536 4.7049569364 4.6899037382 4.6755673589 4.6619477986 4.6490450573 4.6368591350 4.6253900315 4.6146377471 4.6046022816 4.5952836351 4.5866818076 4.5787967990 4.5716286093 4.5651772387 4.5594426870 4.5544249542 4.5501240405 4.5465399457 4.5436726698 4.5415222129 4.5400885750 4.5393717560 4.5393717560 4.5400885750 4.5415222129 4.5436726698 4.5465399457 4.5501240405 4.5544249542 4.5594426870 4.5651772387 4.5716286093 4.5787967990 4.5866818076 4.5952836351 4.6046022816 4.6146377471 4.6253900315 4.6368591350 4.6490450573 4.6619477986 4.6755673589 4.6899037382 4.7049569364 4.7207269536 4.7372137897 4.7544174448 4.7723379189 4.7909752119 4.8103293239 4.8304002549 4.8511880048 4.8726925737 4.8949139615 4.9178521683 4.9415071941 4.9658790388 4.9909677025 5.0167731852 5.0432954868 5.0705346074 5.0984905469 5.1271633054 5.1565528829 5.1866592793 5.2174824947 5.2490225291 5.2812793824 5.3142530547 5.3479435459 5.3823508561 5.4174749853 5.4533159334 5.4898737005 5.5271482866 5.5651396916 5.6038479156 5.6432729585 5.6834148204 5.7242735013 5.7658490011 5.8081413199 5.8511504577 5.8948764144 5.9393191901 5.9844787847 6.0303551984 6.0769484309 6.1242584825 6.1722853530 6.2210290424 6.2704895508 6.3206668782 6.3715610246 6.4231719899 6.4754997742 6.5285443774 6.5823057996 6.6367840408 6.6919791009 6.7478909800 6.8045196780 6.8618651950 6.9199275310 6.9787066860 7.0382026599 7.0984154527 7.1593450645 7.2209914953 7.2833547451 7.3464348138 7.4102317015 7.4747454081 7.5399759337 7.6059232783 7.6725874418 7.7399684243 7.8080662258 7.8768808462 7.9464122855 8.0166605439 8.0876256212 \n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/M00967_43_000000000-A3JHG_1_1101_14010_4122.chimeracheck.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/M00967_43_000000000-A3JHG_1_1101_14010_4122.chimeracheck.svg Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,13 @@ +<svg xmlns:svg="http://www.w3.org/2000/svg" xmlns="http://www.w3.org/2000/svg" width="100%" height="100%" viewBox="0 0 700 255"> +<g> +<text fill="black" class="seri" x="-23" y="25">Plotted IS values for M00967_43_000000000-A3JHG_1_1101_14010_4122</text> +<line x1="75" y1="600" x2="180" y2="600" stroke="black" stroke-width="2"/> +<line x1="75" y1="600" x2="75" y2="125" stroke="black" stroke-width="2"/> +<text fill="black" class="seri" x="80" y="620">25</text> +<text fill="black" class="seri" x="180" y="620">225</text> +<text fill="black" class="seri" x="-23" y="650">Base Positions</text> +<text fill="black" class="seri" x="50" y="580">0</text> +<text fill="black" class="seri" x="50" y="350">IS</text> +<text fill="black" class="seri" x="50" y="135">0</text> +<polyline fill="none" stroke="red" stroke-width="2" points="75,600 80,600 85,600 90,600 95,600 100,600 105,600 110,600 115,600 120,600 125,600 130,600 135,600 140,600 145,600 150,600 155,600 160,600 165,600 170,600 175,600 "/> </g> +</svg> |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.contigs.report --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.contigs.report Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,26 @@ +Name Length Overlap_Length Overlap_Start Overlap_End MisMatches Num_Ns +M00967_43_000000000-A3JHG_1_1101_19936_3208 253 249 2 251 0 0 +M00967_43_000000000-A3JHG_1_1101_15923_3823 253 248 2 250 2 0 +M00967_43_000000000-A3JHG_1_1101_14010_4122 253 250 2 252 18 0 +M00967_43_000000000-A3JHG_1_1101_10776_4204 252 248 2 250 21 8 +M00967_43_000000000-A3JHG_1_1101_22487_4260 253 249 3 252 32 1 +M00967_43_000000000-A3JHG_1_1101_13293_4703 253 248 3 251 4 0 +M00967_43_000000000-A3JHG_1_1101_24357_4866 253 249 2 251 2 0 +M00967_43_000000000-A3JHG_1_1101_23552_5194 253 246 5 251 1 0 +M00967_43_000000000-A3JHG_1_1101_7326_5417 253 248 2 250 3 0 +M00967_43_000000000-A3JHG_1_1101_11148_6457 253 249 3 252 13 0 +M00967_43_000000000-A3JHG_1_1101_7079_6722 253 249 2 251 1 0 +M00967_43_000000000-A3JHG_1_1101_8607_6805 253 250 2 252 3 0 +M00967_43_000000000-A3JHG_1_1101_15208_7185 253 248 2 250 0 0 +M00967_43_000000000-A3JHG_1_1101_4525_7317 253 249 2 251 3 0 +M00967_43_000000000-A3JHG_1_1101_9121_7358 253 249 2 251 0 0 +M00967_43_000000000-A3JHG_1_1101_8480_7498 252 250 1 251 4 0 +M00967_43_000000000-A3JHG_1_1101_11790_7581 253 248 3 251 3 0 +M00967_43_000000000-A3JHG_1_1101_20566_7622 254 246 4 250 0 0 +M00967_43_000000000-A3JHG_1_1101_10073_7632 252 250 1 251 1 0 +M00967_43_000000000-A3JHG_1_1101_5170_7771 253 249 2 251 7 0 +M00967_43_000000000-A3JHG_1_1101_18966_7778 253 249 2 251 1 0 +M00967_43_000000000-A3JHG_1_1101_5494_7973 253 249 2 251 0 0 +M00967_43_000000000-A3JHG_1_1101_10246_8076 253 249 2 251 4 0 +M00967_43_000000000-A3JHG_1_1101_23931_8157 253 249 2 251 10 1 +M00967_43_000000000-A3JHG_1_1101_18269_8162 253 249 2 251 2 0 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.fastq Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,100 @@\n+@M00967:43:000000000-A3JHG:1:1101:19936:3208 1:N:0:280\n+TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA\n++\n+BCCCCFFCFFCFGGGGGGGGGGHGGGGGHHHHHHHHGGGGHHHGGGGGGGGGGGGGGGGHHGHHHHHHHGHHHHHHHHHHGGGGGGGHHHHGGGGCGGGDHHHHHHHHHHHHHGAFFGHHHHHHHGHHGHHHHHHGHGFHGHHGHHHHGHHHCHHHGGGAGGGGGGGDDGGGGBFFGGFGGGGFFFFFFFFFFFFFFFFFFF-AFFFFF0BFBBFFFFEFFFFFFD?FFAF-9FDA/A.DCFFECDFFFF.\n+@M00967:43:000000000-A3JHG:1:1101:15923:3823 1:N:0:280\n+TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAAC\n++\n+3ABBCCCCCBABGGGGGGGGGGHGGGGGHHHHHHGHGEEGHHGGEG?FEHHFHGGGGGHHHGHHHHHHHGHHGHHHHHHHGGGGGGGHHHHHHGGGGGGGGHHHGHHHHHHHHHHHHHHHHHGHHHHHHHHHGGGCGHHHHHHHHHHHHHHHHFHHGGGGGGGGGGGGGGGGGGFGGGGEDDGFFFFFFFFFFFFFFFFFFFFFFFBFFBAFFFFFEFFFFFFFDFFFFFFF-CFF/B9F?FFECFFFFF\n+@M00967:43:000000000-A3JHG:1:1101:14010:4122 1:N:0:280\n+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGGGTAGCGGGGAAAGGCGTAGAGATATGGAGGAACACCAGTGGCAAAGGCGACTTTCGGGGCTGAAACTGCCCCTGAGGCCCGAAAGGGGGGGGAGGAACCG\n++\n+AAAA1FFA@DAFFGGGGGGGGGHGGGCGHHHHHHHG?EEGHHFGEGGGGGGG0BFEFGHHFHHHHHBHDBGHFHHH1GFHEFEGGGGHHHG@<F?/??C<FCGHHBHHG01FHA0/C<GDF1F11<1FHFCHHAG0<C1F1>1<1>=000/</0./<--9;E..999.--.900;0;09C.AFE-B-9-9B/--;9B--9-;@B/B-@;-@---;9/////--;--;-9---9;----9@==----9;---\n+@M00967:43:000000000-A3JHG:1:1101:10776:4204 1:N:0:280\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAGGAAATCCGATTGCGAAGGCAGCCGGCTAAGCTGCAACTGACATTGCGGCTTCAAAGAGAGGGGATCAAACA\n++\n+11AAAA?DAC1C1E10EFGEEGHCCAA/11A2DEFAFGHHF1AE/AAEEECEBGHHDCGHHGHFFGHB2DFGGEGHHHDFBE//>EEHHF0EEGEHFGHFDGFBF1BBFEG2G<FGG1GD2DF1<FGFFF1FHBFGA/?C/CCA<G.0>A..<000-@.-CF0G00CH000:0CGFG..:A-C/00/.C.A?0.-9A.C.;;A-----9BB/B/FBF://9:BFF/-;-9--//;:/---9--9---9//-\n+@M00967:43:000000000-A3JHG:1:1101:22487:4260 1:N:0:280\n+TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACG\n++\n+BCCCCFFBAFCCGGGGGGGGGGHGGGGGHHHHGGHGGGGGHHHGGHHGHHHHHGGGGGGEH@EFEGFFHHCEEGGHGHHFHFFHHHHFFFHHHHGGGGGGDCGEGGG?GGGDGFCDCHGHGGFGEFGG;DFGGG.-.EFFGGFFFFFFFFFFAFFFFF.@DEFFFBDDCFFBF0FFFFFF?FFFFFFFF=AFFFFCFFEFFF=B/9BFFFFEA>DDFFEFF.AF.;AA0A.B@@-.:AADFFF?B.;->9-\n+@M00967:43:000000000-A3JHG:1:1101:13293:4703 1:N:0:280\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACA\n++\n+BBBBBBBDBFFFGGGGGGGGGGHGGGGGHHHHHHHEFGHHHHHGHGGGGGGGHHHGHHGGFHGHHHHHHGCEEGGHHHHHHHHGGGGGGHGHGGHHHHGHHHGGGFHHHHBGHHCGGGGHGGHHHHHGHGGGGGG-CGGBCGGGGGGBEGAEFGFFADFFFFFFFFFFFFFBFFFFFFAFFFFEFFFFCDFAFFFFFFEFFDFFFFFFFFBFFFFDCFFB/BFFFFEFFFFA.;9?EFAFAC:9FFFFFF.\n+@M00967:43:000000000-A3JHG:1:1101:24357:4866 1:N:0:280\n+TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGGATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACA\n++\n+?3AAAFFBBFBBGGGCFGGGGGHGGGFFHHHHH3FCGAFFHHHGGHHGGFHHGCF>/EGEGEEEFGGGEFCDFFFHEGHHEH2FHHHCG2DGFHGGCC@DGGGEGGGFBCDGG?GGEHFHFFF9BFBC.DFGGBDFDGFGGFFFFFFBFB;BEFFFFFDFA-99.BFDFAFFFFFFFFEFFFFFFFFFA9@DFFFFADAAFF@CFFFFBFFEB=?:EFBBFAADFBFF/.A@AACABDAA=A-.-9--@@-\n+@M00967:43:000000000-A3JHG:'..b'FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFECFFFF\n+@M00967:43:000000000-A3JHG:1:1101:10073:7632 1:N:0:280\n+TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAACCATTGTACGCTTTGGAAACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGGGGGGAGCAAACCG\n++\n+CCCBCFFCFFFFCGGGGGGGGGHGGGGGHHHHHHHHGGGGHGCGDGGGGGGGGGGEEF3GHFFHFFGFHHHHFFHH4FGF?3?FFHHFFGHFFF4BFFHGAFF2F2FD2BDGB@D<F=FBGFDFH1=GHHGFG.@DDBGE1GGHBHBFB<<0==0-A<:.GHC0;..::.;00000F0CA.C.//;9A-:C?9-9B./.;--;:B90B0;0/00;0:9:09A....;..:9-BD./:--;CF-CD.BB.:;\n+@M00967:43:000000000-A3JHG:1:1101:5170:7771 1:N:0:280\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACA\n++\n+CCCCCCCCCFFFGGGGGGGGGGHGGGGGHHHHHHHGFGHHHHHGHGGGFGGGGHHGHHGG?GGHHHHHHFGGGGHHHHHHHHHGGGGGHGGHHHHHHGHHHHGDGGHHGGHHHHGGGGGHGHHHHHHHGGGGGCGGGGGGG?FGGFGFFGCECFFFFFDFEBFFF0BFFFFFFFFFFFFFFFFFFFFDDFFFFFF;@FE.ADFFFFFFFFF0FFFF=BFFFFFFFFBFFFFFFFDFFFFFDF.9BBBFFF9\n+@M00967:43:000000000-A3JHG:1:1101:18966:7778 1:N:0:280\n+TACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGGGCGCAGACGGTTACTTAAGCAGGATGTGAAATCCCCGGGCTCAACCCGGGAACTGCGTTCTGAACTGGGTGACTCGAGTGTGTCAGAGGGAGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCTCCTGGGACAACACTGACGTTCATGCCCGAAAGCGTGGGTAGCAAACA\n++\n+ABBBAFFB?FBBGGGGGGGGGGHGGGGGHHHHHHHHGGGGHHGGGGGGGGGGHGGGGGHHHHHHHGFHGHHHHHHHHHHHGGGGGGHHHHHG?GGFGGHHHGGGGGHHHHHHHHFFEHHHGHGHHHHHHHHHHGGGGG;CHHHHHHHHGGHHGGGGGGGGGGGGGGGGGGGGGGGGFFFGGGGFFFFFFFFFFFFFFFFFFFFFFFEFBAFFFEFFFFFFFFFFFFFFFFFFFFFFFF;DFFAFFFFFFF.\n+@M00967:43:000000000-A3JHG:1:1101:5494:7973 1:N:0:280\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACA\n++\n+BBCCCCCCCFFFGGGGGGGGGGHGGGGGHHHHHHHGFGFHHHHGHGGGFGGGHHHHFHHFHHHHHHHHFHHHGHHHHFHHHHGGGGGHHHHGEHGHHHHHHHHHHHHFFHHHHHHHHGHBHHHGHHHHHHHHHGGGDGDCGDGGHHFBFGHGHGHHGGGGFHHHFHHGFCFHFFHHHGGG?EFFFGG?ADDEFGGGADEFADFFFFBFBBFBFFFFFEFFFFFFFFFFFFFF=FFF/;:FFF./;B/BFB.\n+@M00967:43:000000000-A3JHG:1:1101:10246:8076 1:N:0:280\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTTTAGCGGTGAAATGCTTAGATATCACGAGGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACA\n++\n+BBBBBAADBFFFGGCGGGGFEGFGGGGEHHFHHHGGFGHHHFB1GFGGGGGGFHHHHFHHDFGHGHHHHHHFEFGHGHFHHF?/EEEHHHHGEHGHHHFHHHE3FBDEGHGGHG3BGHHHBGB3FGFFHB2@FGAFG@/D?DGGCB.<<<..</=D-@ECGHFH0CFGCBGFFFHFH:.A9?FG0C9;;..;09-AGGEGDDEB?FFFFFF//BFFFFFF/////9BBAEF99.DD///999.9//99BF.\n+@M00967:43:000000000-A3JHG:1:1101:23931:8157 1:N:0:280\n+TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGTGGATATTTAAGTGGGATGTGAAATACTCGGGCTTAACCTGGGTGCTGCATTCCAAACTGGATATCTAGAGTGCAGGAGAGGAAAGTAGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAATACCAGTGGCGAAGGCGACTTTCTGGACTGTAACTGACACTGAGGATCGAAAGCGTGGGGAGCAAACA\n++\n+BBBBAFFB54AFFGGGGGGEGGHGGGGGHHFHHHHCEEEEHHHGCEGGGGGG5FF1E5DGHHHHHHGHC@FHBFHH4F@4@FFGGGHHHHHBGHG?E/B?GGHHB4BGHGDGH33B?FG44?F1FDGH0C?GG/GFBG1@>F2FGFFBDDGFFFHHGGDCFHFGHBD.<<.0DGBDGGHD.GB<=G0GFHHC.-C@BE.A?-;.;FFFGFEFAFFF0009BBB9/9B?/9/;AFDD/A9AB?B?B.AFFA.\n+@M00967:43:000000000-A3JHG:1:1101:18269:8162 1:N:0:280\n+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTCACTGACGCTGAGGCTCGAAAGCGTGGGTAGCGAACA\n++\n+CDCCCFFCFFCFGGGGGGGGGGHGGGGFHHHHHHGHGGGGHHGGGGGGGGGG?GFGGHHHHHHHFGHHHHHHHHGHHHHHHGGGGEGHHHHGGHGGHGGGHHHHHHHHHHHHHHHGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHGHHHHHGGFGGHHHHHGGGGGHHHHGGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFBFDFFFFFFFFFFF-\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +M00967_43_000000000-A3JHG_1_1101_10776_4204 ambig +M00967_43_000000000-A3JHG_1_1101_22487_4260 ambig +M00967_43_000000000-A3JHG_1_1101_23931_8157 ambig |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.fasta Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,50 @@ +>M00967_43_000000000-A3JHG_1_1101_19936_3208 +TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_15923_3823 +TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCGG +>M00967_43_000000000-A3JHG_1_1101_14010_4122 +TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGTCTGTAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_10776_4204 +TACGGAGGATNCGAGGTTATCCGGATTTATTGGGTTTAAAGGGNGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGNGGTGTAGCGGTGAAATGCTTAGATATCACGGGGAANTCCGATTGCGAAGGCAGCCNGCTAAGCNGCAACTGACATTGAGGCTNGAAAGTGTGGGTATCAANCAGG +>M00967_43_000000000-A3JHG_1_1101_22487_4260 +TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAANGCGTGGGGAGCGAACAGG +>M00967_43_000000000-A3JHG_1_1101_13293_4703 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_24357_4866 +TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGG +>M00967_43_000000000-A3JHG_1_1101_23552_5194 +TACAGAGGGTGCGAGCGTTAATCGGATTTACTGGGCGTAAAGCGTGCGTAGGCGGCTTATTAAGTCGGATGTGAAATCCCCGAGCTTAACTTGGGAATTGCATTCGATACTGGTGAGCTAGAGTATGGGAGAGGATGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGATGGCGAAGGCAGCCATCTGGCCTAATACTGACGCTGAGGTACGAAAGCATGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_7326_5417 +TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCTG +>M00967_43_000000000-A3JHG_1_1101_11148_6457 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_7079_6722 +TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_8607_6805 +TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_15208_7185 +TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCGG +>M00967_43_000000000-A3JHG_1_1101_4525_7317 +TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_9121_7358 +TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_8480_7498 +TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAACCATTGTACGCTTTGGAAACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_11790_7581 +TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGG +>M00967_43_000000000-A3JHG_1_1101_20566_7622 +TACGGAGGGTGCAAGCGTTACTCGGAATCACTGGGCGTAAAGAGCGCGTAGGCGGGATAGTCAGTCAGGTGTGAAATCCTATGGCTTAACCATAGAACTGCATTTGAAACTACTATTCTAGAGTGTGGGAGAGGTAGGTGGAATTCTTGGTGTAGGGGTAAAATCCGTAGAGATCAAGAGGAATACTCATTGCGAAGGCGACCTGCTGGAACATTACTGACGCTGATTGCGCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_10073_7632 +TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAACCATTGTACGCTTTGGAAACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACCGG +>M00967_43_000000000-A3JHG_1_1101_5170_7771 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_18966_7778 +TACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGGGCGCAGACGGTTACTTAAGCAGGATGTGAAATCCCCGGGCTCAACCCGGGAACTGCGTTCTGAACTGGGTGACTCGAGTGTGTCAGAGGGAGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCTCCTGGGACAACACTGACGTTCATGCCCGAAAGCGTGGGTAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_5494_7973 +TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_10246_8076 +TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAGGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_23931_8157 +TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGTGGATATTTAAGTGGGATGTGAAATACTCGGGCTTAACCTGGGTGCTGCATTCCAAACTGGANATCTAGAGTGCAGGAGAGGAAAGTAGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAATACCAGTGGCGAAGGCGACTTTCTGGACTGTAACTGACACTGAGGCTCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_18269_8162 +TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTCACTGACGCTGAGGCTCGAAAGCGTGGGTAGCGAACAGG |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,20 @@ +M00967_43_000000000-A3JHG_1_1101_19936_3208 testgroup +M00967_43_000000000-A3JHG_1_1101_15923_3823 testgroup +M00967_43_000000000-A3JHG_1_1101_14010_4122 testgroup +M00967_43_000000000-A3JHG_1_1101_13293_4703 testgroup +M00967_43_000000000-A3JHG_1_1101_24357_4866 testgroup +M00967_43_000000000-A3JHG_1_1101_23552_5194 testgroup +M00967_43_000000000-A3JHG_1_1101_7326_5417 testgroup +M00967_43_000000000-A3JHG_1_1101_11148_6457 testgroup +M00967_43_000000000-A3JHG_1_1101_7079_6722 testgroup +M00967_43_000000000-A3JHG_1_1101_8607_6805 testgroup +M00967_43_000000000-A3JHG_1_1101_19936_3208 testgroup2 +M00967_43_000000000-A3JHG_1_1101_15923_3823 testgroup2 +M00967_43_000000000-A3JHG_1_1101_14010_4122 testgroup2 +M00967_43_000000000-A3JHG_1_1101_13293_4703 testgroup2 +M00967_43_000000000-A3JHG_1_1101_24357_4866 testgroup2 +M00967_43_000000000-A3JHG_1_1101_23552_5194 testgroup2 +M00967_43_000000000-A3JHG_1_1101_7326_5417 testgroup2 +M00967_43_000000000-A3JHG_1_1101_11148_6457 testgroup2 +M00967_43_000000000-A3JHG_1_1101_7079_6722 testgroup2 +M00967_43_000000000-A3JHG_1_1101_8607_6805 testgroup2 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align.report --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align.report Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,23 @@ +QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template +M00967_43_000000000-A3JHG_1_1101_19936_3208 253 E.faecalis.1 541 kmer 100.00 needleman 1 253 177 429 253 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_15923_3823 253 D.radiodurans.1 524 kmer 100.00 needleman 1 253 164 416 253 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_14010_4122 253 B.cereus.1 542 kmer 96.75 needleman 1 253 178 430 253 0 0 0 99.60 +M00967_43_000000000-A3JHG_1_1101_13293_4703 253 P.gingivalis.1 534 kmer 98.78 needleman 1 253 172 424 253 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_24357_4866 253 A.odontolyticus.1 534 kmer 99.59 needleman 1 253 170 422 253 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_23552_5194 253 A.baumannii.1 541 kmer 100.00 needleman 1 253 178 430 253 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_7326_5417 253 D.radiodurans.1 524 kmer 99.19 needleman 1 253 164 416 253 0 0 0 99.60 +M00967_43_000000000-A3JHG_1_1101_11148_6457 253 P.gingivalis.1 534 kmer 98.78 needleman 1 253 172 424 253 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_7079_6722 253 E.coli.1 540 kmer 100.00 needleman 1 253 177 429 253 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_8607_6805 253 S.aureus.1 541 kmer 99.59 needleman 1 253 177 429 253 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_15208_7185 253 D.radiodurans.1 524 kmer 100.00 needleman 1 253 164 416 253 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_4525_7317 253 S.aureus.1 541 kmer 99.59 needleman 1 253 177 429 253 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_9121_7358 253 B.vulgatus.1 532 kmer 99.19 needleman 1 253 172 424 253 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_8480_7498 252 S.agalactiae.1 541 kmer 99.59 needleman 1 252 178 429 252 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_11790_7581 253 A.odontolyticus.1 534 kmer 99.59 needleman 1 253 170 422 253 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_20566_7622 254 H.pylori.1 517 kmer 100.00 needleman 1 254 152 405 254 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_10073_7632 252 S.agalactiae.1 541 kmer 98.37 needleman 1 252 178 429 252 0 0 0 99.60 +M00967_43_000000000-A3JHG_1_1101_5170_7771 253 P.gingivalis.1 534 kmer 98.78 needleman 1 253 172 424 253 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_18966_7778 253 N.meningitidis.1 540 kmer 100.00 needleman 1 253 177 429 253 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_5494_7973 253 B.vulgatus.1 532 kmer 99.19 needleman 1 253 172 424 253 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_10246_8076 253 B.vulgatus.7 532 kmer 99.19 needleman 1 253 172 424 253 0 0 0 100.00 +M00967_43_000000000-A3JHG_1_1101_18269_8162 253 B.cereus.1 542 kmer 80.49 needleman 1 253 178 430 253 0 0 0 96.84 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,20 @@\n+>M00967_43_000000000-A3JHG_1_1101_19936_3208\n+...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................'..b'..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head.names --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head.names Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,10 @@ +M00967_43_000000000-A3JHG_1_1101_19936_3208 M00967_43_000000000-A3JHG_1_1101_19936_3208 +M00967_43_000000000-A3JHG_1_1101_15923_3823 M00967_43_000000000-A3JHG_1_1101_15923_3823 +M00967_43_000000000-A3JHG_1_1101_14010_4122 M00967_43_000000000-A3JHG_1_1101_14010_4122 +M00967_43_000000000-A3JHG_1_1101_13293_4703 M00967_43_000000000-A3JHG_1_1101_13293_4703 +M00967_43_000000000-A3JHG_1_1101_24357_4866 M00967_43_000000000-A3JHG_1_1101_24357_4866 +M00967_43_000000000-A3JHG_1_1101_23552_5194 M00967_43_000000000-A3JHG_1_1101_23552_5194 +M00967_43_000000000-A3JHG_1_1101_7326_5417 M00967_43_000000000-A3JHG_1_1101_7326_5417 +M00967_43_000000000-A3JHG_1_1101_11148_6457 M00967_43_000000000-A3JHG_1_1101_11148_6457 +M00967_43_000000000-A3JHG_1_1101_7079_6722 M00967_43_000000000-A3JHG_1_1101_7079_6722 +M00967_43_000000000-A3JHG_1_1101_8607_6805 M00967_43_000000000-A3JHG_1_1101_8607_6805 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,6 @@\n+>M00967_43_000000000-A3JHG_1_1101_11148_6457\n+................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................'..b'..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.bellerophon.accnos --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.bellerophon.accnos Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,12 @@ +M00967_43_000000000-A3JHG_1_1101_10073_7632 +M00967_43_000000000-A3JHG_1_1101_8480_7498 +M00967_43_000000000-A3JHG_1_1101_23552_5194 +M00967_43_000000000-A3JHG_1_1101_5170_7771 +M00967_43_000000000-A3JHG_1_1101_13293_4703 +M00967_43_000000000-A3JHG_1_1101_11148_6457 +M00967_43_000000000-A3JHG_1_1101_24357_4866 +M00967_43_000000000-A3JHG_1_1101_11790_7581 +M00967_43_000000000-A3JHG_1_1101_15923_3823 +M00967_43_000000000-A3JHG_1_1101_7326_5417 +M00967_43_000000000-A3JHG_1_1101_15208_7185 +M00967_43_000000000-A3JHG_1_1101_7079_6722 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +M00967_43_000000000-A3JHG_1_1101_7326_5417 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,20 @@ +M00967_43_000000000-A3JHG_1_1101_19936_3208 +IS scores: -19 -29 -39 -49 -59 -67 -77 -87 -97 -107 -117 -127 -136 -146 -156 -166 -173 -173 -173 -173 -174 +M00967_43_000000000-A3JHG_1_1101_15923_3823 +IS scores: -19 -29 -39 -49 -59 -69 -79 -89 -99 -107 -117 -126 -136 -146 -156 -160 -160 -160 -160 -160 -160 +M00967_43_000000000-A3JHG_1_1101_14010_4122 +IS scores: -19 -29 -39 -49 -60 -68 -78 -88 -98 -108 -118 -128 -138 -145 -155 -165 -173 -173 -168 -165 -165 +M00967_43_000000000-A3JHG_1_1101_13293_4703 +IS scores: -19 -29 -39 -49 -59 -65 -74 -84 -93 -103 -113 -123 -133 -143 -153 -163 -165 -164 -163 -163 -163 +M00967_43_000000000-A3JHG_1_1101_24357_4866 +IS scores: -19 -29 -39 -49 -59 -69 -79 -89 -98 -107 -117 -126 -136 -146 -156 -166 -166 -166 -166 -166 -166 +M00967_43_000000000-A3JHG_1_1101_23552_5194 +IS scores: -19 -29 -39 -48 -58 -68 -76 -86 -96 -106 -116 -126 -136 -146 -156 -165 -173 -173 -172 -172 -173 +M00967_43_000000000-A3JHG_1_1101_7326_5417 +IS scores: -19 -29 -39 -49 -59 -69 -79 -89 -99 -107 -117 -126 -136 -146 -156 -160 -160 -160 -160 -160 -160 +M00967_43_000000000-A3JHG_1_1101_11148_6457 +IS scores: -19 -29 -39 -49 -59 -65 -74 -84 -93 -103 -113 -123 -133 -143 -153 -163 -165 -164 -163 -163 -163 +M00967_43_000000000-A3JHG_1_1101_7079_6722 +IS scores: -19 -29 -39 -49 -59 -69 -78 -88 -98 -108 -118 -127 -137 -147 -157 -167 -173 -173 -173 -173 -173 +M00967_43_000000000-A3JHG_1_1101_8607_6805 +IS scores: -19 -29 -39 -49 -59 -67 -76 -86 -96 -106 -116 -126 -136 -143 -153 -163 -170 -170 -170 -170 -169 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.chop.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.chop.fasta Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,4 @@\n+>M00967_43_000000000-A3JHG_1_1101_19936_3208\n+................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................'..b'........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................T-------AC---GG-AG-GGT\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.denovo.uchime.chimeras --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.denovo.uchime.chimeras Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,10 @@ +Score Query ParentA ParentB IdQM IdQA IdQB IdAB IdQT LY LN LA RY RN RA Div YN +0.0000 M00967_43_000000000-A3JHG_1_1101_13293_4703/ab=2/ * * * * * * * * * * * * * * N +0.0000 M00967_43_000000000-A3JHG_1_1101_19936_3208/ab=1/ * * * * * * * * * * * * * * N +0.0000 M00967_43_000000000-A3JHG_1_1101_8607_6805/ab=1/ * * * * * * * * * * * * * * N +0.0000 M00967_43_000000000-A3JHG_1_1101_14010_4122/ab=1/ * * * * * * * * * * * * * * N +0.0000 M00967_43_000000000-A3JHG_1_1101_24357_4866/ab=1/ * * * * * * * * * * * * * * N +0.0000 M00967_43_000000000-A3JHG_1_1101_7326_5417/ab=1/ * * * * * * * * * * * * * * N +0.0000 M00967_43_000000000-A3JHG_1_1101_15923_3823/ab=1/ * * * * * * * * * * * * * * N +0.0000 M00967_43_000000000-A3JHG_1_1101_7079_6722/ab=1/ * * * * * * * * * * * * * * N +0.0000 M00967_43_000000000-A3JHG_1_1101_23552_5194/ab=1/ * * * * * * * * * * * * * * N |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.error.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.error.summary Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +query reference weight AA AT AG AC TA TT TG TC GA GT GG GC CA CT CG CC NA NT NG NC Ai Ti Gi Ci Ni dA dT dG dC insertions deletions substitutions ambig matches mismatches total error numparents +M00967_43_000000000-A3JHG_1_1101_11148_6457 P.gingivalis.1 1 60 0 0 0 0 56 0 0 0 0 85 0 0 0 0 52 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 253 0 253 0.000000 1 +M00967_43_000000000-A3JHG_1_1101_7079_6722 E.coli.1 1 64 0 0 0 0 47 0 0 0 0 91 0 0 0 0 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 253 0 253 0.000000 1 +M00967_43_000000000-A3JHG_1_1101_18269_8162 B.cereus.1 1 65 0 0 0 0 53 0 0 0 0 89 0 0 0 0 46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 253 0 253 0.000000 2 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.fasta Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,44 @@ +>M00967_43_000000000-A3JHG_1_1101_19936_3208 +TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_15923_3823 +TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCGG +>M00967_43_000000000-A3JHG_1_1101_14010_4122 +TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGTCTGTAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_13293_4703 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_24357_4866 +TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGG +>M00967_43_000000000-A3JHG_1_1101_23552_5194 +TACAGAGGGTGCGAGCGTTAATCGGATTTACTGGGCGTAAAGCGTGCGTAGGCGGCTTATTAAGTCGGATGTGAAATCCCCGAGCTTAACTTGGGAATTGCATTCGATACTGGTGAGCTAGAGTATGGGAGAGGATGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGATGGCGAAGGCAGCCATCTGGCCTAATACTGACGCTGAGGTACGAAAGCATGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_7326_5417 +TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCTG +>M00967_43_000000000-A3JHG_1_1101_11148_6457 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_7079_6722 +TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_8607_6805 +TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_15208_7185 +TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCGG +>M00967_43_000000000-A3JHG_1_1101_4525_7317 +TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_9121_7358 +TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_8480_7498 +TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAACCATTGTACGCTTTGGAAACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_11790_7581 +TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGG +>M00967_43_000000000-A3JHG_1_1101_20566_7622 +TACGGAGGGTGCAAGCGTTACTCGGAATCACTGGGCGTAAAGAGCGCGTAGGCGGGATAGTCAGTCAGGTGTGAAATCCTATGGCTTAACCATAGAACTGCATTTGAAACTACTATTCTAGAGTGTGGGAGAGGTAGGTGGAATTCTTGGTGTAGGGGTAAAATCCGTAGAGATCAAGAGGAATACTCATTGCGAAGGCGACCTGCTGGAACATTACTGACGCTGATTGCGCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_10073_7632 +TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAACCATTGTACGCTTTGGAAACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACCGG +>M00967_43_000000000-A3JHG_1_1101_5170_7771 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_18966_7778 +TACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGGGCGCAGACGGTTACTTAAGCAGGATGTGAAATCCCCGGGCTCAACCCGGGAACTGCGTTCTGAACTGGGTGACTCGAGTGTGTCAGAGGGAGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCTCCTGGGACAACACTGACGTTCATGCCCGAAAGCGTGGGTAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_5494_7973 +TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_10246_8076 +TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAGGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_18269_8162 +TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTCACTGACGCTGAGGCTCGAAAGCGTGGGTAGCGAACAGG |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.names --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.names Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,9 @@ +M00967_43_000000000-A3JHG_1_1101_19936_3208 M00967_43_000000000-A3JHG_1_1101_19936_3208 +M00967_43_000000000-A3JHG_1_1101_15923_3823 M00967_43_000000000-A3JHG_1_1101_15923_3823 +M00967_43_000000000-A3JHG_1_1101_14010_4122 M00967_43_000000000-A3JHG_1_1101_14010_4122 +M00967_43_000000000-A3JHG_1_1101_13293_4703 M00967_43_000000000-A3JHG_1_1101_13293_4703,M00967_43_000000000-A3JHG_1_1101_11148_6457 +M00967_43_000000000-A3JHG_1_1101_24357_4866 M00967_43_000000000-A3JHG_1_1101_24357_4866 +M00967_43_000000000-A3JHG_1_1101_23552_5194 M00967_43_000000000-A3JHG_1_1101_23552_5194 +M00967_43_000000000-A3JHG_1_1101_7326_5417 M00967_43_000000000-A3JHG_1_1101_7326_5417 +M00967_43_000000000-A3JHG_1_1101_7079_6722 M00967_43_000000000-A3JHG_1_1101_7079_6722 +M00967_43_000000000-A3JHG_1_1101_8607_6805 M00967_43_000000000-A3JHG_1_1101_8607_6805 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +M00967_43_000000000-A3JHG_1_1101_14010_4122 M00967_43_000000000-A3JHG_1_1101_14010_4122 +M00967_43_000000000-A3JHG_1_1101_13293_4703 M00967_43_000000000-A3JHG_1_1101_13293_4703,M00967_43_000000000-A3JHG_1_1101_11148_6457 + |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ng.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ng.fasta Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,20 @@ +>M00967_43_000000000-A3JHG_1_1101_19936_3208 +TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_15923_3823 +TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCGG +>M00967_43_000000000-A3JHG_1_1101_14010_4122 +TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGTCTGTAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_13293_4703 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_24357_4866 +TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGG +>M00967_43_000000000-A3JHG_1_1101_23552_5194 +TACAGAGGGTGCGAGCGTTAATCGGATTTACTGGGCGTAAAGCGTGCGTAGGCGGCTTATTAAGTCGGATGTGAAATCCCCGAGCTTAACTTGGGAATTGCATTCGATACTGGTGAGCTAGAGTATGGGAGAGGATGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGATGGCGAAGGCAGCCATCTGGCCTAATACTGACGCTGAGGTACGAAAGCATGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_7326_5417 +TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCTG +>M00967_43_000000000-A3JHG_1_1101_11148_6457 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_7079_6722 +TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_8607_6805 +TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.pintail.accnos --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.pintail.accnos Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +M00967_43_000000000-A3JHG_1_1101_15923_3823 +M00967_43_000000000-A3JHG_1_1101_13293_4703 +M00967_43_000000000-A3JHG_1_1101_24357_4866 +M00967_43_000000000-A3JHG_1_1101_11148_6457 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,20 @@ +>M00967_43_000000000-A3JHG_1_1101_19936_3208 +CCTGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAGACCAGAGAGCCGCCTTCGCCACTGGTGTTCCTCCATATATCTACGCATTTCACCGCTACACATGGAATTCCACTCTCCTCTTCTGCACTCAAGTCTCCCAGTTTCCAATGACCCTCCCCGGTTGAGCCGGGGGCTTTCACATCAGACTTAAGAAACCGCCTGCGCTCGCTTTACGCCCAATAAATCCGGACAACGCTTGCCACCTACGTA +>M00967_43_000000000-A3JHG_1_1101_15923_3823 +CCGGTTTGCTCCCCACACTTTCGCGCCTCAGCGTCACCTTCTGTCCAGTAACTTGCCTTCGCCATTGGTGTTCCTCCTGGTATCTACGCATTCCACCGCTACACCAGGAATTCCAGTTACCTCTCCAGAGGTCAAGAAATCCAGTATCCAGTCCATCCCCGAGGTTGAGCCCCGGTCTTTAAAACCAGACTTAAATTTCCGCCTACACGCCCTTTACGCCCAGTGATTCCGGGTAACGCTTGCACCCTCCGTA +>M00967_43_000000000-A3JHG_1_1101_14010_4122 +CCTGTTTGCTCCCCACGCTTTCGCGCCTCAGTGTCAGTTACAGACCAGAAAGCCGCCTTCGCCACTGGTGTTCCTCCATATCTCTACGCATTTCACCGCTACACATGGAATTCCACTTTCCTCTTCTGCACTCAAGTCTCCCAGTTTCCAATGACCCTCCACGGTTGAGCCGTGGGCTTTCACATCAGACTTAAGAAACCACCTGCGCGCGCTTTACGCCCAATAATTCCGGATAACGCTTGCCACCTACGTA +>M00967_43_000000000-A3JHG_1_1101_13293_4703 +CCTGTTTGATACCCACGCCTTCGTGCTTCAGTGTCAGTCGCAGTATGGCAAGCTGCCTTCGCAATCGGAGTTCCTCGTGATATCTATGCATTTCACCGCTACACCACGAATTCCGCCTGCCGCCGCTGAACTCAAGCCCGGCAGTTTCAACGGCAGGCTGAACGTTGAGCGCTCAGGTTTCACCGCTGACTTACCGAACAACCTACGCACCCTTTAAACCCAATAAATCCGGATAACGCTCGCATCCTCCGTA +>M00967_43_000000000-A3JHG_1_1101_24357_4866 +CCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTAACGGCCCAGAGACCCGCCTTCGCCACCGGTGTTCTTCCTGATATCTGCGCATTCCACCGCTACACCAGGAGTTCCAGTCTCCCCTACCGCACTCAAGTCAGCCCGTACCCACCGCACGCCCCCAGTTAAGCCAGAGGATTTCACGGCAGACGCGACCAACCGCCTACAAGCCCTTTACGCCCAATAATTCCGGACAACGCTCGCGCCCTACGTA +>M00967_43_000000000-A3JHG_1_1101_23552_5194 +CCTGTTTGCTCCCCATGCTTTCGTACCTCAGCGTCAGTATTAGGCCAGATGGCTGCCTTCGCCATCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCATCCTCTCCCATACTCTAGCTCACCAGTATCGAATGCAATTCCCAAGTTAAGCTCGGGGATTTCACATCCGACTTAATAAGCCGCCTACGCACGCTTTACGCCCAGTAAATCCGATTAACGCTCGCACCCTCTGTA +>M00967_43_000000000-A3JHG_1_1101_7326_5417 +CAGGTTTGCTCCCCACACTTTCGCGCCTCAGCGTCACCTTCTGTCCAGTAACTTGCCTTCGCCATTGGTGTTCCTCCTGGTATCTACGCATTCCACCGCTACACCAGGAATTCCAGTTACCTCTCCAGAGGTCAAGAAATCCAGTATCCAGTCCATCCCCGAGGTTGAGCCCCGGTCTTTAAAACCAGACTTAAATTTCCGCCTACACGCCCTTTACGCCCAGTGATTCCGGGTAACGCTTGCACCCTCCGTA +>M00967_43_000000000-A3JHG_1_1101_11148_6457 +CCTGTTTGATACCCACGCCTTCGTGCTTCAGTGTCAGTCGCAGTATGGCAAGCTGCCTTCGCAATCGGAGTTCCTCGTGATATCTATGCATTTCACCGCTACACCACGAATTCCGCCTGCCGCCGCTGAACTCAAGCCCGGCAGTTTCAACGGCAGGCTGAACGTTGAGCGCTCAGGTTTCACCGCTGACTTACCGAACAACCTACGCACCCTTTAAACCCAATAAATCCGGATAACGCTCGCATCCTCCGTA +>M00967_43_000000000-A3JHG_1_1101_7079_6722 +CCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACGAGACTCAAGCTTGCCAGTATCAGATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCTCCGTA +>M00967_43_000000000-A3JHG_1_1101_8607_6805 +CCTGTTTGATCCCCACGCTTTCGCACATCAGCGTCAGTTACAGACCAGAAAGTCGCCTTCGCCACTGGTGTTCCTCCATATCTCTGCGCATTTCACCGCTACACATGGAATTCCACTTTCCTCTTCTGCACTCAAGTTTTCCAGTTTCCAATGACCCTCCACGGTTGAGCCGTGGGCTTTCACATCAGACTTAAAAAACCGCCTACGCGCGCTTTACGCCCAATAATTCCGGATAACGCTTGCCACCTACGTA |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.accnos --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.accnos Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +M00967_43_000000000-A3JHG_1_1101_18269_8162 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.alns --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.alns Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,36 @@ + +------------------------------------------------------------------------ +Query ( 253 nt) M00967_43_000000000-A3JHG_1_1101_18269_8162 +ParentA ( 542 nt) B.cereus.1 +ParentB ( 541 nt) S.mutans.1 + +A 178 TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCC 257 +Q 1 TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCC 80 +B 178 TACGTAGGTccCgAGCGTTgTCCGGAtTTATTGGGCGTAAAGgGaGCGCAGGcGGTcaggaAAGTCTGgaGTaAAAGgCt 257 +Diffs AA A A A A A A AAAAA AA A A A +Votes ++ + + + + + + +++++ ++ + + + +Model AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +A 258 ACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTG 337 +Q 81 ACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTG 160 +B 258 AtGGCTCAACCaTaGtGtG-CtcTGGAAACTGtctGACTTGAGTGCAGAAGgGGAgAGTGGAATTCCATGTGTAGCGGTG 336 +Diffs A A A A A AA AAA A A +Votes + + + + + ++ +++ + + +Model AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +A 338 AAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAgGCGaCTtTCTGGTCTGTaACTGACaCTGAGGCgCGAAAGCGTG 417 +Q 161 AAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTCACTGACGCTGAGGCTCGAAAGCGTG 240 +B 337 AAATGCGTAGAtATATGGAGGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTCACTGACGCTGAGGCTCGAAAGCGTG 416 +Diffs A B B B B B B +Votes + + + + + + + +Model AAAAAAAAAAAAxxxxxxxxxxxxxxxxxxxxxxxBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB + +A 418 GGgAGCaAACAGG 430 +Q 241 GGTAGCGAACAGG 253 +B 417 GGTAGCGAACAGG 429 +Diffs B B +Votes + + +Model BBBBBBBBBBBBB + +Ids. QA 96.8%, QB 87.7%, AB 84.5%, QModel 100.0%, Div. +3.3% +Diffs Left 32: N 0, A 0, Y 32 (100.0%); Right 8: N 0, A 0, Y 8 (100.0%), Score 2.0408 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Score Query ParentA ParentB IdQM IdQA IdQB IdAB IdQT LY LN LA RY RN RA Div YN +0.0000 M00967_43_000000000-A3JHG_1_1101_11148_6457 * * * * * * * * * * * * * * N +0.0000 M00967_43_000000000-A3JHG_1_1101_7079_6722 * * * * * * * * * * * * * * N +2.0408 M00967_43_000000000-A3JHG_1_1101_18269_8162 B.cereus.1 S.mutans.1 100.0 96.8 87.7 84.5 96.8 32 0 0 8 0 0 3.28 Y |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.slayer.chimeras --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.slayer.chimeras Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,11 @@ +Name LeftParent RightParent DivQLAQRB PerIDQLAQRB BootStrapA DivQLBQRA PerIDQLBQRA BootStrapB Flag LeftWindow RightWindow +M00967_43_000000000-A3JHG_1_1101_19936_3208 no +M00967_43_000000000-A3JHG_1_1101_15923_3823 no +M00967_43_000000000-A3JHG_1_1101_14010_4122 no +M00967_43_000000000-A3JHG_1_1101_13293_4703 no +M00967_43_000000000-A3JHG_1_1101_24357_4866 no +M00967_43_000000000-A3JHG_1_1101_23552_5194 no +M00967_43_000000000-A3JHG_1_1101_7326_5417 no +M00967_43_000000000-A3JHG_1_1101_11148_6457 no +M00967_43_000000000-A3JHG_1_1101_7079_6722 no +M00967_43_000000000-A3JHG_1_1101_8607_6805 no |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.unique.align_head --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.unique.align_head Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,18 @@\n+>M00967_43_000000000-A3JHG_1_1101_19936_3208\n+...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................'..b'..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.qual --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.qual Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,50 @@\n+>M00967_43_000000000-A3JHG_1_1101_19936_3208\t\n+33 34 32 33 33 33 33 33 33 33 29 33 32 12 33 12 32 35 35 35 35 33 33 32 35 35 35 35 35 35 35 35 29 26 30 35 35 35 12 33 35 35 35 35 35 35 32 35 32 35 35 33 32 35 35 35 35 35 32 36 36 35 36 36 36 36 36 35 36 35 36 36 36 36 35 32 32 36 36 36 35 33 36 36 36 36 35 36 36 36 36 35 35 33 33 33 36 35 15 33 35 36 36 36 36 36 36 36 36 36 36 36 36 36 30 35 35 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 35 36 36 33 36 36 36 36 36 36 36 36 36 18 36 36 36 33 36 36 36 36 36 36 32 36 35 35 35 35 35 36 33 33 36 36 36 36 33 35 35 35 36 33 36 36 35 36 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 12 32 35 35 35 35 35 15 33 33 33 32 35 35 35 35 33 35 35 35 35 35 35 33 30 35 35 32 35 12 24 35 33 32 14 32 12 33 33 33 33 33 33 33 33 33 32 33 12 34 34 \n+>M00967_43_000000000-A3JHG_1_1101_15923_3823\t\n+18 32 12 30 30 12 30 24 14 1 12 30 33 32 29 26 14 32 24 12 12 35 35 35 35 32 35 32 35 35 35 35 35 32 32 32 32 32 15 35 32 30 32 30 33 35 30 35 33 30 36 35 36 35 35 35 35 35 35 33 35 35 33 35 35 35 36 36 35 36 36 36 36 36 36 36 36 30 33 36 35 33 35 36 36 36 35 36 36 36 36 33 33 35 35 35 36 33 35 36 35 36 36 36 35 36 36 36 36 33 35 36 36 36 36 36 36 36 36 36 36 36 33 36 36 36 36 36 36 35 36 36 36 35 36 33 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 35 36 36 36 36 36 36 36 35 35 35 35 35 36 36 36 35 35 30 1 35 35 36 36 36 36 35 33 33 36 33 20 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 32 35 35 33 32 35 35 35 35 35 33 35 35 35 35 35 35 35 33 35 35 33 35 33 35 35 12 33 35 35 14 32 24 35 30 33 33 33 33 32 32 30 30 32 33 33 33 \n+>M00967_43_000000000-A3JHG_1_1101_14010_4122\t\n+32 32 24 30 15 12 30 30 29 26 12 12 14 1 14 14 1 32 26 12 24 12 35 14 32 14 24 24 26 1 35 35 35 32 33 32 14 32 30 35 33 26 12 24 24 12 12 24 14 35 35 33 15 12 35 32 26 26 15 15 35 36 33 14 15 36 30 33 15 30 33 15 33 35 36 36 15 32 27 27 12 12 27 29 15 15 29 12 35 12 33 15 27 33 30 14 26 30 15 15 15 15 36 36 33 33 36 35 35 15 15 35 36 30 12 14 27 17 17 33 35 15 33 15 15 18 15 18 18 33 33 33 35 32 35 15 18 33 15 35 15 29 15 27 14 27 26 15 15 15 1 27 14 12 12 14 27 12 1 24 26 33 12 1 24 24 24 12 12 12 12 18 15 15 26 15 26 15 18 33 12 32 35 33 12 33 12 24 12 24 30 14 12 1 26 24 32 12 12 24 1 26 30 33 14 32 1 30 26 1 18 12 12 1 26 24 14 14 14 1 14 1 12 26 12 12 26 12 24 1 12 12 24 26 12 12 1 12 1 30 27 27 12 12 12 37 1 24 26 12 1 12 33 \n+>M00967_43_000000000-A3JHG_1_1101_10776_4204\t\n+16 16 12 24 14 14 14 26 26 12 2 12 15 14 15 14 14 24 12 24 12 24 14 14 30 30 14 12 15 15 12 14 14 1 15 26 26 1 15 12 15 24 1 2 30 12 15 15 26 1 15 30 1 24 24 15 15 15 33 33 35 36 32 33 14 24 12 12 15 15 15 33 32 35 33 12 33 30 12 27 12 14 14 14 14 27 12 15 12 15 15 15 15 33 15 32 36 35 29 15 15 15 15 30 14 15 15 15 15 27 14 15 15 15 15 35 14 35 29 12 33 33 14 26 15 29 15 30 1 15 15 27 15 14 14 27 14 15 30 14 27 29 26 27 14 11 2 29 30 12 12 14 12 12 12 11 17 12 11 17 33 15 15 15 15 15 33 12 15 12 17 15 33 29 30 14 11 1 24 15 12 30 2 12 15 12 12 1 12 14 27 15 12 12 24 30 12 15 12 26 14 15 2 12 12 11 12 24 14 30 2 15 12 33 30 33 24 14 12 24 15 32 35 32 1 12 15 11 15 2 1 12 12 15 24 1 12 1 12 15 12 1 24 11 11 12 24 2 14 12 29 16 \n+>M00967_43_000000000-A3JHG_1_1101_22487_4260\t\n+33 34 34 12 12 1 24 12 12 1 12 1 12 1 24 1 12 12 1 24 12 24 1 32 26 14 1 12 12 1 24 12 38 24 24 12 14 12 12 12 1 14 33 24 14 1 14 26 14 14 24 1 1 1 24 12 24 12 26 12 12 24 1 26 1 12 1 24 1 12 26 14 24 14 14 1 12 26 12 12 1 12 24 12 1 14 12 1 24 1 1 30 30 30 26 26 12 12 30 32 12 33 35 33 33 30 32 12 1 12 24 12 26 12 14 26 1 15 14 14 33 27 27 12 27 12 27 15 12 33 33 27 15 29 12 11 12 15 1 33 27 27 15 14 14 27 15 14 15 30 15 30 1 14 30 30 33 35 12 30 30 14 14 14 32 27 29 17 17 35 33 32 15 15 15 33 32 33 15 35 29 14 14 14 14 29 14 33 29 1 30 30 14 32 32 14 14 29 1 33 33 32 1 14 12 24 14 30 33 14 14 14 30 29 33 30 30 33 30 33 33 12 30 35 12 26 29 15 15 15 11 32 15 15 2 12 24 32 30 33 33 30 29 15 15 12 18 12 27 24 32 11 32 \n+>M00967_43_000000'..b'3JHG_1_1101_18966_7778\t\n+32 33 12 30 30 33 33 32 27 29 30 30 26 24 30 12 15 35 32 26 26 1 14 35 35 32 32 33 35 33 12 33 35 33 32 32 35 15 33 32 12 33 24 32 33 32 32 35 33 30 35 32 35 35 35 35 35 35 26 33 36 36 35 35 15 35 35 35 33 15 26 15 36 36 36 35 33 36 35 12 12 35 36 33 35 35 33 35 33 36 33 33 30 36 36 33 35 35 36 36 36 36 35 36 36 36 36 36 36 36 36 36 36 35 17 33 33 30 36 32 36 35 35 36 36 33 36 35 17 35 36 17 36 36 35 36 35 35 26 33 36 36 36 36 32 35 32 33 33 35 18 36 32 36 36 36 35 36 36 36 36 35 35 33 35 35 36 35 35 36 36 35 36 35 36 35 35 35 35 36 36 36 35 35 33 35 35 35 35 35 35 35 35 35 33 35 35 33 35 15 33 33 35 35 33 35 35 35 33 32 35 33 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 26 33 35 33 30 33 33 33 33 33 33 33 12 34 34 \n+>M00967_43_000000000-A3JHG_1_1101_5494_7973\t\n+33 33 12 33 30 33 33 27 24 30 24 12 26 12 32 30 35 35 35 33 33 35 36 35 35 35 35 32 36 35 36 36 36 36 35 35 35 35 35 33 14 35 35 32 35 33 35 35 35 36 36 36 36 35 35 36 35 36 36 35 35 36 36 36 36 36 36 36 35 36 36 36 35 36 35 36 33 35 36 36 36 36 36 36 36 35 30 36 36 36 36 35 35 36 36 36 36 35 36 36 35 35 36 36 36 36 35 35 35 36 36 36 35 36 36 36 36 36 35 17 35 36 36 36 36 35 36 35 36 36 36 18 35 35 33 33 33 35 33 33 36 33 36 35 36 36 35 15 35 35 36 35 36 35 36 36 36 36 35 35 35 36 36 36 33 36 36 36 35 33 35 36 35 35 35 36 36 36 36 36 30 35 35 35 35 35 35 30 32 33 33 33 35 36 36 36 32 33 35 35 30 33 32 35 35 32 32 35 33 33 35 33 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 27 35 35 35 14 26 24 35 35 33 12 14 26 32 14 32 32 30 12 33 32 \n+>M00967_43_000000000-A3JHG_1_1101_10246_8076\t\n+33 33 12 26 12 1 12 24 12 26 24 26 12 1 26 24 14 15 24 12 12 12 30 32 33 32 24 24 15 14 30 32 26 14 15 15 33 32 15 24 26 26 30 15 12 12 32 35 33 15 15 15 26 14 15 15 15 32 36 33 33 35 36 35 36 36 27 27 15 36 27 33 33 35 33 36 36 36 33 30 33 30 30 14 15 30 30 27 30 14 1 15 15 15 33 36 36 33 35 35 33 36 33 18 32 32 33 33 29 27 36 36 36 33 18 32 35 36 35 15 33 36 32 18 33 35 33 33 15 15 17 26 33 33 14 30 35 30 14 33 30 33 36 35 33 32 12 27 27 27 12 1 27 14 27 33 12 30 33 32 17 36 35 36 15 33 33 35 33 33 35 33 15 15 33 29 14 24 12 30 24 30 30 32 12 30 24 26 14 12 11 26 15 24 12 32 35 35 33 15 33 32 15 32 30 35 15 33 35 33 15 14 14 15 17 32 35 35 33 33 14 14 14 14 14 24 32 30 15 33 35 24 24 12 33 33 14 14 14 24 24 24 12 18 12 12 24 24 30 30 12 32 32 \n+>M00967_43_000000000-A3JHG_1_1101_23931_8157\t\n+33 33 26 12 1 12 12 26 1 18 1 14 24 14 24 12 14 26 12 36 24 12 32 14 14 15 32 35 24 1 33 30 1 32 26 12 15 32 15 32 33 12 12 26 24 12 12 14 26 12 33 33 18 26 26 12 15 14 33 35 26 15 33 27 27 1 14 27 27 27 27 15 30 35 36 36 18 33 27 18 30 33 35 33 35 35 36 36 35 12 35 30 33 14 35 29 27 14 1 30 35 27 33 36 30 18 33 36 36 36 33 35 35 18 2 17 30 35 35 15 18 30 35 15 32 15 33 35 15 33 30 35 33 14 35 33 17 35 15 29 29 35 17 33 15 35 15 32 15 33 36 35 35 35 36 36 36 36 33 33 35 36 35 35 36 32 15 12 27 27 12 12 33 35 17 33 32 36 35 33 12 35 30 15 1 35 15 15 14 35 14 33 12 12 33 30 32 33 12 30 15 12 15 12 15 33 15 33 32 17 15 33 17 17 17 35 15 15 15 24 32 30 33 24 14 24 32 30 1 24 14 26 32 35 33 33 14 32 24 32 32 30 32 29 15 12 30 33 30 29 12 32 32 \n+>M00967_43_000000000-A3JHG_1_1101_18269_8162\t\n+34 35 30 30 24 30 33 33 33 33 12 24 24 12 30 12 14 32 32 24 33 35 35 35 35 35 24 14 35 35 32 12 35 32 35 35 35 32 30 33 33 27 30 30 32 30 30 32 14 35 33 24 12 35 33 32 15 24 15 36 36 35 35 35 24 24 15 35 36 35 36 36 36 36 33 36 36 33 33 30 27 30 35 35 33 32 30 33 30 30 27 12 1 36 36 36 36 36 36 36 36 36 35 36 36 36 35 36 33 36 35 36 36 36 33 35 33 35 36 36 36 36 36 36 36 36 35 35 35 35 36 36 36 36 35 36 30 35 18 36 36 36 36 35 35 36 33 35 1 36 35 35 33 36 36 36 36 36 35 36 36 36 35 36 35 35 35 35 35 36 35 36 36 36 36 36 36 36 36 36 36 35 36 35 35 36 35 32 35 35 35 35 33 33 32 33 15 33 30 35 35 33 17 33 33 33 33 35 35 35 33 33 35 35 20 35 35 35 35 35 33 32 35 35 33 35 35 33 33 33 35 35 32 35 35 35 32 35 33 35 35 32 32 32 32 32 33 33 30 30 12 33 32 \n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R1_001_small.trim.contigs.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.summary Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,26 @@ +seqname start end nbases ambigs polymer numSeqs +M00967_43_000000000-A3JHG_1_1101_19936_3208 1 253 253 0 5 1 +M00967_43_000000000-A3JHG_1_1101_15923_3823 1 253 253 0 4 1 +M00967_43_000000000-A3JHG_1_1101_14010_4122 1 253 253 0 4 1 +M00967_43_000000000-A3JHG_1_1101_10776_4204 1 252 252 8 4 1 +M00967_43_000000000-A3JHG_1_1101_22487_4260 1 253 253 1 5 1 +M00967_43_000000000-A3JHG_1_1101_13293_4703 1 253 253 0 3 1 +M00967_43_000000000-A3JHG_1_1101_24357_4866 1 253 253 0 5 1 +M00967_43_000000000-A3JHG_1_1101_23552_5194 1 253 253 0 4 1 +M00967_43_000000000-A3JHG_1_1101_7326_5417 1 253 253 0 4 1 +M00967_43_000000000-A3JHG_1_1101_11148_6457 1 253 253 0 3 1 +M00967_43_000000000-A3JHG_1_1101_7079_6722 1 253 253 0 6 1 +M00967_43_000000000-A3JHG_1_1101_8607_6805 1 253 253 0 6 1 +M00967_43_000000000-A3JHG_1_1101_15208_7185 1 253 253 0 4 1 +M00967_43_000000000-A3JHG_1_1101_4525_7317 1 253 253 0 6 1 +M00967_43_000000000-A3JHG_1_1101_9121_7358 1 253 253 0 4 1 +M00967_43_000000000-A3JHG_1_1101_8480_7498 1 252 252 0 4 1 +M00967_43_000000000-A3JHG_1_1101_11790_7581 1 253 253 0 5 1 +M00967_43_000000000-A3JHG_1_1101_20566_7622 1 254 254 0 4 1 +M00967_43_000000000-A3JHG_1_1101_10073_7632 1 252 252 0 4 1 +M00967_43_000000000-A3JHG_1_1101_5170_7771 1 253 253 0 3 1 +M00967_43_000000000-A3JHG_1_1101_18966_7778 1 253 253 0 4 1 +M00967_43_000000000-A3JHG_1_1101_5494_7973 1 253 253 0 4 1 +M00967_43_000000000-A3JHG_1_1101_10246_8076 1 253 253 0 4 1 +M00967_43_000000000-A3JHG_1_1101_23931_8157 1 253 253 1 4 1 +M00967_43_000000000-A3JHG_1_1101_18269_8162 1 253 253 0 3 1 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/Mock_S280_L001_R2_001_small.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R2_001_small.fastq Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,100 @@\n+@M00967:43:000000000-A3JHG:1:1101:19936:3208 2:N:0:280\n+CCTGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAGACCAGAGAGCCGCCTTCGCCACTGGTGTTCCTCCATATATCTACGCATTTCACCGCTACACATGGAATTCCACTCTCCTCTTCTGCACTCAAGTCTCCCAGTTTCCAATGACCCTCCCCGGTTGAGCCGGGGGCTTTCACATCAGACTTAAGAAACCGCCTGCGCTCGCTTTACGCCCAATAAATCCGGACAACGCTTGCCACCTACG\n++\n+CCCCBFFFFFFFGGGGGGGGGGGGHGGHHHHGGGGGGHHGHFHGHHHHHHHGHHGGGGGHGGGGGHHHHHHGHHFHGHGHHHHHGHHGGGGGHHHHHGGGGGHH3GGHHHHHHHFHGFHHHHGHHHHHHHHHHHHHHHFHHHHHHHHHHHHHEH1FHFEDGGGGGGGHHHHCFGGGAAEGGGGGGFGGGGGGGGBFFGFGADFFAFAFFFFFFE.FFF?;>FEFFFFFFBDDFFFFA-C.AE?FFFFFFFD\n+@M00967:43:000000000-A3JHG:1:1101:15923:3823 2:N:0:280\n+CCGGTTTGCTCCCCACACTTTCGCGCCTCAGCGTCACCTTCTGTCCAGTAACTTGCCTTCGCCATTGGTGTTCCTCCTGGCATCTACGCATTCCACCGCTACACCAGGAATTCCAGTTACCTCTCCAGAGGTCAAGAAATCCAGTATCCAGTCCATCCCCGAGGTTGAGCCCCGGTCTTTAAAACCAGACTTAAATTTCCGCCTACACGCCCTTTACGCCCAGTGATTCCGGGTAACGCTTGCCCCCTCCG\n++\n+BBBB?ABBFFFFGGGGGGGGGGGCGCGGGHHHGGGGGGHHHHHHHHGHHHHHHHHHGHHHGGGGGHHH5FHGHHHHHHHG1?FFHHHGGGGGHHHHHGGGGGHHHHHGHGHHHHHGHHHFHHHFGHHGGHEHGHHGHGHHHHFBGGGHGGHHGHGDHFGFCCGGGHGHHHFEFGC@GGHHHHHHFGHEEEBFFBFFGFGGGGG?DGGGD?A?AF0CBAAAFFFFFBFBFFFF-.9B/;>AEA.//:B-AD.\n+@M00967:43:000000000-A3JHG:1:1101:14010:4122 2:N:0:280\n+CCTGTTTGCTCCCCACGCTTTCGCGCCTCAGTGTCAGTTACAGACCAGAAAGCCGCCTTCGCCACTGGTGTTCCTCCATATCTCTACGCATTTCACCGCTACACATGGAATTCCACTTTCCTCTTCTGCACTCAAGTCTCCCAGTTTCCAATGACCCTCCACGGTTGAGCCGTGGGCTTTCACATCAGACTTAAGAAACCACCTGCGCGCGCTTTACGCCCAAAAATTCCGGATAAAGCCTGCCACCTACG\n++\n+BBBBBFFFBFDFGGGGGGGGGGGFGGGGFGHGGHHHHHHCHC3EGHHGFHEH3BFGGGGHHGDGGBGHBFGGHF4GGBEGF4FGHHHGGGGGGHHHHGG/EGHHFB??3BBGHH?G4FGGFDGF33B3DDFBHH22>@2FGGFHGFHHDGH1111G<<FDB0C-F.>01><-.<<AEHGFF0CC0CBG0/CGH00;;CH.CEGF/9--:9-;BF?B/ADAFFF.;99/B/F-9.;B///./..;BF?.;B9\n+@M00967:43:000000000-A3JHG:1:1101:10776:4204 2:N:0:280\n+CCTGATTGATACCCACACTTTCGAGCCTCAATGTCAGTTGCCGCTTAGCAGGCTGCCTTCGCAACCGGAGTTCCCCGTGATATCTAAGCATTTCACCGCTACACCCCGAATTCCGCCTGCCTCCACTGCACTCAAGATATCCAGTATCAACTGCAATTTTACGGTTGAGCCGCAAACTTTCACAACTGACTTAAACATCTATATACGCCACCTTAAAATCCAATAAATCCGGATACACCTCGTATCCTCCG\n++\n+1>AA1B311@FD1BBEEE111B0000AFBGG1A2FEFBF111A/AE/FF11/AG0CCFF1AA/B/B/>//BG1B@0/?>F>22@2B1BE1GD22B21////>FFG///E<?<>B0<?//0<1@/@0>1@1FH0?F1F11111<11111@1010>FHB1F111>.0.<//CG-<-AC.CGCC0000.:/CBGFBB0009:;C00;00.C-.9A.00;;00//00;/BFF//:-9-9///9/:---;;///9-\n+@M00967:43:000000000-A3JHG:1:1101:22487:4260 2:N:0:280\n+CCTGTTCGCTCCCCACGCCTTCGCTCCTCAGCGTCAGTAACGGCCCAGAGCCCCCCCTTCGCCCCCGGTGTTCTTCCTGATATCTGCGCATTCCACCGCTCCACCAGGAGTTCCTGTCTCCCCTACCGCACTCAAGCCAGCCCGCACCCACCGCACGCCCCCCCTCAACCCACAGGACTTCACGCCCGCCCCGACCAACACACTACATGCCCGTTAACGCCAACAAATCCCGACCACACCCCCCCCCCAC\n++\n+A1AAAB3>11>AFEFGCC000F00E0AGGGFFCEAE?BFFF///E?/A//0BFE/>//BB/?E/>E/>////BG1EBF1F1GEG22>>B///@DDGF?@//?1?0/0<//0<<F11111>1<EF.0<-<-<<C//00;/.;.:---A?CGGG.A?--;;@@@--9--/--9----;--//9/;--9---;;9--;-9-9---9//;///:B/-----/-99-9----/;B/:-9----9-------9---\n+@M00967:43:000000000-A3JHG:1:1101:13293:4703 2:N:0:280\n+CCTGTTTGATACCCACGCCTTCGTGCTTCAGTGTCAGTCGCAGTATGGCAAGCTGCCTTCGCAATCGGAGTTCCTCGTGATATCTATGCATTTCACCGCTACACCACGAATTCCGCCTGCCGCCGCTGAACTCAAGCCCGGCAGTTTCAACGGCAGGCTGAACGTTGAGCGCTCAGGTTTCACCGCTGACTTACCGAACAACCTACGCAACCCTTAAACCCAATAAAACCGGATAACGCTCGCAACCTCC\n++\n+AAB@BFBFFFFFGGGGEGGGGGHGFGFFGBGGBAFGGHHGGEGGHHFGGHHGGAGHHHHHHGGGGHED?EGHHHFHDGHF3FGGFFHHGHHGHFHHHEEEFEHHGHHGGGAGHHGGFEHHFFGCDCGGCHHHHEHFFGHC<A-AF1FFHGH.@C-<-:GC.0GA::.;:0-;.C./;00;;00:9?@CF/0;BFGB.9@BF.D:/9.-.-9..;BBF//:AE../B///A=BD.;//99..@9=.-;//;\n+@M00967:43:000000000-A3JHG:1:1101:24357:4866 2:N:0:280\n+CCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTAACGGCCCAGAGACCCGCCTTCGCCACCGGTGTTCTTCCTGATATCTGCGCATTCCACCGCTACACCAGGAGTTCCAGTCTCCCCTACCGCACTCAAGTCAGCCCGTACCCACCGCACGCCCCCAGTTAAGCCAGAGGATTTCACGGCAGACGCGACCAACCGCCTACAAGCCCTTTACGCCCACTAATTCCGGACAACGCTCGCGCCCTACG\n++\n+BBB@BFFBBBBBGGGF2EGFGGGGFHGHGFFHGFEGGHHGFGGGGGEHEEFFFH?GGGGHHGGGGHGG/EGGHHFHHBFGFG4FGBGGGGGEHHHHHE?CGGHHH/<FCFGHHHHHF2@GHGGEG?CG?ADGHHHGHHHFFHGGGGFE<0:C.@DGGGEGGG-9FF09FGGF..;..FGGGBB9.;-9.FA;BFFFF?D9--@ADFF/BF?EFFFBFED@BA.9B//;BFF-DBBFFBF9D---@BC-.A.\n+@M00967:43:000000000-A3JHG:1:'..b'GHABCGBDGGGGGEGGGGGGG0FFFFFFAAF09.CDFEEFFFFEF\n+@M00967:43:000000000-A3JHG:1:1101:10073:7632 2:N:0:280\n+CCGGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAGACCAGAGAGCCGCTTTCGCCACCGGTGTTCCTCCATATATCTACGCATTTCACCGCTACACATGGAATTCCACTCTCCCCTTCTGCACTCAAGTCCTCCAGTTTCCAAAGCGTACAATGGTTAAGCCACTGCCTTTAACTTCAGACTTAAAGAACCGCCTGCGCTCGCTTTACGCCCAATAAATCCGGACAACGCTCGGGACCTACGT\n++\n+ABA?ABBBFFFFGGGGGGGGGGFGHGGHHGHHGGGGGHHHHHHHHHHHEHGFGHEGAEGHGGGGGHGG>EFEHHHHHHHGHHHHGHHGGGGGHHEHHGGGGGEH3E3GHHHHHHHHFHHHHHGGHFGHHHHHHHHFGHHHHHGFHFGHHHHEGHDDDDDDDDHFHFHHHHBGCGGHHHGFHHHFFCHGHHHHFCCGCBGD?BCEG-D?EFAAEG0/9DDFFFFFFFFFFAF?CFFF-@.D-@;-9A9FFB;\n+@M00967:43:000000000-A3JHG:1:1101:5170:7771 2:N:0:280\n+CCTGTTTGATACCCACGCCTTCGTGCTTCAGTGTCAGTCGCAGTATGGCAAGCTGCCTTCGCAATCGGAGTTCCTCGTGATATCTATGCATTTCACCGCTACACCACGAATTCCGCCTGCCGCCGCTGAACTCAAGCCCGGCAGTTTCAACGGCAGGCTGAACGTTGAGCGCTCAGGGTTCACCGCTGCCTTACCGAACAACCTCCGGACCCTTTAAACCCAATAAATCCGGATAACGCTCGCCTCCCACG\n++\n+>ABBBFFFFFFFGFGGGGCGGGHFGAFHGGG5DGHBGG52EGGGHEHHFGHGHFHHHGFHEGGGFHGGEGGG5GH5EGFGHFFDGFFF3FGHHFFHGGEFGGGHCH/?EFHHHHHG?GEFHGGGC/B@DF2FHHGHHGHGCGGGHHFHGHD.@?-CFGCGCGHAGB../;;@.9./C.99;0CFBDFG..9FB/BDA-9-9.AB/.;-.;;AFFF/9;/9DE..//;BB/9>D.A//.-..---.....9-\n+@M00967:43:000000000-A3JHG:1:1101:18966:7778 2:N:0:280\n+CCTGTTTGCTACCCACGCTTTCGGGCATGAACGTCAGTGTTGTCCCAGGAGGCTGCCTTCGCCATCGGTATTCCTCCACATCTCTACGCATTTCACTGCTACACGTGGAATTCTACCTCCCTCTGACACACTCGAGTCACCCAGTTCAGAACGCAGTTCCCGGGTTGAGCCCGGGGATTTCACATCCTGCTTAAGTAACCGTCTGCGCCCGCTTTACGCCCAGTAATTCCGCTTAACGCTCGCACCCTACG\n++\n+CCCCCFFFFFFFGGGGGGGGGGGGGGGHHHGHHHHGGHHHHDHHHHHHFHGDE1GFHHFHGGGGGHGGEHGHHHHHHFHGHGHHFFHFFEGGHHHHGHHHBG3GEBAFAGHHHHFFGHGHG2GF2FGDGHGFHAH?GF2FHHGHHHHHHHFHGGGGGFHHHECGDFCFGCHG--EGCEHHH0;0CFGF0FFGGB;FFGFFFAF?EGABDB:D-AE0FAABFB.BFEBBFF/.;;AF0.@:;BA>>FDFFA.\n+@M00967:43:000000000-A3JHG:1:1101:5494:7973 2:N:0:280\n+CCTGTTTGATACCCACACTTTCGAGCCTCAATGTCAGTTGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTCTTCGTGATATCTAAGCATTTCACCGCTACACCACGAATTCCGCCTGCCTCAACTGCACTCAAGATATCCAGTATCAACTGCAATTTTACGGTTGAGCCGCAAACTTTCACAACTGACTTAAACATCCATCTACGCTCCCTTTAAACCCAATAAATCCGGATAACGCTCGGATCCTCCG\n++\n+ABAABFFFFFFFGGGGFGGGGGGGHGGHHGHGHHHHGHHHHHHHHHGBGHBEEHHGHHHHGGGGGHGGGGGHHHHHGHFHHHGHHHHHFHHHHGGHHGGGGGHGH1GGGGHHHHFGGEEGF3GGHFHFHHHHF2FHHHHHEHHHGGFGHHGFFHHEHHHHHGGGHG?GHHHGGGGGCGFHGHGHHGHGHHHHFHHHGHFFHHHHGGGCEAEE/BGGGGFGGGGFGBFFFGGGDDFGF?A.;-9A9>FFBF.\n+@M00967:43:000000000-A3JHG:1:1101:10246:8076 2:N:0:280\n+CCTGTTTGATACCCACACTTTCGAGCCTCAATGTCAGTTGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTCCTCGTGATATCTAAGCATTTCACCGCTACACCACGAATTCCGCCTGCCTCAACTGCACTCAAGATATCCAGTATCAACTGCAATTTTACCGTTGAGCCGCAAACTTTCACAACTGACTTAAACATCCATCTACGCTCCCTTTAAACCCAATAAATCCGGATAACGCCCGGATCCCCCG\n++\n+AAAAAFF113DFGGGGGGGGGGGF0AEFHHHHFFFGHB21FB1FGD1GHF1CE0FFFGHHHG/E/FBA/AAFFD2F/>B00DGHHFFHHGGH2EFGHEC@EE1GECGGGGHEHHBEGA/CC<F11FFFFGGHH0FHFGGDGHH<>FFGBGFGCFHBGHE1111/?<?A1FG@C?CGHHDHFD<G0<=GHFHHHCGB000/;000CGA-.CC;;90BF00/;AA/0:9BCBA-..90/9;--;9;-9---;-\n+@M00967:43:000000000-A3JHG:1:1101:23931:8157 2:N:0:280\n+CCTGTTTGCTCCCCACGCTTTCGAGCCTCAGTGTCAGTTACAGTCCAGAAAGTCGCCTTCGCCACTGGGATTCTTCCTAATCTCTACGCATTTCACCGCTACACTAGGAATTCTACTTTCCTCTCCTGCACTCTAGATCTCCAGTTTGGAATGCCGCACCCAGGTTAAGCCCGAGTATTTCACATCCAACTTAAATATCCACCTACGCTCCCTTTACGCCAAGAAAATCCGGAAACAGCTTGACCCCTCCG\n++\n+AAAAAFDF1BFFGGGGGGGGGGGGHGEHHHHAFHHHHH222F12BF1F1F1G1BEFGGGHHG/E/1BG/0BGHHFHBG2FF1FHHH1FGGGGHHHHHGGGGGHH1F1G1FGHHBBF2FGHDGGFHFD1BGHFH1FGH21>FGHHHHHGCGD<GH1><CG/CCF.FGHGFEGECG@EGHHHB0==<</0<<C0;FH000;;:CC.;/.-:;..CC0C0.;AA@E.:FB0//A-9-;//-9/:/;9/;----;\n+@M00967:43:000000000-A3JHG:1:1101:18269:8162 2:N:0:280\n+CCTGTTCGCTACCCACGCTTTCGAGCCTCAGCGTCAGTGACAGACCAGAGAGCCGCTTTCGCCACTGGTGTTCCTCCATATCTCTACGCATTTCACCGCTACACCTGGAATTCCACTTTCCTCTTCTGCACTCAAGTCTCCCAGTTTCCAATGACCCTCCCCGGTTGAGCCGTGGGCTTTCACATCAGACTTAAGAAACCACCTGCGCGCGCTTTACGCCCAATAATTCCGGATAACGCTTGCCACCTACG\n++\n+ABB@AFFBBBBBGGGGGGGGGGGCFFGHCHHBFGGGGH5GHFFGHHCFFC2EGH?E0EADEGGGGBFHFGHGHHHHHHHHHGGHGFFEEGFGHHHHHGGGCFFH3FCGFFGHHH3F?GFHHHHFFFFHHHHHHHGFDGDGGHEGBGFHHHEHHHHHHHHG..<@@D?CCGG@<@CCGHEHHGHFHF0::FFFGG090BFG.9CF/A??B?@=BD?BFEFAF.AFF/9FFFFFD9AB/.@.::.FFFF?9BA\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/abrecovery.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abrecovery.fasta Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,2301 @@\n+>AY457915\n+CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGC\n+ATTTAAGACAGATTACTTCGGTTTGAAGTCTTTTATGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGT\n+AACCTGCCTCATACAGGGGGATAGCAGCTGGAAACGGCTGGTAATACCGCATAAGCGCACAGTACCACAT\n+GGTACAGTGTGAAAAACTCCGGTGGTATGAGATGGACCCGCGTCTGATTAGCTTGTTGGCGGGGTAACGG\n+CCCACCAAGGCGACGATCAGTAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCA\n+GACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGAGGAAACTCTGATGCAGCGACGCCGCGTG\n+AGTGAAGAAGTAGTTCGCTATGTAAAGCTCTATCAGCAGGGAAGATAGAGACGGTACCTGACTAAGAAGC\n+TCCGGCAAATC\n+\n+>AY457914\n+CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGC\n+ATTTAGAACAGATTACTTCGGTTTGAAGTTCTTTATGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGT\n+AACCTGCCTTGTACTGGGGGATAGCAGCTGGAAACGGCTGGTAATACCGCATAAGCGCACAATGTTGCAT\n+GACATGGTGTGAAAAACTCCGGTGGTATAAGATGGACCCGCGTCTGATTAGCTAGTTGGTGAGATAACAG\n+CCCACCAAGGCGACGATCAGTAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCA\n+GACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGAGGAAACTCTGATGCAGCGACGCCGCGTG\n+AGTGAAGAAGTAATTCGTTATGTAAAGCTCTATCAGCAGGGAAGATAGAGACGGTACCTAACTAAGAAGC\n+TCCGGCTAA\n+\n+>AY457913\n+CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGC\n+ACTTTTACAGATTTCTTCGGAATGAAGTTTTAGTGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGTAA\n+CCTGCCTCACACAGGGGGATAACAGTTGGAAACGGCTGCTAATACCGCATAAGCGCACAGTACCGCATGG\n+TACAGTGTGAAAAACTCCGGTGGTGTGAGATGGACCCGCGTCTGATTAGCTAGTTGGCAGGGTAACGGCC\n+TACCAAGGCGACGATCAGTAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCAAA\n+CTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAG\n+CGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAGAAATGACGGTACCTGACTAAGAAGC\n+ACCGGCAAATCTG\n+\n+>AY457912\n+CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGC\n+ATTTGCGACAGATTTCTTCGGATTGAAGTTGCTTATGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGT\n+AACCTGCCTCACACAGGGGGATAGCAGTTGGAAACGGCTGATAATACCGCATAAGCGCACAGTACCGCAT\n+GGTACAGTGTGAAAAACTCCGGTGGTGTGAGATGGACCCGCGTCTGATTAGCTTGTTGGCAGGGTAACGG\n+CCTACCAAGGCAACGATCAGTAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCA\n+GACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGAGGAAACTCTGATGCAGCGACGCCGCGTG\n+AGTGAAGAAGTAATTCGTTATGTAAAGCTCTATCAGCAGGGAAGATAGTGACGGTACCTGACTAAGAAGC\n+TCCGGCTAATCGT\n+\n+>AY457911\n+CCCTTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGCGCCTAACACATGCAAGTCGAACGAGCG\n+AGAGAGAGTTTACTTTTTCGAGCGAGTGGCGAACGGGTGAGTAACGCGTGAGGAACCTGCCTCAAAGAGG\n+GGGACAACAGTTGGAAACGACTGCTAATACCGCATAAGCCCACGACCCGGCATCGGGTAGAGGGAAAAGG\n+AGCAATCCGCTTTGAGATGGCCTCGCGTCCGATTAGCTAGTTGGTGAGGTAACGGCCCACCAAGGCGACG\n+ATCGGTAGCCGGACTGAGAGGTTGAACGGCCACATTGGGACTGAGACACGGCCCGGACTCCTACGGGAGG\n+CAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGGAGGAAGAAGGTCTT\n+CGGATTGTAAACTCCTGTTGTTGGGGGAGATAATGACGGTACTCAACAGGGAAGGACGGCTACTCTG\n+\n+>AY457910\n+CCCTTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGCGCCTAACACATGCAAGTCGAACGAGAG\n+AGAGGGAGCTTGCTTCCTTGATCGAGTGGCGAACGGGTGAGTAACGCGTGAGGAACCTGCCTCAAAGAGG\n+GGGACAACAGTTGGAAACGACTGCTAATACCGCATAAGCCCACGACCCGGCATCGGGTAGAGGGAAAAGG\n+AGCAATCCGCTTTGAGATGGCCTCGCGTCCGATTAGCTAGTTGGTGAGGTAATGGCCCACCAAGGCGACG\n+ATCGGTAGCCGGACTGAGAGGTTGAACGGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAGG\n+CAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGGAGGAAGAAGGTCTT\n+CGGATTGTAAACTCCTGTTGTGAGGAAGATAAAGACGGTCTCAACAAGGAAGGACGGCTACTC\n+\n+>AY457909\n+CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTAGCTACAGGCTTAACACATGCAAGTCGAGGGGCAG\n+CATGGTCTTAGCTTGCTAAGGCCGATGGCGACCGGCGCACGGGTGAGTAACGCGTATCCAACCTGCCTTA\n+CACTCTTGGACAGCCTTCTGAAAGGGAGATTAATACAAGATGTTATCATGAGTAAGCATTTTCGCATGAT\n+TAAAGGTTTACCGGTGTAAGATGGGGATGCGTTCCATTAGATAGTAGGCGGGGTAACGGCCCACCTAGTC\n+TTCGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAAGCTCCTACGG\n+GAGGCAGCAGTGAGGAATATTGGTCAATGGACGAGAGTCTGAACCAGCCAAGTAGCGTGAAGGATGAAGG\n+TTCTATGGATTGTAAACTTCTTTTATACGGGAATAAACGAATCCACGTGTGGATTTAGCAGTACCGATGA\n+ATA\n+\n+>AY457908\n+CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGC\n+ACTTTGATCGATTTCTTCGGATTGGAATTTTAGTGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGTAA\n+CCTGCCTCACACAGGGGGATAACAGTTGGAAACGGCTGCTAATACCGCATAAGCGCACAGTACCGCATGG\n+TACAGTGTGAAAAACTCCGGTGGTGTGAGATGGACCCGCGTCTGATTAGCTAGTTGGCAGGGTAACGGCC\n+TACCAAGGCGAC'..b'TCGCAAGACCAAAGTGGGGGACCTTCGGGC\n+CTCATGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGAGGTAACGGCTCACCTAGGCGACGATC\n+CCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAG\n+CAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGG\n+GTTGTAAAGCACTTTCAGCGGGGAGGAAGGCGTTAAGGTTAATAACCTTGGCGATTGACGTACCCGCAGA\n+AGAAGCCACCGGCAACTCC\n+\n+>AY457680\n+CCCTTAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAA\n+CAGGAAGCAGCTTGCTGCTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGG\n+AGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGG\n+GCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGA\n+TCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGGCACGGTCCAGACTCCTACGGGAGGC\n+AGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTC\n+GGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGCTGAGGTTAATAACCTCAGCAATTGGCGTACCCGCA\n+GAAGAAGCCCGCACTCG\n+\n+>AY457679\n+GCCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTAGCGACAGGCTTAACACATGCAAGTCGAGGGGCA\n+GCACAGGTAGTAATACCGGGTGGCGACCGGCGCACGGGTGAGTAACGCGTATGCAACTTGCCTATCAGAG\n+GGGGATAACCCGGCGAAAGTCGGACTAATACCGCATGAAGCAGGGGCCCCGCATGGGGATATTTGCTAAA\n+GATTCATCGCTGATAGATAGGCATGCGTTCCATTAGGCAGTTGGCGGGGTAACGGCCCACCAAACCGACG\n+ATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGTACTGAGACACGGACCAAACTCCTACGGGAGG\n+CAGCAGTGAGGAATATTGGTCAATGGCCGAGAGGCTGAACCAGCCAAGTCGCGTGAGGGATGAAGGTTCT\n+ATGGATCGTAAACCTCTTTTATAAGGGAATAAAGTGTGGGACGTGTCCTATTTTGTATGTACCTTAGAAT\n+AAGGATCGGCAA\n+\n+>AY457678\n+CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTAGCGACAGGCTTAACACATGCAAGTCGAGGGGCAG\n+CGGGGGTAGCAATACCCGCCGGCGACCGGCGCACGGGTGAGTAACGCGTATGCAACTTACCTATCAGAGG\n+GGGATAACCCGGCGAAAGTCGGACTAATACCGCATGGAGCAGGGATCCCGCATGGGAATATTTGCTAAAG\n+ATTCATCGCTGATAGATAGGCATGCGTTCCATTAGGCAGTTGGCGGGGTAACGGCCCACCAAACCGACGA\n+TGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGTACTGAGACACGGACCAAACTCCTACGGGAGGC\n+AGCAGTGAGGAATATTGGTCAATGGCCGAGAGGCTGAACCAGCCCAGTCGCGTGAGGGATGAAGGTTCTA\n+TGGATCGTAAACCTCTTTTATAAGGGAATAAAGTGCGGGACGTGTCCCGTTTGTATGTACCTATGATAGA\n+TGGTA\n+\n+>AY457677\n+GCCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTAGCGACAGGCTTAACACATGCAAGTCGAGGGGCA\n+GCGGGGGTAGCAATACCCGCCGGCGACCGGCGCACGGGTGAGTAACGCGTATGCAACTTACCTATCAGAG\n+GGGGATAACCCGGCGAAAGTCGGACTAATACCGCATGAAGCAGGGATCCCGCATGGGAATATTTGCTAAA\n+GAATTATCGCTGATAGATGGGCATGCGTTCCATTAGATAGTTGGTGAGGTAACGGCTCACCAAGTCCACG\n+ATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACACTGGTACTGAGACACGGACCAGACTCCTACGGGAGG\n+CAGCAGTGAGGAATATTGGTCAATGGGCGAGAGCCTGAACCAGCCAAGTCGCGTGAAGGATGAAGGATCT\n+ATGGTTTGTAAACTTCTTTTATATGGGAATAAAGTGAGGAACGTGTTCCTTTAGTATGTACCATAGAATA\n+AGCATGGCAACTCT\n+\n+>AY457676\n+GCCCTTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGCGCCTAACACATGCAAGTCGAACGAGA\n+GATGAGGAGCTTGCTCTTCAAATCGAGTGGCGAACGGGTGAGTAACGCGTGAGGAACCTGCCTCAAAGAG\n+GGGGACAACAGTTGGAAACGACTGCTAATACCGCATAAGCCCACGGCTCGGCATCGAGCAGAGGGAAAAG\n+GAGCAATCCGCTTTGAGATGGCCTCGCGTCCGATTAGCTAGTTGGTGAGGTAACGGCCCACCAAGGCGAC\n+GATCGGTAGCCGGACTGAGAGGTTGAACGGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAG\n+GCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGGAGGAAGAAGGTCT\n+TCGGATTGTAAACTCCTGTTGTGAGGAAGATAAAGACGGTACTCAACAAGGAAGCA\n+\n+>AY457675\n+GCTCAGGATGAACGCTAGCGACAGGCTTAACACATGCAAGTCGAGGGGCAGCACGATGTAGCAATACATT\n+GGTGGCGACCGGCGCACGGGTGAGTAACGCGTATGCAACCTACCTATCAGAGGGGAATAACCCGGCGAAA\n+GTCGGACTAATACCGCATAAAACAGGGGTTCCACATGGAAATATTTGTTAAAGAATTATCGCTGATAGAT\n+GGGCATGCGTTCCATTAGATAGTTGGTGAGGTAACGGCTCACCAAGTCCACGATGGATAGGGGTTCTGAG\n+AGGAAGGTCCCCCACACTGGTACTGAGACACGGACCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTG\n+GTCAATGGGCGAGAGCCTGAACCAGCCAAGTCGCGTGAAGGATGAAGGATCTATGGTTTGTAAACTTCTT\n+TTATATGGGAATAAAGTGAGGAACGTGTTCCTTTAGTATGTACCATAGAATAGCATGG\n+\n+>AY457674\n+CCCTTAGAGTTCGATCCTGGCTCAGGATGAACGCTAGCGACAGGCTTAACACATGCAAGTCGAGGGGCAG\n+CACAGGTAGCAATTCCGGGTGGCGACCGGCGCACGGGTGAGTAACGCGTATGCAACTTACCTATCAGAGG\n+GGGATAACCCGGCGAAAGTCGGACTAATACCGCATGAAGCAGGGGCCCCGCATGGGGATATTTGCTAAAG\n+ATTCATCGCTGATAGATAGGCATGCGTTCCATTAGGCAGTTGGCGGGGTAACGGCCCACCAAACCGACGA\n+TGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGTACTGAGACACGGACCAAACTCCTACGGGAGGC\n+AGCAGTGAGGAATATTGGTCAATGGCCGAGAGGCTGAACCAGCCAAGTCGCGTGAGGGATGAAGGTTCTA\n+TGGATCGTAAACCTCTTTTATAAGGGAATAAAGTGCGGGACGTGTCCCGTTAGTATGTACCTATAATAGC\n+ATCGGC\n+\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/abrecovery.groups --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abrecovery.groups Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,242 @@ +AY457915 A +AY457914 A +AY457913 A +AY457912 A +AY457911 A +AY457910 A +AY457909 A +AY457908 A +AY457907 A +AY457906 A +AY457905 A +AY457904 A +AY457903 A +AY457902 A +AY457901 A +AY457900 A +AY457899 A +AY457898 A +AY457897 A +AY457896 A +AY457895 A +AY457894 A +AY457893 A +AY457892 A +AY457891 A +AY457890 A +AY457889 A +AY457888 A +AY457887 A +AY457886 A +AY457885 A +AY457884 A +AY457883 A +AY457882 A +AY457881 A +AY457880 A +AY457879 A +AY457878 A +AY457877 A +AY457876 A +AY457875 A +AY457874 A +AY457873 A +AY457872 A +AY457871 A +AY457870 A +AY457869 A +AY457868 A +AY457867 A +AY457866 A +AY457865 A +AY457864 A +AY457863 A +AY457862 A +AY457861 A +AY457860 A +AY457859 A +AY457858 A +AY457857 A +AY457856 A +AY457855 A +AY457854 A +AY457853 A +AY457852 A +AY457851 A +AY457850 A +AY457849 A +AY457848 A +AY457847 A +AY457846 A +AY457845 A +AY457844 A +AY457843 A +AY457842 A +AY457841 A +AY457840 A +AY457839 A +AY457838 A +AY457837 A +AY457836 A +AY457835 A +AY457834 A +AY457833 A +AY457832 A +AY457831 B +AY457830 B +AY457829 B +AY457828 B +AY457827 B +AY457826 B +AY457825 B +AY457824 B +AY457823 B +AY457822 B +AY457821 B +AY457820 B +AY457819 B +AY457818 B +AY457817 B +AY457816 B +AY457815 B +AY457814 B +AY457813 B +AY457812 B +AY457811 B +AY457810 B +AY457809 B +AY457808 B +AY457807 B +AY457806 B +AY457805 B +AY457804 B +AY457803 B +AY457802 B +AY457801 B +AY457800 B +AY457799 B +AY457798 B +AY457797 B +AY457796 B +AY457795 B +AY457794 B +AY457793 B +AY457792 B +AY457791 B +AY457790 B +AY457789 B +AY457788 B +AY457787 B +AY457786 B +AY457785 B +AY457784 B +AY457783 B +AY457782 B +AY457781 B +AY457780 B +AY457779 B +AY457778 B +AY457777 B +AY457776 B +AY457775 B +AY457774 B +AY457773 B +AY457772 B +AY457771 B +AY457770 B +AY457769 B +AY457768 B +AY457767 B +AY457766 B +AY457765 B +AY457764 B +AY457763 B +AY457762 B +AY457761 B +AY457760 B +AY457759 B +AY457758 B +AY457757 B +AY457756 B +AY457755 B +AY457754 B +AY457753 B +AY457752 B +AY457751 B +AY457750 B +AY457749 B +AY457748 B +AY457747 C +AY457746 C +AY457745 C +AY457744 C +AY457743 C +AY457742 C +AY457741 C +AY457740 C +AY457739 C +AY457738 C +AY457737 C +AY457736 C +AY457735 C +AY457734 C +AY457733 C +AY457732 C +AY457731 C +AY457730 C +AY457729 C +AY457728 C +AY457727 C +AY457726 C +AY457725 C +AY457724 C +AY457723 C +AY457722 C +AY457721 C +AY457720 C +AY457719 C +AY457718 C +AY457717 C +AY457716 C +AY457715 C +AY457714 C +AY457713 C +AY457712 C +AY457711 C +AY457710 C +AY457709 C +AY457708 C +AY457707 C +AY457706 C +AY457705 C +AY457704 C +AY457703 C +AY457702 C +AY457701 C +AY457700 C +AY457699 C +AY457698 C +AY457697 C +AY457696 C +AY457695 C +AY457694 C +AY457693 C +AY457692 C +AY457691 C +AY457690 C +AY457689 C +AY457688 C +AY457687 C +AY457686 C +AY457685 C +AY457684 C +AY457683 C +AY457682 C +AY457681 C +AY457680 C +AY457679 C +AY457678 C +AY457677 C +AY457676 C +AY457675 C +AY457674 C |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/abrecovery.names --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abrecovery.names Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,242 @@ +AY457915 AY457915 +AY457914 AY457914 +AY457913 AY457913 +AY457912 AY457912 +AY457911 AY457911 +AY457910 AY457910 +AY457909 AY457909 +AY457908 AY457908 +AY457907 AY457907 +AY457906 AY457906 +AY457905 AY457905 +AY457904 AY457904 +AY457903 AY457903 +AY457902 AY457902 +AY457901 AY457901 +AY457900 AY457900 +AY457899 AY457899 +AY457898 AY457898 +AY457897 AY457897 +AY457896 AY457896 +AY457895 AY457895 +AY457894 AY457894 +AY457893 AY457893 +AY457892 AY457892 +AY457891 AY457891 +AY457890 AY457890 +AY457889 AY457889 +AY457888 AY457888 +AY457887 AY457887 +AY457886 AY457886 +AY457885 AY457885 +AY457884 AY457884 +AY457883 AY457883 +AY457882 AY457882 +AY457881 AY457881 +AY457880 AY457880 +AY457879 AY457879 +AY457878 AY457878 +AY457877 AY457877 +AY457876 AY457876 +AY457875 AY457875 +AY457874 AY457874 +AY457873 AY457873 +AY457872 AY457872 +AY457871 AY457871 +AY457870 AY457870 +AY457869 AY457869 +AY457868 AY457868 +AY457867 AY457867 +AY457866 AY457866 +AY457865 AY457865 +AY457864 AY457864 +AY457863 AY457863 +AY457862 AY457862 +AY457861 AY457861 +AY457860 AY457860 +AY457859 AY457859 +AY457858 AY457858 +AY457857 AY457857 +AY457856 AY457856 +AY457855 AY457855 +AY457854 AY457854 +AY457853 AY457853 +AY457852 AY457852 +AY457851 AY457851 +AY457850 AY457850 +AY457849 AY457849 +AY457848 AY457848 +AY457847 AY457847 +AY457846 AY457846 +AY457845 AY457845 +AY457844 AY457844 +AY457843 AY457843 +AY457842 AY457842 +AY457841 AY457841 +AY457840 AY457840 +AY457839 AY457839 +AY457838 AY457838 +AY457837 AY457837 +AY457836 AY457836 +AY457835 AY457835 +AY457834 AY457834 +AY457833 AY457833 +AY457832 AY457832 +AY457831 AY457831 +AY457830 AY457830 +AY457829 AY457829 +AY457828 AY457828 +AY457827 AY457827 +AY457826 AY457826 +AY457825 AY457825 +AY457824 AY457824 +AY457823 AY457823 +AY457822 AY457822 +AY457821 AY457821 +AY457820 AY457820 +AY457819 AY457819 +AY457818 AY457818 +AY457817 AY457817 +AY457816 AY457816 +AY457815 AY457815 +AY457814 AY457814 +AY457813 AY457813 +AY457812 AY457812 +AY457811 AY457811 +AY457810 AY457810 +AY457809 AY457809 +AY457808 AY457808 +AY457807 AY457807 +AY457806 AY457806 +AY457805 AY457805 +AY457804 AY457804 +AY457803 AY457803 +AY457802 AY457802 +AY457801 AY457801 +AY457800 AY457800 +AY457799 AY457799 +AY457798 AY457798 +AY457797 AY457797 +AY457796 AY457796 +AY457795 AY457795 +AY457794 AY457794 +AY457793 AY457793 +AY457792 AY457792 +AY457791 AY457791 +AY457790 AY457790 +AY457789 AY457789 +AY457788 AY457788 +AY457787 AY457787 +AY457786 AY457786 +AY457785 AY457785 +AY457784 AY457784 +AY457783 AY457783 +AY457782 AY457782 +AY457781 AY457781 +AY457780 AY457780 +AY457779 AY457779 +AY457778 AY457778 +AY457777 AY457777 +AY457776 AY457776 +AY457775 AY457775 +AY457774 AY457774 +AY457773 AY457773 +AY457772 AY457772 +AY457771 AY457771 +AY457770 AY457770 +AY457769 AY457769 +AY457768 AY457768 +AY457767 AY457767 +AY457766 AY457766 +AY457765 AY457765 +AY457764 AY457764 +AY457763 AY457763 +AY457762 AY457762 +AY457761 AY457761 +AY457760 AY457760 +AY457759 AY457759 +AY457758 AY457758 +AY457757 AY457757 +AY457756 AY457756 +AY457755 AY457755 +AY457754 AY457754 +AY457753 AY457753 +AY457752 AY457752 +AY457751 AY457751 +AY457750 AY457750 +AY457749 AY457749 +AY457748 AY457748 +AY457747 AY457747 +AY457746 AY457746 +AY457745 AY457745 +AY457744 AY457744 +AY457743 AY457743 +AY457742 AY457742 +AY457741 AY457741 +AY457740 AY457740 +AY457739 AY457739 +AY457738 AY457738 +AY457737 AY457737 +AY457736 AY457736 +AY457735 AY457735 +AY457734 AY457734 +AY457733 AY457733 +AY457732 AY457732 +AY457731 AY457731 +AY457730 AY457730 +AY457729 AY457729 +AY457728 AY457728 +AY457727 AY457727 +AY457726 AY457726 +AY457725 AY457725 +AY457724 AY457724 +AY457723 AY457723 +AY457722 AY457722 +AY457721 AY457721 +AY457720 AY457720 +AY457719 AY457719 +AY457718 AY457718 +AY457717 AY457717 +AY457716 AY457716 +AY457715 AY457715 +AY457714 AY457714 +AY457713 AY457713 +AY457712 AY457712 +AY457711 AY457711 +AY457710 AY457710 +AY457709 AY457709 +AY457708 AY457708 +AY457707 AY457707 +AY457706 AY457706 +AY457705 AY457705 +AY457704 AY457704 +AY457703 AY457703 +AY457702 AY457702 +AY457701 AY457701 +AY457700 AY457700 +AY457699 AY457699 +AY457698 AY457698 +AY457697 AY457697 +AY457696 AY457696 +AY457695 AY457695 +AY457694 AY457694 +AY457693 AY457693 +AY457692 AY457692 +AY457691 AY457691 +AY457690 AY457690 +AY457689 AY457689 +AY457688 AY457688 +AY457687 AY457687 +AY457686 AY457686 +AY457685 AY457685 +AY457684 AY457684 +AY457683 AY457683 +AY457682 AY457682 +AY457681 AY457681 +AY457680 AY457680 +AY457679 AY457679 +AY457678 AY457678 +AY457677 AY457677 +AY457676 AY457676 +AY457675 AY457675 +AY457674 AY457674 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/abrecovery.pds.wang.taxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abrecovery.pds.wang.taxonomy Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,242 @@\n+AY457915\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiracea_incertae_sedis(88);\n+AY457914\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiracea_incertae_sedis(100);\n+AY457913\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(100);\n+AY457912\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiracea_incertae_sedis(96);\n+AY457911\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457910\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457909\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457908\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(100);\n+AY457907\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457906\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457905\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457904\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457903\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457902\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457901\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(100);\n+AY457900\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457899\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457898\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiracea_incertae_sedis(67);\n+AY457897\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457896\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457895\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiracea_incertae_sedis(98);\n+AY457894\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiracea_incertae_sedis(90);\n+AY457893\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457892\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457891\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiracea_incertae_sedis(88);\n+AY457890\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457889\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457888\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiracea_incertae_sedis(89);\n+AY457887\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457886\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457885\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457884\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457883\tBacteria(100);"Bact'..b'0);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457703\tBacteria(100);"Proteobacteria"(100);Betaproteobacteria(100);Burkholderiales(100);Sutterellaceae(100);Sutterella(100);\n+AY457702\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Citrobacter(67);\n+AY457701\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457700\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457699\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Enterobacter(45);\n+AY457698\tBacteria(100);"Proteobacteria"(100);Betaproteobacteria(100);Burkholderiales(100);Sutterellaceae(100);Sutterella(100);\n+AY457697\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Citrobacter(54);\n+AY457696\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Enterobacter(36);\n+AY457695\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457694\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457693\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457692\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457691\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Escherichia_Shigella(95);\n+AY457690\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457689\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Citrobacter(54);\n+AY457688\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Enterobacter(39);\n+AY457687\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457686\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457685\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Enterobacter(69);\n+AY457684\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Citrobacter(64);\n+AY457683\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457682\tBacteria(100);Firmicutes(88);Clostridia(76);Clostridiales(76);Ruminococcaceae(46);Pseudoflavonifractor(16);\n+AY457681\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Klebsiella(99);\n+AY457680\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Citrobacter(78);\n+AY457679\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457678\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457677\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457676\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457675\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457674\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/abrecovery.pds.wang.tree.sum --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abrecovery.pds.wang.tree.sum Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,174 @@ +#1.36.1 +171 +6 +0 Root 3 Bacteria 2 unclassified 59 unknown 1 +1 unknown 1 unclassified 117 +1 Bacteria 6 "Actinobacteria" 32 "Bacteroidetes" 3 "Proteobacteria" 13 Firmicutes 8 TM7 40 unclassified 60 +2 "Bacteroidetes" 2 "Bacteroidia" 4 unclassified 66 +3 "Bacteroidia" 2 "Bacteroidales" 5 unclassified 67 +4 "Bacteroidales" 3 "Porphyromonadaceae" 6 Bacteroidaceae 22 unclassified 68 +5 "Porphyromonadaceae" 2 Parabacteroides 7 unclassified 69 +6 Parabacteroides 1 unclassified 70 +2 Firmicutes 4 Clostridia 9 Erysipelotrichia 55 Negativicutes 47 unclassified 88 +3 Clostridia 2 Clostridiales 10 unclassified 89 +4 Clostridiales 4 Lachnospiraceae 28 Peptostreptococcaceae 30 Ruminococcaceae 11 unclassified 90 +5 Ruminococcaceae 4 Faecalibacterium 12 Pseudoflavonifractor 19 Subdoligranulum 53 unclassified 100 +6 Faecalibacterium 1 unclassified 101 +2 "Proteobacteria" 3 Betaproteobacteria 24 Gammaproteobacteria 14 unclassified 73 +3 Gammaproteobacteria 3 "Enterobacteriales" 15 Pasteurellales 37 unclassified 78 +4 "Enterobacteriales" 2 Enterobacteriaceae 16 unclassified 79 +5 Enterobacteriaceae 5 Citrobacter 17 Enterobacter 20 Escherichia_Shigella 21 Klebsiella 18 unclassified 80 +6 Citrobacter 1 unclassified 81 +6 Klebsiella 1 unclassified 84 +6 Pseudoflavonifractor 1 unclassified 102 +6 Enterobacter 1 unclassified 82 +6 Escherichia_Shigella 1 unclassified 83 +5 Bacteroidaceae 2 Bacteroides 23 unclassified 71 +6 Bacteroides 1 unclassified 72 +3 Betaproteobacteria 2 Burkholderiales 25 unclassified 74 +4 Burkholderiales 2 Sutterellaceae 26 unclassified 75 +5 Sutterellaceae 2 Sutterella 27 unclassified 76 +6 Sutterella 1 unclassified 77 +5 Lachnospiraceae 7 Blautia 45 Clostridium_XlVa 51 Coprococcus 54 Dorea 46 Lachnospiracea_incertae_sedis 29 Roseburia 52 unclassified 91 +6 Lachnospiracea_incertae_sedis 1 unclassified 96 +5 Peptostreptococcaceae 2 Clostridium_XI 31 unclassified 98 +6 Clostridium_XI 1 unclassified 99 +2 "Actinobacteria" 2 Actinobacteria 33 unclassified 61 +3 Actinobacteria 2 Bifidobacteriales 34 unclassified 62 +4 Bifidobacteriales 2 Bifidobacteriaceae 35 unclassified 63 +5 Bifidobacteriaceae 2 Bifidobacterium 36 unclassified 64 +6 Bifidobacterium 1 unclassified 65 +4 Pasteurellales 2 Pasteurellaceae 38 unclassified 85 +5 Pasteurellaceae 2 Haemophilus 39 unclassified 86 +6 Haemophilus 1 unclassified 87 +2 TM7 2 TM7_class_incertae_sedis 41 unclassified 112 +3 TM7_class_incertae_sedis 2 TM7_order_incertae_sedis 42 unclassified 113 +4 TM7_order_incertae_sedis 2 TM7_family_incertae_sedis 43 unclassified 114 +5 TM7_family_incertae_sedis 2 TM7_genus_incertae_sedis 44 unclassified 115 +6 TM7_genus_incertae_sedis 1 unclassified 116 +6 Blautia 1 unclassified 92 +6 Dorea 1 unclassified 95 +3 Negativicutes 2 Selenomonadales 48 unclassified 108 +4 Selenomonadales 2 Acidaminococcaceae 49 unclassified 109 +5 Acidaminococcaceae 2 Phascolarctobacterium 50 unclassified 110 +6 Phascolarctobacterium 1 unclassified 111 +6 Clostridium_XlVa 1 unclassified 93 +6 Roseburia 1 unclassified 97 +6 Subdoligranulum 1 unclassified 103 +6 Coprococcus 1 unclassified 94 +3 Erysipelotrichia 2 Erysipelotrichales 56 unclassified 104 +4 Erysipelotrichales 2 Erysipelotrichaceae 57 unclassified 105 +5 Erysipelotrichaceae 2 Turicibacter 58 unclassified 106 +6 Turicibacter 1 unclassified 107 +1 unclassified 1 unclassified 118 +2 unclassified 1 unclassified 123 +3 unclassified 1 unclassified 127 +4 unclassified 1 unclassified 130 +5 unclassified 1 unclassified 132 +6 unclassified 0 +7 unclassified 0 +3 unclassified 1 unclassified 133 +4 unclassified 1 unclassified 136 +5 unclassified 1 unclassified 138 +6 unclassified 0 +7 unclassified 0 +6 unclassified 0 +7 unclassified 0 +3 unclassified 1 unclassified 139 +4 unclassified 1 unclassified 142 +5 unclassified 1 unclassified 144 +6 unclassified 0 +7 unclassified 0 +4 unclassified 1 unclassified 145 +5 unclassified 1 unclassified 147 +6 unclassified 0 +7 unclassified 0 +7 unclassified 0 +7 unclassified 0 +7 unclassified 0 +5 unclassified 1 unclassified 148 +6 unclassified 0 +7 unclassified 0 +3 unclassified 1 unclassified 149 +4 unclassified 1 unclassified 152 +5 unclassified 1 unclassified 154 +6 unclassified 0 +7 unclassified 0 +7 unclassified 0 +7 unclassified 0 +7 unclassified 0 +7 unclassified 0 +7 unclassified 0 +6 unclassified 0 +7 unclassified 0 +6 unclassified 0 +7 unclassified 0 +7 unclassified 0 +7 unclassified 0 +4 unclassified 1 unclassified 155 +5 unclassified 1 unclassified 157 +6 unclassified 0 +7 unclassified 0 +4 unclassified 1 unclassified 158 +5 unclassified 1 unclassified 160 +6 unclassified 0 +7 unclassified 0 +3 unclassified 1 unclassified 161 +4 unclassified 1 unclassified 164 +5 unclassified 1 unclassified 166 +6 unclassified 0 +7 unclassified 0 +2 unclassified 1 unclassified 167 +2 unclassified 1 unclassified 119 +3 unclassified 1 unclassified 120 +4 unclassified 1 unclassified 121 +5 unclassified 1 unclassified 122 +6 unclassified 0 +3 unclassified 1 unclassified 124 +4 unclassified 1 unclassified 125 +5 unclassified 1 unclassified 126 +6 unclassified 0 +4 unclassified 1 unclassified 128 +5 unclassified 1 unclassified 129 +6 unclassified 0 +5 unclassified 1 unclassified 131 +6 unclassified 0 +6 unclassified 0 +4 unclassified 1 unclassified 134 +5 unclassified 1 unclassified 135 +6 unclassified 0 +5 unclassified 1 unclassified 137 +6 unclassified 0 +6 unclassified 0 +4 unclassified 1 unclassified 140 +5 unclassified 1 unclassified 141 +6 unclassified 0 +5 unclassified 1 unclassified 143 +6 unclassified 0 +6 unclassified 0 +5 unclassified 1 unclassified 146 +6 unclassified 0 +6 unclassified 0 +6 unclassified 0 +4 unclassified 1 unclassified 150 +5 unclassified 1 unclassified 151 +6 unclassified 0 +5 unclassified 1 unclassified 153 +6 unclassified 0 +6 unclassified 0 +5 unclassified 1 unclassified 156 +6 unclassified 0 +6 unclassified 0 +5 unclassified 1 unclassified 159 +6 unclassified 0 +6 unclassified 0 +4 unclassified 1 unclassified 162 +5 unclassified 1 unclassified 163 +6 unclassified 0 +5 unclassified 1 unclassified 165 +6 unclassified 0 +6 unclassified 0 +3 unclassified 1 unclassified 168 +4 unclassified 1 unclassified 169 +5 unclassified 1 unclassified 170 +6 unclassified 0 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/abrecovery.tre --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abrecovery.tre Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ 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|
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.accnos.otulabels --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.accnos.otulabels Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +U68589 +U68590 +U68591 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.align_head --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.align_head Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,6 @@\n+>U68589\n+.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................'..b'...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................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|
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.align_head.count_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.align_head.count_table Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Representative_Sequence total +U68589 1 +U68590 1 +U68591 1 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.align_head.list --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.align_head.list Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +label numOtus Otu1 Otu2 Otu3 +unique 3 U68589 U68590 U68591 +0.30 2 U68589,U68590 U68591 +0.33 1 U68589,U68590,U68591 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.align_head.names --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.align_head.names Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +U68589 U68589 +U68590 U68590 +U68591 U68591 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.align_head.wang.taxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.align_head.wang.taxonomy Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +U68589 Bacteria(92);"Proteobacteria"(40);Gammaproteobacteria(40);"Enterobacteriales"(40);Enterobacteriaceae(40);Escherichia_Shigella(40); +U68590 Bacteria(94);Firmicutes(69);Erysipelotrichia(68);Erysipelotrichales(68);Erysipelotrichaceae(68);Turicibacter(68); +U68591 Bacteria(97);"Proteobacteria"(55);Gammaproteobacteria(55);"Enterobacteriales"(55);Enterobacteriaceae(55);Escherichia_Shigella(55); |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.align_head_short --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.align_head_short Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,6 @@ +>U68589 +.......... +>U68590 +.......... +>U68591 +.......... |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.an.0.03.-.0.05.otu.hierarchy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.an.0.03.-.0.05.otu.hierarchy Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,78 @@ +U68688,U68665,U68679,U68663 U68688,U68665,U68679,U68663 +U68658,U68638,U68620,U68618 U68658,U68638,U68620,U68618 +U68683,U68652,U68610 U68652 U68683 U68610 +U68673,U68667,U68641 U68673,U68667,U68641 +U68636,U68631 U68636,U68631 +U68637,U68602 U68637 U68602 +U68628,U68601 U68601 U68628 +U68614,U68596 U68596 U68614 +U68666,U68595 U68666 U68595 +U68672,U68621 U68672 U68621 +U68686,U68635 U68686 U68635 +U68678,U68619 U68678 U68619 +U68680,U68615 U68680,U68615 +U68681,U68677 U68681 U68677 +U68654 U68654 +U68653 U68653 +U68651 U68651 +U68649 U68649 +U68648 U68648 +U68647 U68647 +U68646 U68646 +U68645 U68645 +U68685 U68685 +U68644 U68644 +U68643 U68643 +U68642 U68642 +U68640 U68640 +U68639 U68639 +U68687 U68687 +U68676 U68676 +U68675 U68675 +U68674 U68674 +U68671 U68671 +U68670 U68670 +U68669 U68669 +U68668 U68668 +U68664 U68664 +U68662 U68662 +U68661 U68661 +U68660 U68660 +U68682 U68682 +U68659 U68659 +U68684 U68684 +U68657 U68657 +U68656 U68656 +U68655 U68655 +U68607 U68607 +U68608 U68608 +U68600 U68600 +U68609 U68609 +U68599 U68599 +U68606 U68606 +U68598 U68598 +U68611 U68611 +U68612 U68612 +U68613 U68613 +U68605 U68605 +U68616 U68616 +U68617 U68617 +U68597 U68597 +U68603 U68603 +U68594 U68594 +U68589 U68589 +U68634 U68634 +U68590 U68590 +U68633 U68633 +U68632 U68632 +U68591 U68591 +U68592 U68592 +U68630 U68630 +U68629 U68629 +U68627 U68627 +U68626 U68626 +U68625 U68625 +U68624 U68624 +U68623 U68623 +U68622 U68622 +U68593 U68593 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.an.jclass.unique.tre --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.an.jclass.unique.tre Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +(pasture:0.5,forest:0.5):0; |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.an.list --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.an.list Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,37 @@\n+label\tnumOtus\tOtu01\tOtu02\tOtu03\tOtu04\tOtu05\tOtu06\tOtu07\tOtu08\tOtu09\tOtu10\tOtu11\tOtu12\tOtu13\tOtu14\tOtu15\tOtu16\tOtu17\tOtu18\tOtu19\tOtu20\tOtu21\tOtu22\tOtu23\tOtu24\tOtu25\tOtu26\tOtu27\tOtu28\tOtu29\tOtu30\tOtu31\tOtu32\tOtu33\tOtu34\tOtu35\tOtu36\tOtu37\tOtu38\tOtu39\tOtu40\tOtu41\tOtu42\tOtu43\tOtu44\tOtu45\tOtu46\tOtu47\tOtu48\tOtu49\tOtu50\tOtu51\tOtu52\tOtu53\tOtu54\tOtu55\tOtu56\tOtu57\tOtu58\tOtu59\tOtu60\tOtu61\tOtu62\tOtu63\tOtu64\tOtu65\tOtu66\tOtu67\tOtu68\tOtu69\tOtu70\tOtu71\tOtu72\tOtu73\tOtu74\tOtu75\tOtu76\tOtu77\tOtu78\tOtu79\tOtu80\tOtu81\tOtu82\tOtu83\tOtu84\tOtu85\tOtu86\tOtu87\tOtu88\tOtu89\tOtu90\tOtu91\tOtu92\tOtu93\tOtu94\tOtu95\tOtu96\tOtu97\tOtu98\n+unique\t96\tU68667,U68641\tU68620,U68618\tU68663\tU68662\tU68661\tU68660\tU68659\tU68658\tU68657\tU68656\tU68655\tU68654\tU68653\tU68652\tU68651\tU68649\tU68648\tU68647\tU68646\tU68645\tU68644\tU68643\tU68642\tU68640\tU68639\tU68688\tU68687\tU68686\tU68685\tU68684\tU68683\tU68682\tU68681\tU68680\tU68679\tU68678\tU68677\tU68676\tU68675\tU68674\tU68673\tU68672\tU68671\tU68670\tU68669\tU68668\tU68666\tU68665\tU68664\tU68613\tU68612\tU68611\tU68610\tU68609\tU68608\tU68607\tU68606\tU68605\tU68603\tU68602\tU68601\tU68600\tU68599\tU68598\tU68597\tU68596\tU68595\tU68594\tU68593\tU68592\tU68591\tU68590\tU68589\tU68638\tU68637\tU68636\tU68635\tU68634\tU68633\tU68632\tU68631\tU68630\tU68629\tU68628\tU68627\tU68626\tU68625\tU68624\tU68623\tU68622\tU68621\tU68619\tU68617\tU68616\tU68615\tU68614\n+0.01\t93\tU68688,U68665\tU68636,U68631\tU68667,U68641\tU68620,U68618\tU68680,U68615\tU68661\tU68660\tU68659\tU68658\tU68657\tU68656\tU68655\tU68654\tU68653\tU68652\tU68651\tU68649\tU68648\tU68647\tU68646\tU68645\tU68644\tU68643\tU68642\tU68640\tU68639\tU68687\tU68686\tU68685\tU68684\tU68683\tU68682\tU68681\tU68679\tU68678\tU68677\tU68676\tU68675\tU68674\tU68673\tU68672\tU68671\tU68670\tU68669\tU68668\tU68666\tU68664\tU68663\tU68662\tU68613\tU68612\tU68611\tU68610\tU68609\tU68608\tU68607\tU68606\tU68605\tU68603\tU68602\tU68601\tU68600\tU68599\tU68598\tU68597\tU68596\tU68595\tU68594\tU68593\tU68592\tU68591\tU68590\tU68589\tU68638\tU68637\tU68635\tU68634\tU68633\tU68632\tU68630\tU68629\tU68628\tU68627\tU68626\tU68625\tU68624\tU68623\tU68622\tU68621\tU68619\tU68617\tU68616\tU68614\n+0.02\t90\tU68688,U68665,U68679,U68663\tU68673,U68667,U68641\tU68636,U68631\tU68620,U68618\tU68680,U68615\tU68658\tU68657\tU68656\tU68655\tU68686\tU68654\tU68653\tU68652\tU68651\tU68649\tU68648\tU68647\tU68646\tU68645\tU68644\tU68643\tU68642\tU68640\tU68639\tU68638\tU68687\tU68683\tU68682\tU68681\tU68684\tU68678\tU68677\tU68676\tU68675\tU68674\tU68685\tU68672\tU68671\tU68670\tU68669\tU68668\tU68666\tU68664\tU68662\tU68661\tU68660\tU68659\tU68612\tU68611\tU68610\tU68609\tU68608\tU68607\tU68606\tU68605\tU68603\tU68602\tU68601\tU68600\tU68599\tU68598\tU68597\tU68596\tU68595\tU68594\tU68593\tU68592\tU68591\tU68590\tU68589\tU68637\tU68635\tU68634\tU68633\tU68632\tU68630\tU68629\tU68628\tU68627\tU68626\tU68625\tU68624\tU68623\tU68622\tU68621\tU68619\tU68617\tU68616\tU68614\tU68613\n+0.03\t88\tU68688,U68665,U68679,U68663\tU68658,U68638,U68620,U68618\tU68673,U68667,U68641\tU68636,U68631\tU68680,U68615\tU68686\tU68657\tU68656\tU68655\tU68654\tU68653\tU68652\tU68651\tU68649\tU68648\tU68647\tU68646\tU68645\tU68644\tU68643\tU68642\tU68640\tU68639\tU68637\tU68687\tU68683\tU68682\tU68681\tU68684\tU68678\tU68677\tU68676\tU68675\tU68674\tU68685\tU68672\tU68671\tU68670\tU68669\tU68668\tU68666\tU68664\tU68662\tU68661\tU68660\tU68659\tU68613\tU68612\tU68611\tU68610\tU68609\tU68608\tU68607\tU68606\tU68605\tU68603\tU68602\tU68601\tU68600\tU68599\tU68598\tU68597\tU68596\tU68595\tU68594\tU68593\tU68592\tU68591\tU68590\tU68589\tU68635\tU68634\tU68633\tU68632\tU68630\tU68629\tU68628\tU68627\tU68626\tU68625\tU68624\tU68623\tU68622\tU68621\tU68619\tU68617\tU68616\tU68614\n+0.04\t83\tU68688,U68665,U68679,U68663\tU68658,U68638,U68620,U68618\tU68673,U68667,U68641\tU68636,U68631\tU68637,U68602\tU68652,U68610\tU68614,U68596\tU68678,U68619\tU68680,U68615\tU68681,U68677\tU68656\tU68655\tU68654\tU68653\tU68685\tU68651\tU68649\tU68648\tU68647\tU68646\tU68645\tU68644\tU68643\tU68642\tU68640\tU68639\tU68686\tU68687\tU68676\tU68675\tU68674\tU68682\tU68672\tU68671\tU68670\tU68669\tU68668\tU68666\tU68664\tU68662\tU68661\tU68660\tU68683\tU68659\tU68684\tU68657\tU68613\tU68612\tU68611\tU68609\tU68608\tU68607\tU68606\tU68605\tU68603\tU68601\tU68600\tU68599\tU68598\tU68597\tU68595\tU68594\tU68593\tU68592\tU68591\tU68590\tU68589\tU68635\tU68634\t'..b'677,U68669,U68589,U68642,U68599,U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618,U68659,U68624,U68655,U68651,U68640,U68633,U68612,U68648,U68632,U68605,U68597,U68684,U68654,U68593,U68649,U68639,U68606,U68646,U68590,U68644,U68680,U68615,U68670,U68611,U68625,U68672,U68621,U68656,U68668,U68662,U68661,U68594,U68687,U68592,U68685,U68683,U68652,U68610,U68671,U68666,U68595,U68636,U68631\tU68682,U68657,U68675,U68627,U68609,U68603,U68643\tU68600,U68591\tU68664\tU68622\tU68608\n+0.36\t5\tU68688,U68665,U68679,U68663,U68653,U68676,U68660,U68647,U68626,U68623,U68674,U68630,U68634,U68628,U68601,U68607,U68629,U68617,U68614,U68596,U68616,U68681,U68677,U68669,U68589,U68642,U68599,U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618,U68659,U68624,U68655,U68651,U68640,U68633,U68612,U68648,U68632,U68605,U68597,U68684,U68654,U68593,U68649,U68639,U68606,U68646,U68590,U68644,U68680,U68615,U68670,U68611,U68625,U68672,U68621,U68656,U68668,U68662,U68661,U68594,U68687,U68592,U68685,U68683,U68652,U68610,U68671,U68666,U68595,U68636,U68631,U68600,U68591\tU68682,U68657,U68675,U68627,U68609,U68603,U68643\tU68622\tU68664\tU68608\n+0.38\t4\tU68688,U68665,U68679,U68663,U68653,U68676,U68660,U68647,U68626,U68623,U68674,U68630,U68634,U68628,U68601,U68607,U68629,U68617,U68614,U68596,U68616,U68681,U68677,U68669,U68589,U68642,U68599,U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618,U68659,U68624,U68655,U68651,U68640,U68633,U68612,U68648,U68632,U68605,U68597,U68684,U68654,U68593,U68649,U68639,U68606,U68646,U68590,U68644,U68680,U68615,U68670,U68611,U68625,U68672,U68621,U68656,U68668,U68662,U68661,U68594,U68687,U68592,U68685,U68683,U68652,U68610,U68671,U68666,U68595,U68636,U68631,U68600,U68591,U68622\tU68682,U68657,U68675,U68627,U68609,U68603,U68643\tU68664\tU68608\n+0.41\t3\tU68688,U68665,U68679,U68663,U68653,U68676,U68660,U68647,U68626,U68623,U68674,U68630,U68634,U68628,U68601,U68607,U68629,U68617,U68614,U68596,U68616,U68681,U68677,U68669,U68589,U68642,U68599,U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618,U68659,U68624,U68655,U68651,U68640,U68633,U68612,U68648,U68632,U68605,U68597,U68684,U68654,U68593,U68649,U68639,U68606,U68646,U68590,U68644,U68680,U68615,U68670,U68611,U68625,U68672,U68621,U68656,U68668,U68662,U68661,U68594,U68687,U68592,U68685,U68683,U68652,U68610,U68671,U68666,U68595,U68636,U68631,U68600,U68591,U68622,U68682,U68657,U68675,U68627,U68609,U68603,U68643\tU68664\tU68608\n+0.45\t2\tU68688,U68665,U68679,U68663,U68653,U68676,U68660,U68647,U68626,U68623,U68674,U68630,U68634,U68628,U68601,U68607,U68629,U68617,U68614,U68596,U68616,U68681,U68677,U68669,U68589,U68642,U68599,U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618,U68659,U68624,U68655,U68651,U68640,U68633,U68612,U68648,U68632,U68605,U68597,U68684,U68654,U68593,U68649,U68639,U68606,U68646,U68590,U68644,U68680,U68615,U68670,U68611,U68625,U68672,U68621,U68656,U68668,U68662,U68661,U68594,U68687,U68592,U68685,U68683,U68652,U68610,U68671,U68666,U68595,U68636,U68631,U68600,U68591,U68622,U68682,U68657,U68675,U68627,U68609,U68603,U68643,U68664\tU68608\n+0.55\t1\tU68688,U68665,U68679,U68663,U68653,U68676,U68660,U68647,U68626,U68623,U68674,U68630,U68634,U68628,U68601,U68607,U68629,U68617,U68614,U68596,U68616,U68681,U68677,U68669,U68589,U68642,U68599,U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618,U68659,U68624,U68655,U68651,U68640,U68633,U68612,U68648,U68632,U68605,U68597,U68684,U68654,U68593,U68649,U68639,U68606,U68646,U68590,U68644,U68680,U68615,U68670,U68611,U68625,U68672,U68621,U68656,U68668,U68662,U68661,U68594,U68687,U68592,U68685,U68683,U68652,U68610,U68671,U68666,U68595,U68636,U68631,U68600,U68591,U68622,U68682,U68657,U68675,U68627,U68609,U68603,U68643,U68664,U68608\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.an.rabund --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.an.rabund Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,36 @@ +unique 96 2 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 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 +0.01 93 2 2 2 2 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 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 +0.02 90 4 3 2 2 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 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 +0.03 88 4 4 3 2 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 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 +0.04 83 4 4 3 2 2 2 2 2 2 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 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 +0.05 78 4 4 3 3 2 2 2 2 2 2 2 2 2 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 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +0.06 69 4 4 4 4 3 3 2 2 2 2 2 2 2 2 2 2 2 2 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 1 1 1 +0.07 65 7 4 4 4 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 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 +0.08 56 11 7 4 4 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 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 +0.09 55 11 7 5 4 4 3 3 2 2 2 2 2 2 2 2 2 2 2 2 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 +0.10 49 16 7 5 4 4 4 4 4 2 2 2 2 2 2 2 2 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 +0.11 45 16 8 8 5 4 4 4 3 3 2 2 2 2 2 2 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 +0.12 43 17 8 8 5 4 4 4 3 3 3 2 2 2 2 2 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 +0.13 40 17 8 8 8 5 5 4 3 3 2 2 2 2 2 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 +0.14 36 19 8 8 8 6 5 4 3 3 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +0.15 35 21 8 8 8 6 5 4 3 3 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +0.16 34 21 8 8 8 6 5 4 3 3 3 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +0.17 33 21 10 8 8 6 5 4 3 3 3 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +0.18 31 21 10 8 8 6 5 4 4 3 3 3 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +0.19 30 21 10 8 8 6 5 4 4 3 3 3 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +0.20 27 23 11 10 8 6 5 4 4 3 3 3 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +0.21 25 23 11 10 9 9 5 4 4 3 3 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 +0.22 23 23 11 11 10 9 5 4 4 4 3 2 1 1 1 1 1 1 1 1 1 1 1 1 +0.23 21 23 21 11 9 5 5 4 4 3 2 1 1 1 1 1 1 1 1 1 1 1 +0.24 17 36 21 11 5 5 5 4 2 1 1 1 1 1 1 1 1 1 +0.25 15 36 21 11 6 5 5 5 2 1 1 1 1 1 1 1 +0.26 13 36 26 11 6 5 5 2 2 1 1 1 1 1 +0.27 12 36 26 11 10 6 2 2 1 1 1 1 1 +0.29 9 73 11 6 2 2 1 1 1 1 +0.32 7 75 11 7 2 1 1 1 +0.33 6 86 7 2 1 1 1 +0.36 5 88 7 1 1 1 +0.38 4 89 7 1 1 +0.41 3 96 1 1 +0.45 2 97 1 +0.55 1 98 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.an.rabund2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.an.rabund2 Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +0.03 88 4 4 3 2 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 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 +0.05 78 4 4 3 3 2 2 2 2 2 2 2 2 2 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 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.an.relabund --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.an.relabund Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,73 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|
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.an.sabund --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.an.sabund Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,36 @@ +unique 2 94 2 +0.01 2 88 5 +0.02 4 85 3 1 1 +0.03 4 83 2 1 2 +0.04 4 73 7 1 2 +0.05 4 64 10 2 2 +0.06 4 50 13 2 4 +0.07 7 45 14 2 3 0 0 1 +0.08 11 35 14 3 2 0 0 1 0 0 0 1 +0.09 11 35 13 2 2 1 0 1 0 0 0 1 +0.10 16 32 9 0 5 1 0 1 0 0 0 0 0 0 0 0 1 +0.11 16 29 7 2 3 1 0 0 2 0 0 0 0 0 0 0 1 +0.12 17 27 6 3 3 1 0 0 2 0 0 0 0 0 0 0 0 1 +0.13 17 25 6 2 1 2 0 0 3 0 0 0 0 0 0 0 0 1 +0.14 19 20 7 2 1 1 1 0 3 0 0 0 0 0 0 0 0 0 0 1 +0.15 21 20 6 2 1 1 1 0 3 0 0 0 0 0 0 0 0 0 0 0 0 1 +0.16 21 19 5 3 1 1 1 0 3 0 0 0 0 0 0 0 0 0 0 0 0 1 +0.17 21 19 4 3 1 1 1 0 2 0 1 0 0 0 0 0 0 0 0 0 0 1 +0.18 21 17 3 3 2 1 1 0 2 0 1 0 0 0 0 0 0 0 0 0 0 1 +0.19 21 15 4 3 2 1 1 0 2 0 1 0 0 0 0 0 0 0 0 0 0 1 +0.20 23 14 2 3 2 1 1 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 +0.21 23 13 2 2 2 1 0 0 0 2 1 1 0 0 0 0 0 0 0 0 0 0 0 1 +0.22 23 12 1 1 3 1 0 0 0 1 1 2 0 0 0 0 0 0 0 0 0 0 0 1 +0.23 23 11 1 1 2 2 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 1 +0.24 36 9 1 0 1 3 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +0.25 36 7 1 0 0 3 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +0.26 36 5 2 0 0 2 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 +0.27 36 5 2 0 0 0 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 +0.29 73 4 2 0 0 0 1 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 1 +0.32 75 3 1 0 0 0 0 1 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 1 +0.33 86 3 1 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 0 0 0 0 0 1 +0.36 88 3 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 0 0 0 0 0 0 0 1 +0.38 89 2 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 0 0 0 0 0 0 0 0 1 +0.41 96 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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 +0.45 97 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 1 +0.55 98 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.an.sabund2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.an.sabund2 Fri May 19 05:26:45 2017 -0400 |
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0.3803 0.3783\n+ 0.3700 0.3824 0.3949 0.3365 0.4508 0.3926 0.3204 0.3694 0.3711\n+ 0.4122 0.3221 0.3075 0.3254 0.4581 0.3383 0.3535 0.3900 0.3307\n+ 0.3336 0.3656 0.4200 0.4257 0.3212 0.4051 0.3718 0.4083 0.3730\n+U68592 0.4155 0.3198 0.4148 0.0000 0.2842 0.3326 0.2299 0.3633\n+ 0.3252 0.2652 0.3390 0.3643 0.3504 0.2667 0.4185 0.3312 0.3012\n+ 0.3844 0.5872 0.4165 0.2159 0.3197 0.3597 0.2546 0.3328 0.3390\n+ 0.3264 0.3475 0.2817 0.3122 0.2817 0.3732 0.3597 0.3652 0.3019\n+ 0.3625 0.3821 0.4203 0.3564 0.3422 0.3402 0.1795 0.3269 0.2984\n+ 0.3025 0.2606 0.1645 0.2758 0.2681 0.3556 0.3034 0.2952 0.3471\n+ 0.5563 0.3534 0.2815 0.3542 0.3553 0.3450 0.3281 0.2975 0.2135\n+ 0.3261 0.3236 0.3118 0.3366 0.4250 0.2995 0.2778 0.3740 0.3994\n+ 0.3624 0.3696 0.4420 0.3808 0.2115 0.2952 0.3265 0.3703 0.3633\n+ 0.1765 0.3656 0.2376 0.3093 0.3784 0.3468 0.3311 0.2884 0.3858\n+ 0.3365 0.3633 0.4019 0.1811 0.2960 0.1160 0.2765 0.0659 0.3824\n+U68593 0.2873 0.1690 0.3362 0.2842 0.0000 0.2769 0.2831 0.2918\n+ 0.2174 0.1894 0.2942 0.3024 0.2846 0.2196 0.3851 0.2575 0.1229\n+ 0.3240 0.5188 0.3912 0.2846 0.2539 0.2732 0.2139 0.2678 0.2743\n+ 0.2711 0.2911 0.2146 0.2406 0.2146 0.2236 0.3441 0.2473 0.2364\n+ 0.2225 0.2542 0.3966 0.2898 0.2785 0.2599 0.2832 0.2255 0.2448\n+ 0.2681 0.2028 0.2698 0.2141 0.1969 0.1134 0.2321 0.2310 0.3243\n+ 0.4861 0.2113 0.2501 0.1830 0.2924 0.2326 0.1121 0.2294 0.3037\n+ 0.2600 0.0787 0.2485 0.3127 0.3650 0.2276 0.2835 0.3146 0.3340\n+ 0.2882 0.3299 0.3826 0.2870 0.2957 0.2310 0.2758 0.2858 0.2845\n+ 0.2702 0.2408 0.1779 0.2396 0.3425'..b'1979 0.1639 0.2876 0.2931 0.2594 0.1844 0.4162 0.2239 0.1163\n+ 0.3280 0.5025 0.3974 0.3049 0.2436 0.2382 0.1881 0.2514 0.2661\n+ 0.2654 0.2599 0.1838 0.2098 0.1838 0.1956 0.3388 0.2580 0.2094\n+ 0.2042 0.2614 0.4086 0.2715 0.2550 0.2416 0.3071 0.2028 0.2178\n+ 0.2470 0.1876 0.2873 0.1937 0.1635 0.1330 0.2133 0.2070 0.3056\n+ 0.4695 0.1817 0.2121 0.1979 0.2639 0.2168 0.1216 0.1802 0.3103\n+ 0.2306 0.1229 0.2534 0.2555 0.3635 0.2031 0.2291 0.2962 0.3166\n+ 0.2526 0.2874 0.4059 0.2715 0.3218 0.2070 0.2200 0.2824 0.2819\n+ 0.2698 0.2137 0.1765 0.2195 0.3309 0.2388 0.2552 0.1872 0.2644\n+ 0.2669 0.2782 0.3729 0.2932 0.0000 0.3094 0.1868 0.3584 0.2862\n+U68685 0.3654 0.3135 0.4051 0.1160 0.3003 0.3093 0.2277 0.3496\n+ 0.3194 0.2925 0.3441 0.3480 0.3291 0.2820 0.4781 0.3340 0.3094\n+ 0.3606 0.5865 0.4103 0.2122 0.3588 0.3754 0.2769 0.3361 0.3676\n+ 0.3346 0.3299 0.2957 0.3267 0.2957 0.3480 0.3463 0.3555 0.3356\n+ 0.3508 0.3791 0.4154 0.3349 0.3226 0.3330 0.1852 0.3390 0.3159\n+ 0.2992 0.2804 0.1706 0.2778 0.2767 0.3653 0.3071 0.3233 0.3331\n+ 0.5698 0.3252 0.3185 0.3404 0.3536 0.3407 0.3370 0.3011 0.2097\n+ 0.3137 0.3200 0.3244 0.3295 0.4127 0.3119 0.3117 0.3641 0.3732\n+ 0.3778 0.3712 0.4079 0.3700 0.2026 0.3233 0.3049 0.3404 0.3966\n+ 0.1696 0.3378 0.2553 0.2870 0.4061 0.3319 0.3201 0.3179 0.3653\n+ 0.3680 0.3464 0.3919 0.1665 0.3094 0.0000 0.2967 0.1188 0.3730\n+U68686 0.3229 0.2232 0.3718 0.2765 0.1919 0.2815 0.3002 0.2865\n+ 0.2251 0.0857 0.3339 0.3500 0.2575 0.0935 0.3868 0.2365 0.2182\n+ 0.3178 0.5229 0.3640 0.2862 0.2888 0.2114 0.0738 0.2756 0.3101\n+ 0.2884 0.2800 0.0798 0.0927 0.0798 0.2751 0.3551 0.2855 0.1344\n+ 0.2416 0.3018 0.3716 0.2681 0.2538 0.2825 0.2805 0.1829 0.1593\n+ 0.2530 0.0438 0.2594 0.0710 0.0610 0.2299 0.1474 0.1066 0.2949\n+ 0.4858 0.2623 0.0963 0.2870 0.2777 0.1989 0.2108 0.1129 0.2972\n+ 0.2170 0.2171 0.1032 0.2635 0.3554 0.0880 0.1146 0.2760 0.3551\n+ 0.3153 0.3041 0.4148 0.2981 0.3003 0.1066 0.2686 0.2776 0.3305\n+ 0.2902 0.2664 0.0877 0.2468 0.3481 0.2575 0.2559 0.0837 0.2915\n+ 0.3108 0.2974 0.3472 0.2719 0.1868 0.2967 0.0000 0.2967 0.2973\n+U68687 0.4123 0.3135 0.4083 0.0659 0.3579 0.3866 0.2289 0.3674\n+ 0.3673 0.2714 0.3893 0.3758 0.3601 0.2626 0.4420 0.3442 0.3348\n+ 0.4376 0.5980 0.4067 0.2133 0.3592 0.3885 0.2629 0.3497 0.4039\n+ 0.3757 0.3499 0.2815 0.3181 0.2815 0.3875 0.3817 0.4058 0.3094\n+ 0.4027 0.4170 0.4036 0.3611 0.3504 0.4067 0.1803 0.3357 0.3016\n+ 0.3191 0.2774 0.1606 0.2575 0.2708 0.3746 0.3163 0.2921 0.3710\n+ 0.5616 0.4053 0.3254 0.3744 0.3575 0.3543 0.3682 0.3214 0.2303\n+ 0.3361 0.3635 0.3111 0.3263 0.4080 0.3119 0.3809 0.3781 0.3913\n+ 0.3959 0.3770 0.4891 0.4118 0.2125 0.2921 0.3243 0.3772 0.3747\n+ 0.1693 0.3806 0.2332 0.3569 0.3839 0.3514 0.3470 0.2906 0.4195\n+ 0.4059 0.3854 0.3835 0.1690 0.3584 0.1188 0.2967 0.0000 0.3855\n+U68688 0.3236 0.3167 0.3730 0.3824 0.3361 0.2738 0.3902 0.2219\n+ 0.2942 0.2865 0.2916 0.3499 0.2332 0.3026 0.3862 0.2955 0.2745\n+ 0.2576 0.5619 0.4359 0.3736 0.2782 0.3501 0.2957 0.2070 0.3049\n+ 0.2080 0.1983 0.3079 0.3301 0.3079 0.2708 0.3958 0.1578 0.3109\n+ 0.3502 0.1635 0.4262 0.2200 0.2228 0.2366 0.3597 0.2942 0.3295\n+ 0.2168 0.2744 0.3399 0.3133 0.2850 0.3087 0.2648 0.3331 0.3018\n+ 0.4751 0.3125 0.3195 0.3550 0.1068 0.3204 0.2803 0.2715 0.3768\n+ 0.0685 0.2883 0.3419 0.3181 0.4176 0.3349 0.3243 0.0838 0.3754\n+ 0.3550 0.0203 0.4384 0.0081 0.3910 0.3331 0.2962 0.2419 0.3287\n+ 0.3558 0.2534 0.2690 0.2305 0.4061 0.0726 0.2074 0.3321 0.0100\n+ 0.3132 0.2380 0.4186 0.3631 0.2862 0.3730 0.2973 0.3855 0.0000\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.fasta Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,196 @@\n+>U68589\n+TAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG\n+>U68590\n+TAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC\n+>U68591\n+CGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT\n+>U68592\n+TAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT\n+>U68593\n+TAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG\n+>U68594\n+TAATCCCAAGGGTGCAANCGTTACTCGGAATTACTGGGCGTAAAGCGTGCG'..b'GGGCGTAAAGGGTGCGTANGCGGCGCGGTAAGTCGGGTGTGAAATCTCGGAGCTTAACTCCGAAACTGCATTCGATACTGCCGTGCTTGAGGACTGGAGANGAGACTGGAATTTACGGTGTAGCGGTGAAATGCGTATATATCGTAAGGAAGACCAGTGGCGAAGGCGGGTCTCTGGACAGTTCCTGACGCTGANGCACGAAGGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCAGTAAACGGTGCACCTTTGGTGTGGGAGGATTCGACCCCTTCCGTGCCGGAGCTAACGCGTTAAACCTTGCCGCCTGGTGGAGTACGGTCCGCAAGATTAAAACTCACACAAATTGACGGGGGCCCGCACAAGCGGTGGAGTATGTGGCTTAATTCCATGCAACGCGAAGAACCTTTATCCATGGCCCTGACATGCATCTCTTAGTTGGTGAAAGCCACG\n+>U68684\n+TAATACGGGGGGGGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGGGCTCGTAGGTGGCCAACTAAGTCATACGTGAAATCCCTCGGCTTAACCGGGGAACTGCGTCTGATACTGGATGGCTTGAGTTTGGGAGAGGGACGCGGAATTCCAGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCGTCCTGGACCAACACTGACACTGATGGGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAAACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAACATGTGGTTCAATTCGACGCAACGCGAAGAACCTTACCTGGGCTCGAAATGGANTGGAATCCGGTGGAAACATCNGCGCCCGCAAGGGCCGCTCTATAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCGTTAGTTGCCATCGGGTCAAGCCGGGCACTCTAGCGAAACCGCCTCGGATAACGGGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCTTTATGTCCAGGGCTACACACGTGCTACAATGCACGGTACAAACCGTCGCAAACCCGCGAGGGGGAGCTAATCGGAAAAAGCCGTGCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGAATCGCTAGTAATCGCAGATCAGAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGTGGACCATACTAGAAGCAGGTGGGCCAACCGCAAGGGGGCAGCCTTCCAAGGTATAGTTCATGATTGGGGTG\n+>U68685\n+TAATACAGANGTCCCAAGCGTTGTTCGGATTCACTGGGCGTAAAGGGCGCGTANGTGGCTGGGTAAGTTTGATGTGAAATCTCCGAGCCTAACTCGGAAAATGCATTGAATACTATCCAGCTTGAGGATTGGAGGGGAGACTGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACCAGTGGCGAAGGCGAGTCTCTGGACAATTCCTGACACTGAGGCGCGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCTTAAACGGTGCACATTTGCTGTAAGAAGAATCGACCCCTCTTGTGGCGAAGCTAACGCGTTAAATGTGCCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCGGTGGAGTATGTGGCTTAATTCGATGCAACGCGAAGAACCTTACCTGGCCTTGACATGTAGGTAGTAGAACCTGAAAGGGTGACGAGAGTAACAATACTCACTTACACAGGTGN\n+>U68686\n+TAATACAGAAGGTGCAAGCGTTGTTCGGAATTATTGGGCGTAAAGGGCGCGTAGGCGGTGCGGTAAGTCTCTAGTGAAATCTCCGGGCTCAACTCGGAGCCTGCTAGGGAAACTGCCGTGCTTGAGTGTGGGAGAGGTGAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCTGTGGCGAAAGCGGCTCACTGGACCACAACTGACGCTGAGGCGCGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCCTAAACGATGATTGCTTGGTGTAGCAGGTACCCAATCCTGCCGTGCCGAAGCTAACGCGATAAGCAATCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAACATGTGGTTCAATTCGACCCACGCGAAGAACCTTACCTGGGCTCGAAGCGCAGTGGACTGCGGTAGAAATATCGCTTTCCCGCAAGGGACTGCTGCGTT\n+>U68687\n+TAATACAGAGGTCCCAAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGAGGTAAGTCGGATGTGAAATCTCCGAGCTCAACTCGGAAACTGCATTGGAAACTACCTTGCTCGAGGGTTGGAGGGGGGACTGGAATGCTTGGTGTAGCAGTGAAATGCGTAGGTATCAAGCGGAACACCAGTGGCGAAGGCGAGTCCCTGGACAACTCCTGACACTGATGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAAAGGAATCGACCCCTTTTGTGGCGTACCAACGCGTTAAACGTGCCGCCTGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCGGTGGAGTATGTGGCTCAATTCGATGCAACGCGAAGAACCTTACCTGGCCTTGACATGCNACNTAGTAGAAGGGTGAAAGCCTGAAGAAGTTAGCAATACCAGTGTGCAACGGGTGTTGAAGGGCTGTTGTCAAGNTCGTTTGNGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCNTGNNTCCTGTCGCCACTCGTTCGCAAGACCGAAGCACTCGGGACAGACTGCTTCGCTTAAACGAGGAGGAAGGTGGGGATGACGTCAAGTCAGTATGGCCCTTACGGCCAGGGCTGCACANGTACCACAATGCCCGGCACAAAGGGAAGCGAGACCGTAAGGTGGAGCAAATCCCCAAAAACCGGGCCCAGTTCAGATTGTCGTCTGCAACTCGACGGCATGAAGCTGGAATCGCTAGTAATGGCGCATCAGCTACGGCGCCGTGAATACGTTCCCAGGCCTTGNACACACCGCCCGTCACATCATGAAAGCNGTTTGTACCNGAAGTCACCCCTTAAAAGGTGCCGAAGGTATGGATGGTGATTGGGATG\n+>U68688\n+TAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTCCTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGGGACTTGAGTGCAGGAGANAAAAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTTTTTGGCCTGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGANGGTTTCCGCCCTTTAGTGCTGAAGTAAACGCATTAAGCACTCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTCAAAGGAATCGACGGGGACCGCACAAGCGGTGGGGCATGTGGTTTAATTCGAAACAACGCGAAGAACCTTACCAGGTCTTGACATCCTCTGACAATCCTAGAGATAGGACTTCCCCTTCCGGGGGACAGA\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.fasta_head --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.fasta_head Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,10 @@ +>U68589 +TAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG +>U68590 +TAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC +>U68591 +CGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT +>U68592 +TAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT +>U68593 +TAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.fragclust.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.fragclust.fasta Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,192 @@\n+>U68622\n+TAAGACGAACCGTGCGAACGTTGTTCGGAATCACTGGGCTTAAAGGGCGCGTAGGCGGGCCATCAAGTCCGGGGTGAAATCCTCCAGCTCAACTGGAGAAGTGCCTTGGATACTGATGGCCTCGAGGAAGGTAGGGGAGCGCGGAACGGATGGTGGAGCGGTGAAATGTGTTGATATCATCCGGAACTCCGGTGGCGAAGGCGGCGCTCTGGACCTTTTCTGACGCTGAGGCGCGAAAGCCAGGGGAGAGAACGGGATTAGATACCCCGGTATTCCTGGCCCTAAACGATGAGTACTAGGTTGTAGACTAGACATGGGTTTACAGCCGAAGCAAAAGTGCTAAGTACTCCGCCTGGGGAGTATGGTCGCAAGGCTGAAACTCCAAGGAATTGACGGGGGCTCACACAAGCGGTGGAGCATGTGGCTTAATTCGANGCTACGCCGAAGAACCTTATCCTGGTCTTGANATGTTCGAAAAGANGTNNGNAAGTAGCGTGCGGGAAACGTTAACGGCGATCAGTAANGTCTGGAACCTATCACAGGTGCTGCATGGCTGTTGTCAGCTCGTGTCGTGAGATGTCGGGTTAAGTCCCTTAAACGAGCGAAACCCCTTGCTTTTCAGTTGCTACGGGGTAATGCCGAAGGACTCTGGGAGGACTGCCGGTGTTAAACCGGAGGAAGGTGGGGGACGTCAAGTCCTCATGGCCTTTATGACCAGGGCTGCACACGTGCTACAATGGCGTGAACAAAGGGACGCGAACGCGCGAGCGGGAGCAAATCCCAAAAAACACGCCCCAGTTCAGATCGAAGGCTGCAACTCGCCTTCGTGAAGTTGGAATCGCTAGTAATCGCAGGTCAGCAACACTGCGGTGAATGTGTTCCTGAGCCTTGTACACACCGCCCGTCAAGCCACGAAAGGGAGGGGCACCTGAAGTCGCTTTTACCAGTGCCGAAGGTGAACTTCCTGATTGGGATTAA\n+>U68608\n+TAAGACGTATAGAGCCAGTGTTATTTTTCGTGATTTGGCGTAAAGGGTGCGTAGGCGGTATGTTAAACAGAGAAGAGTGAGACATGGGTCGAACTGTGGCAGCTTTTTCTGAAATGGCAAACTAGAATTTTTTGGAAGTAAGCGGTATTTATAGGGTACAGGTGAAAAGGGTAGATCCTATAGGAACCATCAATTGCGAAGGCGGCTTACTATAAAGAATCGACGCTGAGGCACGAAGGCATGGGTATCGAATGGGATTAGACACCCCAGTAGTCCATGCGGACAACTATGGGAATTGGATTTCAAGGATCCGAGCTAGCGTGTGAAATTCCCCGCCTGGGGATGTACGATCGCAAGGTTTAAACCCAAGGGAATTGACGGGGGCTTAATCAAGCGGTGGAACATGTGGTTTAATTCGATACAACACGCAAAATCTTACCAACGTTCCGAGAAGAAAATATAAGGGGGTGNGAAAACACAGCAATAGGAAAATAGTTTGAGAAAAGAATTACTTCCTAAACCTTCGGCTTCATAGGCGCTGCATGGTNGTGGTTAGTCCGTGTCTTGAGATGTACGGTTCGATCCTATAACGGACAATACCCGTGTTTCTAATTAATAAAATAGAAAAATCACCACCTAAAGTTTGGATGAAGGGCGATTACCTCAAATCTTCATGGCCCGATCAAACGTTGGGCTACACACGTGTTACAATGGCCGTCACAAAGCGTGGCAAGAGTGCAAACTGGAGCAAATCGTGAATCGTGGTCGTAGTTCGAATTATTTTCTGGAACTCGAAAATATGAAGTTGAAATCGCAAGTAATCGGAGATCATGGAGCTTCGGTGAATGCAACCTTAGGTCTTATACACACCGCCCGTCACATTNTGAAAGTCGATCACATGTTAAGCTCTAATAATTATACGGTTTTAAATTCCGTTATAGTATCAGGAGTGCGAGTGTGGTTGGTAATTAGAGTG\n+>U68599\n+TAATACGGAGGGTGCGAGCATTAATCGGATTTATTGGGCGTAAAGGGCGCGTAGGCGGGAGCATAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGAATAGCATATGATACTGTGAATCTAGAGGATAGGCGGAGGAAATGGAATTCCACAAGTAGCGGTGAAATGCGTAGATATGTGGAAGAACACCGGTGGCGAAAGCGATTTTCTAGCTTATACCTGACGCTGAGGCGCGAAAGCAAGGGGATCAAACAGGATTAGATACCCTGGTAGTCCTTGCTGTAAACGATGTATACTTGGTGTAACCGGACTCAACCCTGGTTGTGCCGAAGCTAACGCGATATAGTATACCGCCTGGGGAGTACAGTCGCAAGGCTGAAACTCCAAAGAATTGACGGGGACCGCACAAGCAGTGGAGCATGTGGTTTAATTCGATGCACGCGAAAAACCTTACCAGGCTTGAACATGCACTTGGAAGATTAGCAGAGATGTTATTGCCCTTTAGGGGCTGGTGCACAGGTGCTGCATGGCTGTCGTCAGCTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGNNAAACGGAGCGGCAACCCTTCATCATTAGTTGCCAACAACGTGAAAGGTGGGGAACTCTAATGAGACTGCCTGGGTTAACCAGGAGGAAGGTGAGGTGACGTCAAGTCCGCATGGCCCTTATGTCTGGGGCTACACACGTGCTACAATGGACGGTGCAGAAGGCAGCAAAACCGCGAGGTGAAGCAAATCCTAAGAAAGCCGTCCTCAGTTCAGATTGTAGTCTGCAACTCGACTACATGAAGACGGAGTTGCTAGTAATGGCGAGTCAGCAACATCGCCGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACATCATGGGAGTTGGTTTTACCCGAAGCCGCTGGCCTAACCGCAAGGGGGGAGGCGTCTAAGGTGAGGCCGATGTCGCGGATG\n+>U68646\n+TAATACGTAGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTAGGCGGCAATTCAAGTCAGCTGTGAAATCTCCGAGCTTAACTCGGAACGGTCAGCTGATACTGTCTTGCTTGAGTGCGGAAGGGGCAATCGGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCAAGAGGAACACCTGAGGTGAAGACGGGTTGCTGGGCCGACACTGACGCTGACAGCGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGAATACTTGGTGTCTGGAGTCTCTATAGCTCCGGGTGCCGTCGCTAACGTTTTTAGTATTCCGCCTGGGGAGTACGCACGCAAGTGTGAAACTCAAAGGAATTGACCGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGCAACGCGAAGAACCTTACNTGGANTAGAATGTGNAGGGGATCTTGGGTAANCGCCAAGAGTNTGGGAAACCANACCCAAAACAAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTATTGATAGTCGCTAACATTAAGTTGAGAACTCTATCAAGACTGCTGTTGATAAAACGGAGGAAGGTGGGGATGATGTCAAGTCATCATGGCCTTTATGTTCAGGGCTACACACGTGCTACAATGGCCGGTACAAAACGTCGCAATCTCGCAAGAGGGAGCTAATCGCAAAAACCGGTCTCAGTTCGGATTGAAGTCTGCAACTCGACTTCATGAAGTTGGAATCGCTAGTAATCGCAAATCAGCATGTTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGTAGGTTGTACTAGAAGTGGCCGGACCAACTCGCAAGAGAGGTAGGTTACCACGGTATGATTTATGATTGGGGTG\n+>U68623\n+TAATACGTAGGGGGCAAGCGTTGTCCGGAATT'..b'AGTGGCGAAGGCGACTTTCTGGACGATAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGATGGATACTANGTGTNNGAGGTNTCGACCCCTTCTGTGCCGGAGTTAACACAATAAGTTTCCCNCCTGGGGAGTNCCGCCGCNAGGTTGAAACTCAAANGAATTGACCGGGGCCCGCACCACCCACTTGGAATTATGTGGTTTAATTCCAAGCCACGCGAAGAACCTTNCCAAGGGCTTGACATAATGGTGGATA\n+>U68675\n+TAGCGTTGTTCGGATTCACTGGGTTTAAAGGGTGCGTAGGAGGGCAGGTAAGTCAGTGTGAAATCCTGGGGCTTAACCCCAGAACTGCCATTGATACTCTCTGTCTTGAATACAGTGGAGGTGAGCGGAATATGTCATGTAGCGGTGAAATGCTTAGATATGACATAGAACACCAATTGCGAAGGCAGCTCGCTACACTACTATTGACTCTGAGGCACGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGGATACTCGACATACGCGATACACTGTGTGTGTCTGAGCGAAAGCATTAAGTATCCCACCTGGGAAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGGCGGGGGTCCGCACAAGCGGTGGAACATGTGGTTTAATTCGATGATACGCGAGGAACCTTACCTGGGCTANAATGCTGGTGGAACGTGGGTGAAAACTCACTTTG\n+>U68633\n+TAATACGAGGGGGGCAAGCGTTGTTCGGAATTATTGGGTGTAAAGGGTTCGTACGCGGTGTGGCAAGTCGGGAGTGAAATCTCTGGGCTTAACTCAGAGGCTGCTTCCGAAACTGCTGTGCTTGAGTGTGGGAGAAGCGCGTGGAATTGCAGGTGTANCGGTGAAATGCGTANATATCTGCGGGAACACCCGTGGCGAAAGCGGCGCGCTGGACCACAACTGACGCTGAGGAACNAAANCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCCTAAACGATCAGGACTTGGGGTGGCGCCCGTTCGGGCGTCGTCCCNGAGCTAACCGCGTTAAATCCTGCACCCTGGGGGAGTACGGTCGCAAGACTGACACTCCAAAGGAATTGACGGGGGGCCCGCACCAACCGGTGGAAACATGTTGGTTCAAATTCGAACGCTACGCCGAGGAACCTTTACCTGGGCTCC\n+>U68677\n+TAATACGTAGGGGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCGCGTAGGCGGTCCGATAAGTCGGCTGTGAAAGTCAGGGGCTCAACCCTTGAAAGCCGGCCGACACTGTCGGACTAGAGTCCGGAAGANGCAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGCAGATATCGGGAGGAACACCAATGGCGAAGGCAGCTTGCTGGGACGGTACTGACGCTGANGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTATTCCNCGCCGTAAACGATGGGCACTACGTGTGGGAGGTGTCGACTCCTCCCGTGCCGCAGCTAACGCATTAAGTGCCCCGCCTGGGGAGTACGCCGCTANGCTAAAACTCAAAGGAATCNGCCGGGGCCCGCACAAACAGCGGAACATGTGGTTTAATTCCACGCACCGCAAATAACCTACCTGGGCTTGACATGTT\n+>U68676\n+TAATACGTNGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTCCTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCNTTGGAAACTGGGGGACTTGAGTACAGAAGAAGAAAGCGGAATTCCACGTGTAGCGGTGAAATGCGTATAGATGTGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGTCTGTAACTGACGCTGANGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGAGGAATGCTAAGTGTTAGAAGGTTTCCGCCCTTTAATGCTGCACTAACCCATTTAGCACTCCGCCTGGGGAGTACGGCCGCCAGGCTGAAACTCAAATGAATTGACCGGGGCCGCCCAANCGGTGGAACATGTTTGTTTATATTCTAATCCACCGCCAAGAACTTTACANG\n+>U68673\n+TAATACAGAGGGTGCGAGCGTTGTTCGGAATTATTGGGCGTAAAGGGCGCGTANGCGGTGCGGTAAGTCACCTGTGAAATCTCCTGGCTCAACTGGGAGCTTGCAGGCGAAACTGCCGTGCTGGAGTGTGGGAGAGGTGCGTGGAATTCCCGGTGTAGCGGTGAAATGCGTATATATCGGGAGGAACACCTGTGGCGAAAGCGGCGCACTGGACCACAACTGACGCTGAGGCGCGAAAGCTAGGGGAGCAAACGGGATTAGATACCCTGGTAGTCCTAGCCCTAAACTATGGATGCTTGGTGTGATGGGTACCCAATCCCATCGTGCCGCAGCTAACGCGTTAAGCATCCCGCCTGGGGAGTACCGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCCCAAGCGTGGACATGTTGTCAATTCGACGCACGCGAAGATACTT\n+>U68647\n+CGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTCCTTTAAGTCTGANGTGAAAGCCCTCGGCTCAACCGAGGAGGGTCATTGGAAACTGGAGGACTTGAGTGCNNAATACGAAAGTGGAATTCCAAGTGTACCGGTGAAATGCGTNCAGATTTGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTATCTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTTTTCCCCGCCGTAAACAATTAAGTGCTAAGTGTTNTGGGGTTTCCGCCCCTTANTGCTGCAGCTAACGCATTATNCTCTCCGCCTGGGGAGTACTGTCGCCAGACTGACACTCCCATGAATTGACTGGGGCCCGCACAANCGGTGGAGCATGTGGTTTAATTCCAACCAACNCGAAAAAACTT\n+>U68682\n+TAATACCGAAGGTGCAAGCGTTATCCGGATTCACTGGGTTTAAAGGGTGCNTANGTGGACTANTAANTCAGTGGTGAAATCTCCGGGCTTAACTCGGAGACTGCCATTGATACTATCTGTCTTGAATATCCTGGAGGTGAGCGGAATATGTCATGTANCGGTGAAATGCCTAGATATGACATACGAACACCAATTGCGAAGGCNGCTCACTACGGGGTTATTGACACTGAGGCACGAAAGCGTGGGGATCAAACNGGATTAGATACCCTGCGTAGTCCACCGCCCTAAACGAAGGGATACTCGACATCANCGATACACTGTTGGTGTCTGAACGAAAAGCATTAAGTTTCCCCACCCTGGGGAAGTTCGAACCGCCAAGGTTGAAAACCTCCAAACGAATTGACCGGGGGTCCGCCCACAAGCGCGTGGG\n+>U68653\n+TAATACGTACGTGGCAAGCGTTGTCCGGAATTATTGGGTGTAAAGNGCNCGCAGGNGGTCCNTTANATCTGATGTGAAANCCCACGGCTCAACCCTGGNCGGTCATTGGATACTGGGGGACTTGAGTGCAGNAGAGAAGAATGGAATTCCACGTGTNGCGGTGAAATGCGTAGATATNTGGAGGAACACCNGTGGCGAAGGCGACTCTCTGGNCTGTAACTGACGCTGAAGCAGCGAAAGCGTGGGGAGCAAACAGGATTAGATATCCTGGNATCCACCCGTAAACGATTGAGTGCTAAGTGTTGGGAGTNGTTTCCGCCCATTCCGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGGAGTACCGGCGCCAAGCTGAAAACTCAAAAGAATTGACGGGGNNCCGCACAAGCGGTGGG\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.fragclust.names --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.fragclust.names Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,96 @@ +U68622 U68622 +U68608 U68608 +U68599 U68599 +U68646 U68646 +U68623 U68623 +U68644 U68644 +U68680 U68680 +U68621 U68621 +U68597 U68597 +U68594 U68594 +U68649 U68649 +U68593 U68593 +U68662 U68662 +U68607 U68607 +U68639 U68639 +U68674 U68674 +U68654 U68654 +U68615 U68615 +U68606 U68606 +U68612 U68612 +U68684 U68684 +U68659 U68659 +U68679 U68679 +U68687 U68687 +U68626 U68626 +U68672 U68672 +U68665 U68665 +U68632 U68632 +U68625 U68625 +U68652 U68652 +U68648 U68648 +U68630 U68630 +U68616 U68616 +U68664 U68664 +U68589 U68589 +U68600 U68600 +U68591 U68591 +U68605 U68605 +U68614 U68614 +U68611 U68611 +U68645 U68645 +U68602 U68602 +U68596 U68596 +U68681 U68681 +U68619 U68619 +U68670 U68670 +U68661 U68661 +U68617 U68617 +U68592 U68592 +U68669 U68669 +U68603 U68603 +U68610 U68610 +U68642 U68642 +U68631 U68631 +U68685 U68685 +U68595 U68595 +U68666 U68666 +U68651 U68651 +U68624 U68624 +U68686 U68686 +U68640 U68640 +U68628 U68628 +U68601 U68601 +U68641 U68641,U68667 +U68609 U68609 +U68678 U68678 +U68688 U68688 +U68627 U68627 +U68629 U68629 +U68643 U68643 +U68637 U68637 +U68618 U68618,U68620 +U68655 U68655 +U68656 U68656 +U68663 U68663 +U68636 U68636 +U68657 U68657 +U68658 U68658 +U68613 U68613 +U68635 U68635 +U68671 U68671 +U68683 U68683 +U68638 U68638 +U68598 U68598 +U68590 U68590 +U68660 U68660 +U68668 U68668 +U68634 U68634 +U68675 U68675 +U68633 U68633 +U68677 U68677 +U68676 U68676 +U68673 U68673 +U68647 U68647 +U68682 U68682 +U68653 U68653 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.groupaccnos --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.groupaccnos Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +forest +pasture |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.groups --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.groups Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +U68589 forest U68590 forest U68591 forest U68592 forest U68593 forest U68594 forest U68595 forest U68596 forest U68597 forest U68598 forest U68599 forest U68600 forest U68601 forest U68602 forest U68603 forest U68605 forest U68606 forest U68607 forest U68608 forest U68609 forest U68610 forest U68611 forest U68612 forest U68613 forest U68614 forest U68615 forest U68616 forest U68617 forest U68618 forest U68619 forest U68620 forest U68621 forest U68622 forest U68623 forest U68624 forest U68625 forest U68626 forest U68627 forest U68628 forest U68629 forest U68630 forest U68631 forest U68632 forest U68633 forest U68634 forest U68635 forest U68636 forest U68637 forest U68638 forest U68639 pasture U68640 pasture U68641 pasture U68642 pasture U68643 pasture U68644 pasture U68645 pasture U68646 pasture U68647 pasture U68648 pasture U68649 pasture U68651 pasture U68652 pasture U68653 pasture U68654 pasture U68655 pasture U68656 pasture U68657 pasture U68658 pasture U68659 pasture U68660 pasture U68661 pasture U68662 pasture U68663 pasture U68664 pasture U68665 pasture U68666 pasture U68667 pasture U68668 pasture U68669 pasture U68670 pasture U68671 pasture U68672 pasture U68673 pasture U68674 pasture U68675 pasture U68676 pasture U68677 pasture U68678 pasture U68679 pasture U68680 pasture U68681 pasture U68682 pasture U68683 pasture U68684 pasture U68685 pasture U68686 pasture U68687 pasture U68688 pasture \ No newline at end of file |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.head.names --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.head.names Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,5 @@ +U68593 U68593 +U68592 U68592 +U68591 U68591 +U68590 U68590 +U68589 U68589 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.metadata --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.metadata Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +group feature +forest 98 +pasture 98 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.mothur.shared --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.mothur.shared Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +label Group numOtus Otu01 Otu02 Otu03 Otu04 Otu05 Otu06 Otu07 Otu08 Otu09 Otu10 +0.10 forest 10 0 5 2 3 1 1 3 3 1 0 +0.10 pasture 10 7 2 5 1 3 2 0 0 1 2 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.names --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.names Fri May 19 05:26:45 2017 -0400 |
| b |
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| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.pcoa.loadings --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.pcoa.loadings Fri May 19 05:26:45 2017 -0400 |
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| @@ -0,0 +1,99 @@ +axis loading +1 5.209297 +2 4.419977 +3 3.507522 +4 2.856806 +5 2.267862 +6 2.073816 +7 1.852071 +8 1.742582 +9 1.675175 +10 1.559590 +11 1.476943 +12 1.423754 +13 1.400448 +14 1.373608 +15 1.288984 +16 1.278740 +17 1.220963 +18 1.192054 +19 1.168860 +20 1.144852 +21 1.085866 +22 1.054236 +23 1.036880 +24 1.020942 +25 0.992328 +26 0.987332 +27 0.971493 +28 0.968304 +29 0.951738 +30 0.937392 +31 0.915684 +32 0.911642 +33 0.894907 +34 0.886563 +35 0.881383 +36 0.879600 +37 0.869992 +38 0.862822 +39 0.854810 +40 0.851234 +41 0.846873 +42 0.836880 +43 0.832258 +44 0.827443 +45 0.823466 +46 0.821408 +47 0.819031 +48 0.817872 +49 0.810424 +50 0.807200 +51 0.805901 +52 0.798921 +53 0.791782 +54 0.791228 +55 0.785156 +56 0.784003 +57 0.783116 +58 0.783116 +59 0.781252 +60 0.778979 +61 0.777788 +62 0.775128 +63 0.771603 +64 0.768684 +65 0.765272 +66 0.762280 +67 0.758008 +68 0.756816 +69 0.754255 +70 0.749665 +71 0.746768 +72 0.743431 +73 0.742548 +74 0.736557 +75 0.734655 +76 0.727909 +77 0.723521 +78 0.713732 +79 0.713287 +80 0.710682 +81 0.706210 +82 0.695652 +83 0.690801 +84 0.680253 +85 0.675806 +86 0.670920 +87 0.659053 +88 0.657299 +89 0.649407 +90 0.635317 +91 0.625939 +92 0.612844 +93 0.566212 +94 0.559919 +95 0.545322 +96 0.361096 +97 0.000000 +98 0.000000 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.silva.wang.tax.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.silva.wang.tax.summary Fri May 19 05:26:45 2017 -0400 |
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| @@ -0,0 +1,23 @@ +taxlevel rankID taxon daughterlevels total +0 0 Root 1 3 +1 0.1 Bacteria 2 3 +2 0.1.2 Actinobacteria 1 2 +3 0.1.2.1 Actinobacteria 1 2 +4 0.1.2.1.2 Actinobacteridae 1 2 +5 0.1.2.1.2.1 Actinomycetales 2 2 +6 0.1.2.1.2.1.8 Micrococcineae 1 1 +7 0.1.2.1.2.1.8.11 Microbacteriaceae 1 1 +8 0.1.2.1.2.1.8.11.24 Zimmermannella 1 1 +9 0.1.2.1.2.1.8.11.24.1 unclassified 0 1 +6 0.1.2.1.2.1.12 Pseudonocardineae 1 1 +7 0.1.2.1.2.1.12.2 Pseudonocardiaceae 1 1 +8 0.1.2.1.2.1.12.2.9 Saccharomonospora 1 1 +9 0.1.2.1.2.1.12.2.9.1 unclassified 0 1 +2 0.1.34 Firmicutes 1 1 +3 0.1.34.2 Clostridia 1 1 +4 0.1.34.2.1 Clostridiales 1 1 +5 0.1.34.2.1.9 Gracilibacteraceae 1 1 +6 0.1.34.2.1.9.1 Gracilibacter 1 1 +7 0.1.34.2.1.9.1.1 unclassified 1 1 +8 0.1.34.2.1.9.1.1.1 unclassified 1 1 +9 0.1.34.2.1.9.1.1.1.1 unclassified 0 1 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.square.pcoa.axes --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.square.pcoa.axes Fri May 19 05:26:45 2017 -0400 |
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| @@ -0,0 +1,3 @@ +group axis1 axis2 axis3 +forest 0.045166 0.143659 -0.000000 +pasture 0.129005 -0.103932 -0.000000 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.unique.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.unique.fasta Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,192 @@\n+>U68589\n+TAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG\n+>U68590\n+TAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC\n+>U68591\n+CGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT\n+>U68592\n+TAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT\n+>U68593\n+TAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG\n+>U68594\n+TAATCCCAAGGGTGCAANCGTTACTCGGAATTACTGGGCGTAAAGCGTGCG'..b'GGGCGTAAAGGGTGCGTANGCGGCGCGGTAAGTCGGGTGTGAAATCTCGGAGCTTAACTCCGAAACTGCATTCGATACTGCCGTGCTTGAGGACTGGAGANGAGACTGGAATTTACGGTGTAGCGGTGAAATGCGTATATATCGTAAGGAAGACCAGTGGCGAAGGCGGGTCTCTGGACAGTTCCTGACGCTGANGCACGAAGGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCAGTAAACGGTGCACCTTTGGTGTGGGAGGATTCGACCCCTTCCGTGCCGGAGCTAACGCGTTAAACCTTGCCGCCTGGTGGAGTACGGTCCGCAAGATTAAAACTCACACAAATTGACGGGGGCCCGCACAAGCGGTGGAGTATGTGGCTTAATTCCATGCAACGCGAAGAACCTTTATCCATGGCCCTGACATGCATCTCTTAGTTGGTGAAAGCCACG\n+>U68684\n+TAATACGGGGGGGGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGGGCTCGTAGGTGGCCAACTAAGTCATACGTGAAATCCCTCGGCTTAACCGGGGAACTGCGTCTGATACTGGATGGCTTGAGTTTGGGAGAGGGACGCGGAATTCCAGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCGTCCTGGACCAACACTGACACTGATGGGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAAACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAACATGTGGTTCAATTCGACGCAACGCGAAGAACCTTACCTGGGCTCGAAATGGANTGGAATCCGGTGGAAACATCNGCGCCCGCAAGGGCCGCTCTATAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCGTTAGTTGCCATCGGGTCAAGCCGGGCACTCTAGCGAAACCGCCTCGGATAACGGGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCTTTATGTCCAGGGCTACACACGTGCTACAATGCACGGTACAAACCGTCGCAAACCCGCGAGGGGGAGCTAATCGGAAAAAGCCGTGCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGAATCGCTAGTAATCGCAGATCAGAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGTGGACCATACTAGAAGCAGGTGGGCCAACCGCAAGGGGGCAGCCTTCCAAGGTATAGTTCATGATTGGGGTG\n+>U68685\n+TAATACAGANGTCCCAAGCGTTGTTCGGATTCACTGGGCGTAAAGGGCGCGTANGTGGCTGGGTAAGTTTGATGTGAAATCTCCGAGCCTAACTCGGAAAATGCATTGAATACTATCCAGCTTGAGGATTGGAGGGGAGACTGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACCAGTGGCGAAGGCGAGTCTCTGGACAATTCCTGACACTGAGGCGCGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCTTAAACGGTGCACATTTGCTGTAAGAAGAATCGACCCCTCTTGTGGCGAAGCTAACGCGTTAAATGTGCCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCGGTGGAGTATGTGGCTTAATTCGATGCAACGCGAAGAACCTTACCTGGCCTTGACATGTAGGTAGTAGAACCTGAAAGGGTGACGAGAGTAACAATACTCACTTACACAGGTGN\n+>U68686\n+TAATACAGAAGGTGCAAGCGTTGTTCGGAATTATTGGGCGTAAAGGGCGCGTAGGCGGTGCGGTAAGTCTCTAGTGAAATCTCCGGGCTCAACTCGGAGCCTGCTAGGGAAACTGCCGTGCTTGAGTGTGGGAGAGGTGAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCTGTGGCGAAAGCGGCTCACTGGACCACAACTGACGCTGAGGCGCGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCCTAAACGATGATTGCTTGGTGTAGCAGGTACCCAATCCTGCCGTGCCGAAGCTAACGCGATAAGCAATCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAACATGTGGTTCAATTCGACCCACGCGAAGAACCTTACCTGGGCTCGAAGCGCAGTGGACTGCGGTAGAAATATCGCTTTCCCGCAAGGGACTGCTGCGTT\n+>U68687\n+TAATACAGAGGTCCCAAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGAGGTAAGTCGGATGTGAAATCTCCGAGCTCAACTCGGAAACTGCATTGGAAACTACCTTGCTCGAGGGTTGGAGGGGGGACTGGAATGCTTGGTGTAGCAGTGAAATGCGTAGGTATCAAGCGGAACACCAGTGGCGAAGGCGAGTCCCTGGACAACTCCTGACACTGATGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAAAGGAATCGACCCCTTTTGTGGCGTACCAACGCGTTAAACGTGCCGCCTGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCGGTGGAGTATGTGGCTCAATTCGATGCAACGCGAAGAACCTTACCTGGCCTTGACATGCNACNTAGTAGAAGGGTGAAAGCCTGAAGAAGTTAGCAATACCAGTGTGCAACGGGTGTTGAAGGGCTGTTGTCAAGNTCGTTTGNGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCNTGNNTCCTGTCGCCACTCGTTCGCAAGACCGAAGCACTCGGGACAGACTGCTTCGCTTAAACGAGGAGGAAGGTGGGGATGACGTCAAGTCAGTATGGCCCTTACGGCCAGGGCTGCACANGTACCACAATGCCCGGCACAAAGGGAAGCGAGACCGTAAGGTGGAGCAAATCCCCAAAAACCGGGCCCAGTTCAGATTGTCGTCTGCAACTCGACGGCATGAAGCTGGAATCGCTAGTAATGGCGCATCAGCTACGGCGCCGTGAATACGTTCCCAGGCCTTGNACACACCGCCCGTCACATCATGAAAGCNGTTTGTACCNGAAGTCACCCCTTAAAAGGTGCCGAAGGTATGGATGGTGATTGGGATG\n+>U68688\n+TAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTCCTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGGGACTTGAGTGCAGGAGANAAAAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTTTTTGGCCTGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGANGGTTTCCGCCCTTTAGTGCTGAAGTAAACGCATTAAGCACTCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTCAAAGGAATCGACGGGGACCGCACAAGCGGTGGGGCATGTGGTTTAATTCGAAACAACGCGAAGAACCTTACCAGGTCTTGACATCCTCTGACAATCCTAGAGATAGGACTTCCCCTTCCGGGGGACAGA\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.unique.names --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.unique.names Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,96 @@ +U68589 U68589 +U68590 U68590 +U68591 U68591 +U68592 U68592 +U68593 U68593 +U68594 U68594 +U68595 U68595 +U68596 U68596 +U68597 U68597 +U68598 U68598 +U68599 U68599 +U68600 U68600 +U68601 U68601 +U68602 U68602 +U68603 U68603 +U68605 U68605 +U68606 U68606 +U68607 U68607 +U68608 U68608 +U68609 U68609 +U68610 U68610 +U68611 U68611 +U68612 U68612 +U68613 U68613 +U68614 U68614 +U68615 U68615 +U68616 U68616 +U68617 U68617 +U68618 U68618,U68620 +U68619 U68619 +U68621 U68621 +U68622 U68622 +U68623 U68623 +U68624 U68624 +U68625 U68625 +U68626 U68626 +U68627 U68627 +U68628 U68628 +U68629 U68629 +U68630 U68630 +U68631 U68631 +U68632 U68632 +U68633 U68633 +U68634 U68634 +U68635 U68635 +U68636 U68636 +U68637 U68637 +U68638 U68638 +U68639 U68639 +U68640 U68640 +U68641 U68641,U68667 +U68642 U68642 +U68643 U68643 +U68644 U68644 +U68645 U68645 +U68646 U68646 +U68647 U68647 +U68648 U68648 +U68649 U68649 +U68651 U68651 +U68652 U68652 +U68653 U68653 +U68654 U68654 +U68655 U68655 +U68656 U68656 +U68657 U68657 +U68658 U68658 +U68659 U68659 +U68660 U68660 +U68661 U68661 +U68662 U68662 +U68663 U68663 +U68664 U68664 +U68665 U68665 +U68666 U68666 +U68668 U68668 +U68669 U68669 +U68670 U68670 +U68671 U68671 +U68672 U68672 +U68673 U68673 +U68674 U68674 +U68675 U68675 +U68676 U68676 +U68677 U68677 +U68678 U68678 +U68679 U68679 +U68680 U68680 +U68681 U68681 +U68682 U68682 +U68683 U68683 +U68684 U68684 +U68685 U68685 +U68686 U68686 +U68687 U68687 +U68688 U68688 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.wang.knn.tax.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.wang.knn.tax.summary Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,8 @@ +taxlevel rankID taxon daughterlevels total +0 0 Root 1 98 +1 0.3 unknown 1 98 +2 0.3.1 unclassified 1 98 +3 0.3.1.1 unclassified 1 98 +4 0.3.1.1.1 unclassified 1 98 +5 0.3.1.1.1.1 unclassified 1 98 +6 0.3.1.1.1.1.1 unclassified 0 98 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon.wang.wang.taxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.wang.wang.taxonomy Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,98 @@\n+U68589\tBacteria(92);"Proteobacteria"(40);Gammaproteobacteria(40);"Enterobacteriales"(40);Enterobacteriaceae(40);Escherichia_Shigella(40);\n+U68590\tBacteria(94);Firmicutes(69);Erysipelotrichia(68);Erysipelotrichales(68);Erysipelotrichaceae(68);Turicibacter(68);\n+U68591\tBacteria(97);"Proteobacteria"(55);Gammaproteobacteria(55);"Enterobacteriales"(55);Enterobacteriaceae(55);Escherichia_Shigella(55);\n+U68592\tBacteria(93);"Proteobacteria"(31);Gammaproteobacteria(31);"Enterobacteriales"(31);Enterobacteriaceae(31);Escherichia_Shigella(31);\n+U68593\tBacteria(98);Firmicutes(55);Erysipelotrichia(31);Erysipelotrichales(31);Erysipelotrichaceae(31);Turicibacter(31);\n+U68594\tBacteria(93);Firmicutes(72);Clostridia(46);Clostridiales(46);Lachnospiraceae(46);Dorea(22);\n+U68595\tBacteria(88);TM7(37);TM7_class_incertae_sedis(37);TM7_order_incertae_sedis(37);TM7_family_incertae_sedis(37);TM7_genus_incertae_sedis(37);\n+U68596\tBacteria(74);TM7(29);TM7_class_incertae_sedis(29);TM7_order_incertae_sedis(29);TM7_family_incertae_sedis(29);TM7_genus_incertae_sedis(29);\n+U68597\tBacteria(100);Firmicutes(87);Clostridia(54);Clostridiales(54);Lachnospiraceae(54);Clostridium_XlVa(28);\n+U68598\tBacteria(80);TM7(39);TM7_class_incertae_sedis(39);TM7_order_incertae_sedis(39);TM7_family_incertae_sedis(39);TM7_genus_incertae_sedis(39);\n+U68599\tBacteria(98);Firmicutes(57);Erysipelotrichia(30);Erysipelotrichales(30);Erysipelotrichaceae(30);Turicibacter(30);\n+U68600\tBacteria(98);"Proteobacteria"(60);Gammaproteobacteria(60);"Enterobacteriales"(60);Enterobacteriaceae(60);Escherichia_Shigella(60);\n+U68601\tBacteria(82);Firmicutes(31);Erysipelotrichia(14);Erysipelotrichales(14);Erysipelotrichaceae(14);Turicibacter(14);\n+U68602\tBacteria(89);"Proteobacteria"(30);Gammaproteobacteria(30);"Enterobacteriales"(30);Enterobacteriaceae(30);Escherichia_Shigella(30);\n+U68603\tBacteria(91);Firmicutes(76);Erysipelotrichia(51);Erysipelotrichales(51);Erysipelotrichaceae(51);Turicibacter(51);\n+U68605\tBacteria(86);Firmicutes(79);Clostridia(70);Clostridiales(70);Lachnospiraceae(70);Clostridium_XlVa(39);\n+U68606\tBacteria(98);TM7(41);TM7_class_incertae_sedis(41);TM7_order_incertae_sedis(41);TM7_family_incertae_sedis(41);TM7_genus_incertae_sedis(41);\n+U68607\tBacteria(87);TM7(24);TM7_class_incertae_sedis(24);TM7_order_incertae_sedis(24);TM7_family_incertae_sedis(24);TM7_genus_incertae_sedis(24);\n+U68608\tBacteria(98);TM7(45);TM7_class_incertae_sedis(45);TM7_order_incertae_sedis(45);TM7_family_incertae_sedis(45);TM7_genus_incertae_sedis(45);\n+U68609\tBacteria(74);Firmicutes(46);Erysipelotrichia(46);Erysipelotrichales(46);Erysipelotrichaceae(46);Turicibacter(46);\n+U68610\tBacteria(83);Firmicutes(48);Clostridia(40);Clostridiales(40);Lachnospiraceae(40);Clostridium_XlVa(30);\n+U68611\tBacteria(80);TM7(32);TM7_class_incertae_sedis(32);TM7_order_incertae_sedis(32);TM7_family_incertae_sedis(32);TM7_genus_incertae_sedis(32);\n+U68612\tBacteria(97);TM7(47);TM7_class_incertae_sedis(47);TM7_order_incertae_sedis(47);TM7_family_incertae_sedis(47);TM7_genus_incertae_sedis(47);\n+U68613\tBacteria(81);Firmicutes(36);Erysipelotrichia(14);Erysipelotrichales(14);Erysipelotrichaceae(14);Turicibacter(14);\n+U68614\tBacteria(79);Firmicutes(53);Erysipelotrichia(15);Erysipelotrichales(15);Erysipelotrichaceae(15);Turicibacter(15);\n+U68615\tBacteria(97);Firmicutes(69);Clostridia(50);Clostridiales(50);Lachnospiraceae(50);Dorea(32);\n+U68616\tBacteria(94);Firmicutes(69);Erysipelotrichia(33);Erysipelotrichales(33);Erysipelotrichaceae(33);Turicibacter(33);\n+U68617\tBacteria(79);Firmicutes(36);Erysipelotrichia(14);Erysipelotrichales(14);Erysipelotrichaceae(14);Turicibacter(14);\n+U68618\tBacteria(73);Firmicutes(31);Erysipelotrichia(25);Erysipelotrichales(25);Erysipelotrichaceae(25);Turicibacter(25);\n+U68619\tBacteria(86);TM7(41);TM7_class_incertae_sedis(41);TM7_order_incertae_sedis(41);TM7_family_incertae_sedis(41);TM7_genus_incertae_sedis(41);\n+U68620\tBacteria(67);Firmicutes(24);Erysipelotrichia(18);Erysipelotrichales(18);Erysipel'..b'657\tBacteria(70);Firmicutes(44);Erysipelotrichia(32);Erysipelotrichales(32);Erysipelotrichaceae(32);Turicibacter(32);\n+U68658\tBacteria(61);Firmicutes(23);Erysipelotrichia(17);Erysipelotrichales(17);Erysipelotrichaceae(17);Turicibacter(17);\n+U68659\tBacteria(97);Firmicutes(36);Erysipelotrichia(28);Erysipelotrichales(28);Erysipelotrichaceae(28);Turicibacter(28);\n+U68660\tBacteria(95);Firmicutes(85);Clostridia(72);Clostridiales(72);Lachnospiraceae(72);Dorea(40);\n+U68661\tBacteria(94);Firmicutes(52);Erysipelotrichia(24);Erysipelotrichales(24);Erysipelotrichaceae(24);Turicibacter(24);\n+U68662\tBacteria(98);TM7(42);TM7_class_incertae_sedis(42);TM7_order_incertae_sedis(42);TM7_family_incertae_sedis(42);TM7_genus_incertae_sedis(42);\n+U68663\tBacteria(95);Firmicutes(89);Erysipelotrichia(49);Erysipelotrichales(49);Erysipelotrichaceae(49);Turicibacter(49);\n+U68664\tBacteria(100);Firmicutes(61);Clostridia(44);Clostridiales(44);Lachnospiraceae(44);Coprococcus(17);\n+U68665\tBacteria(100);Firmicutes(83);Erysipelotrichia(20);Erysipelotrichales(20);Erysipelotrichaceae(20);Turicibacter(20);\n+U68666\tBacteria(91);TM7(27);TM7_class_incertae_sedis(27);TM7_order_incertae_sedis(27);TM7_family_incertae_sedis(27);TM7_genus_incertae_sedis(27);\n+U68667\tBacteria(78);Firmicutes(33);Erysipelotrichia(26);Erysipelotrichales(26);Erysipelotrichaceae(26);Turicibacter(26);\n+U68668\tBacteria(56);Firmicutes(28);Erysipelotrichia(14);Erysipelotrichales(14);Erysipelotrichaceae(14);Turicibacter(14);\n+U68669\tBacteria(67);Firmicutes(50);Erysipelotrichia(34);Erysipelotrichales(34);Erysipelotrichaceae(34);Turicibacter(34);\n+U68670\tBacteria(69);Firmicutes(30);Clostridia(30);Clostridiales(30);Lachnospiraceae(30);Coprococcus(21);\n+U68671\tBacteria(98);Firmicutes(59);Clostridia(41);Clostridiales(41);Lachnospiraceae(41);Clostridium_XlVa(24);\n+U68672\tBacteria(89);Firmicutes(57);Erysipelotrichia(21);Erysipelotrichales(21);Erysipelotrichaceae(21);Turicibacter(21);\n+U68673\tBacteria(89);"Proteobacteria"(41);Gammaproteobacteria(41);"Enterobacteriales"(41);Enterobacteriaceae(41);Escherichia_Shigella(41);\n+U68674\tBacteria(99);"Proteobacteria"(57);Gammaproteobacteria(57);"Enterobacteriales"(57);Enterobacteriaceae(57);Escherichia_Shigella(57);\n+U68675\tBacteria(79);Firmicutes(55);Erysipelotrichia(37);Erysipelotrichales(37);Erysipelotrichaceae(37);Turicibacter(37);\n+U68676\tBacteria(85);Firmicutes(65);Clostridia(54);Clostridiales(54);Lachnospiraceae(54);Dorea(38);\n+U68677\tBacteria(49);TM7(22);TM7_class_incertae_sedis(22);TM7_order_incertae_sedis(22);TM7_family_incertae_sedis(22);TM7_genus_incertae_sedis(22);\n+U68678\tBacteria(85);Firmicutes(49);Erysipelotrichia(41);Erysipelotrichales(41);Erysipelotrichaceae(41);Turicibacter(41);\n+U68679\tBacteria(98);Firmicutes(94);Clostridia(62);Clostridiales(62);Lachnospiraceae(62);Dorea(40);\n+U68680\tBacteria(99);Firmicutes(43);Clostridia(33);Clostridiales(33);Lachnospiraceae(33);Dorea(25);\n+U68681\tBacteria(59);TM7(16);TM7_class_incertae_sedis(16);TM7_order_incertae_sedis(16);TM7_family_incertae_sedis(16);TM7_genus_incertae_sedis(16);\n+U68682\tBacteria(82);TM7(26);TM7_class_incertae_sedis(26);TM7_order_incertae_sedis(26);TM7_family_incertae_sedis(26);TM7_genus_incertae_sedis(26);\n+U68683\tBacteria(86);Firmicutes(49);Erysipelotrichia(24);Erysipelotrichales(24);Erysipelotrichaceae(24);Turicibacter(24);\n+U68684\tBacteria(100);TM7(39);TM7_class_incertae_sedis(39);TM7_order_incertae_sedis(39);TM7_family_incertae_sedis(39);TM7_genus_incertae_sedis(39);\n+U68685\tBacteria(88);TM7(59);TM7_class_incertae_sedis(59);TM7_order_incertae_sedis(59);TM7_family_incertae_sedis(59);TM7_genus_incertae_sedis(59);\n+U68686\tBacteria(85);"Proteobacteria"(37);Gammaproteobacteria(37);"Enterobacteriales"(37);Enterobacteriaceae(37);Escherichia_Shigella(37);\n+U68687\tBacteria(100);Firmicutes(46);Erysipelotrichia(34);Erysipelotrichales(34);Erysipelotrichaceae(34);Turicibacter(34);\n+U68688\tBacteria(95);Firmicutes(88);Erysipelotrichia(34);Erysipelotrichales(34);Erysipelotrichaceae(34);Turicibacter(34);\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon1.count_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon1.count_table Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,99 @@ +Representative_Sequence total +U68630 1 +U68595 1 +U68600 1 +U68591 1 +U68647 1 +U68661 1 +U68605 1 +U68622 1 +U68612 1 +U68608 1 +U68610 1 +U68656 1 +U68655 1 +U68668 1 +U68686 1 +U68683 1 +U68635 1 +U68627 1 +U68672 1 +U68621 1 +U68638 1 +U68613 1 +U68618 1 +U68620 1 +U68602 1 +U68637 1 +U68641 1 +U68667 1 +U68673 1 +U68658 1 +U68664 1 +U68687 1 +U68592 1 +U68671 1 +U68636 1 +U68631 1 +U68652 1 +U68666 1 +U68674 1 +U68685 1 +U68625 1 +U68682 1 +U68609 1 +U68603 1 +U68640 1 +U68680 1 +U68615 1 +U68670 1 +U68662 1 +U68678 1 +U68598 1 +U68619 1 +U68633 1 +U68651 1 +U68645 1 +U68643 1 +U68611 1 +U68657 1 +U68599 1 +U68642 1 +U68590 1 +U68644 1 +U68684 1 +U68606 1 +U68639 1 +U68654 1 +U68593 1 +U68679 1 +U68607 1 +U68597 1 +U68653 1 +U68646 1 +U68616 1 +U68677 1 +U68681 1 +U68623 1 +U68669 1 +U68589 1 +U68665 1 +U68663 1 +U68688 1 +U68617 1 +U68628 1 +U68629 1 +U68660 1 +U68614 1 +U68632 1 +U68634 1 +U68676 1 +U68649 1 +U68648 1 +U68626 1 +U68596 1 +U68624 1 +U68594 1 +U68659 1 +U68601 1 +U68675 1 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon1.names --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon1.names Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,98 @@ +U68630 U68630 +U68595 U68595 +U68600 U68600 +U68591 U68591 +U68647 U68647 +U68661 U68661 +U68605 U68605 +U68622 U68622 +U68612 U68612 +U68608 U68608 +U68610 U68610 +U68656 U68656 +U68655 U68655 +U68668 U68668 +U68686 U68686 +U68683 U68683 +U68635 U68635 +U68627 U68627 +U68672 U68672 +U68621 U68621 +U68638 U68638 +U68613 U68613 +U68618 U68618 +U68620 U68620 +U68602 U68602 +U68637 U68637 +U68641 U68641 +U68667 U68667 +U68673 U68673 +U68658 U68658 +U68664 U68664 +U68687 U68687 +U68592 U68592 +U68671 U68671 +U68636 U68636 +U68631 U68631 +U68652 U68652 +U68666 U68666 +U68674 U68674 +U68685 U68685 +U68625 U68625 +U68682 U68682 +U68609 U68609 +U68603 U68603 +U68640 U68640 +U68680 U68680 +U68615 U68615 +U68670 U68670 +U68662 U68662 +U68678 U68678 +U68598 U68598 +U68619 U68619 +U68633 U68633 +U68651 U68651 +U68645 U68645 +U68643 U68643 +U68611 U68611 +U68657 U68657 +U68599 U68599 +U68642 U68642 +U68590 U68590 +U68644 U68644 +U68684 U68684 +U68606 U68606 +U68639 U68639 +U68654 U68654 +U68593 U68593 +U68679 U68679 +U68607 U68607 +U68597 U68597 +U68653 U68653 +U68646 U68646 +U68616 U68616 +U68677 U68677 +U68681 U68681 +U68623 U68623 +U68669 U68669 +U68589 U68589 +U68665 U68665 +U68663 U68663 +U68688 U68688 +U68617 U68617 +U68628 U68628 +U68629 U68629 +U68660 U68660 +U68614 U68614 +U68632 U68632 +U68634 U68634 +U68676 U68676 +U68649 U68649 +U68648 U68648 +U68626 U68626 +U68596 U68596 +U68624 U68624 +U68594 U68594 +U68659 U68659 +U68601 U68601 +U68675 U68675 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon_withgroups.count_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon_withgroups.count_table Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,97 @@ +Representative_Sequence total forest pasture +U68630 1 1 0 +U68595 1 1 0 +U68600 1 1 0 +U68591 1 1 0 +U68647 1 0 1 +U68661 1 0 1 +U68605 1 1 0 +U68622 1 1 0 +U68612 1 1 0 +U68608 1 1 0 +U68610 1 1 0 +U68656 1 0 1 +U68655 1 0 1 +U68668 1 0 1 +U68686 1 0 1 +U68683 1 0 1 +U68635 1 1 0 +U68627 1 1 0 +U68672 1 0 1 +U68621 1 1 0 +U68638 1 1 0 +U68613 1 1 0 +U68618 2 2 0 +U68602 1 1 0 +U68637 1 1 0 +U68641 2 0 2 +U68673 1 0 1 +U68658 1 0 1 +U68664 1 0 1 +U68687 1 0 1 +U68592 1 1 0 +U68671 1 0 1 +U68636 1 1 0 +U68631 1 1 0 +U68652 1 0 1 +U68666 1 0 1 +U68674 1 0 1 +U68685 1 0 1 +U68625 1 1 0 +U68682 1 0 1 +U68609 1 1 0 +U68603 1 1 0 +U68640 1 0 1 +U68680 1 0 1 +U68615 1 1 0 +U68670 1 0 1 +U68662 1 0 1 +U68678 1 0 1 +U68598 1 1 0 +U68619 1 1 0 +U68633 1 1 0 +U68651 1 0 1 +U68645 1 0 1 +U68643 1 0 1 +U68611 1 1 0 +U68657 1 0 1 +U68599 1 1 0 +U68642 1 0 1 +U68590 1 1 0 +U68644 1 0 1 +U68684 1 0 1 +U68606 1 1 0 +U68639 1 0 1 +U68654 1 0 1 +U68593 1 1 0 +U68679 1 0 1 +U68607 1 1 0 +U68597 1 1 0 +U68653 1 0 1 +U68646 1 0 1 +U68616 1 1 0 +U68677 1 0 1 +U68681 1 0 1 +U68623 1 1 0 +U68669 1 0 1 +U68589 1 1 0 +U68665 1 0 1 +U68663 1 0 1 +U68688 1 0 1 +U68617 1 1 0 +U68628 1 1 0 +U68629 1 1 0 +U68660 1 0 1 +U68614 1 1 0 +U68632 1 1 0 +U68634 1 1 0 +U68676 1 0 1 +U68649 1 0 1 +U68648 1 0 1 +U68626 1 1 0 +U68596 1 1 0 +U68624 1 1 0 +U68594 1 1 0 +U68659 1 0 1 +U68601 1 1 0 +U68675 1 0 1 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon_withgroups.redundant.groups --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon_withgroups.redundant.groups Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,98 @@ +U68589_1 forest +U68590_1 forest +U68591_1 forest +U68592_1 forest +U68593_1 forest +U68594_1 forest +U68595_1 forest +U68596_1 forest +U68597_1 forest +U68598_1 forest +U68599_1 forest +U68600_1 forest +U68601_1 forest +U68602_1 forest +U68603_1 forest +U68605_1 forest +U68606_1 forest +U68607_1 forest +U68608_1 forest +U68609_1 forest +U68610_1 forest +U68611_1 forest +U68612_1 forest +U68613_1 forest +U68614_1 forest +U68615_1 forest +U68616_1 forest +U68617_1 forest +U68618_1 forest +U68618_2 forest +U68619_1 forest +U68621_1 forest +U68622_1 forest +U68623_1 forest +U68624_1 forest +U68625_1 forest +U68626_1 forest +U68627_1 forest +U68628_1 forest +U68629_1 forest +U68630_1 forest +U68631_1 forest +U68632_1 forest +U68633_1 forest +U68634_1 forest +U68635_1 forest +U68636_1 forest +U68637_1 forest +U68638_1 forest +U68639_1 pasture +U68640_1 pasture +U68641_1 pasture +U68641_2 pasture +U68642_1 pasture +U68643_1 pasture +U68644_1 pasture +U68645_1 pasture +U68646_1 pasture +U68647_1 pasture +U68648_1 pasture +U68649_1 pasture +U68651_1 pasture +U68652_1 pasture +U68653_1 pasture +U68654_1 pasture +U68655_1 pasture +U68656_1 pasture +U68657_1 pasture +U68658_1 pasture +U68659_1 pasture +U68660_1 pasture +U68661_1 pasture +U68662_1 pasture +U68663_1 pasture +U68664_1 pasture +U68665_1 pasture +U68666_1 pasture +U68668_1 pasture +U68669_1 pasture +U68670_1 pasture +U68671_1 pasture +U68672_1 pasture +U68673_1 pasture +U68674_1 pasture +U68675_1 pasture +U68676_1 pasture +U68677_1 pasture +U68678_1 pasture +U68679_1 pasture +U68680_1 pasture +U68681_1 pasture +U68682_1 pasture +U68683_1 pasture +U68684_1 pasture +U68685_1 pasture +U68686_1 pasture +U68687_1 pasture +U68688_1 pasture |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/amazon_withgroups_pasture.count_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon_withgroups_pasture.count_table Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,49 @@ +Representative_Sequence total pasture +U68647 1 1 +U68661 1 1 +U68656 1 1 +U68655 1 1 +U68668 1 1 +U68686 1 1 +U68683 1 1 +U68672 1 1 +U68641 2 2 +U68673 1 1 +U68658 1 1 +U68664 1 1 +U68687 1 1 +U68671 1 1 +U68652 1 1 +U68666 1 1 +U68674 1 1 +U68685 1 1 +U68682 1 1 +U68640 1 1 +U68680 1 1 +U68670 1 1 +U68662 1 1 +U68678 1 1 +U68651 1 1 +U68645 1 1 +U68643 1 1 +U68657 1 1 +U68642 1 1 +U68644 1 1 +U68684 1 1 +U68639 1 1 +U68654 1 1 +U68679 1 1 +U68653 1 1 +U68646 1 1 +U68677 1 1 +U68681 1 1 +U68669 1 1 +U68665 1 1 +U68663 1 1 +U68688 1 1 +U68660 1 1 +U68676 1 1 +U68649 1 1 +U68648 1 1 +U68659 1 1 +U68675 1 1 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/biosample.source --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biosample.source Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,24 @@ +if (package == "soil") { + out << "#MIMARKS.survey.soil.4.0" << endl; + if (requiredonly) { + out << "#{sample name} {description of sample} {sample title} {description of library_construction_protocol} {http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&keep=1&srchmode=1&unlock}" << endl; + out << "#{text} {text} {text} {text} {controlled vacabulary}" << endl; + out << "*sample_name *description *sample_title *seq_methods *organism" << endl; + }else { + out << "#{sample name} {description of sample} {sample title} {description of library_construction_protocol} {http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&keep=1&srchmode=1&unlock} {soil classification from the FAO World Reference Database for Soil Resources}" << endl; + out << "#{text} {text} {text} {text} {controlled vacabulary} {{term}}" << endl; + out << "*sample_name *description *sample_title *seq_methods *organism fao_class" << endl; + } +} + +if ((package == "soil") ) {} + +vector<string> requiredFieldsForPackage; +requiredFieldsForPackage.push_back("sample_name"); +requiredFieldsForPackage.push_back("description"); +requiredFieldsForPackage.push_back("sample_title"); +requiredFieldsForPackage.push_back("seq_methods"); +requiredFieldsForPackage.push_back("organism"); + + +if (packageType == "MIMARKS.survey.soil.4.0") {} |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/biosample.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biosample.tsv Fri May 19 05:26:45 2017 -0400 |
| [ |
| @@ -0,0 +1,10 @@ +#This is a tab-delimited file. Additional Documentation can be found at http://www.mothur.org/wiki/MIMarks_Data_Packages. +#Please fill all the required fields indicated with '*' +#Unknown or inapplicable fields can be assigned 'missing' value. +#You may add extra custom fields to this template. Make sure all the fields are separated by tabs. +#You may remove any fields not required (marked with '*'). Make sure all the fields are separated by tabs. +#You can edit this template using Microsoft Excel or any other editor. But while saving the file please make sure to save them as 'TAB-DELIMITED' TEXT FILE. +#MIMARKS.survey.miscellaneous.4.0 +#{sample name} {description of sample} {sample title} {description of library_construction_protocol} {http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&keep=1&srchmode=1&unlock} {Date of sampling, in "DD-Mmm-YYYY", "Mmm-YYYY" or "YYYY" format (eg., 30-Oct-1990, Oct-1990 or 1990) or ISO 8601 standard "YYYY-mm-dd", "YYYY-mm" or "YYYY-mm-ddThh:mm:ss" (eg., 1990-10-30, 1990-10 or 1990-10-30T14:41:36)} {descriptor of the broad ecological context of a sample. Examples include: desert, taiga, deciduous woodland, or coral reef. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO} {descriptor of the local environment. Examples include: harbor, cliff, or lake. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO} {material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO} {Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps"} {The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W} {alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate} {The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.} {concentration of ammonium} {amount of biomass; should include the name for the part of biomass measured, e.g. microbial, total. can include multiple measurements} {concentration of bromide} {concentration of calcium} {list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v1.72), please see http://bioportal.bioontology.org/visualize/44603} {concentration of chloride} {concentration of chlorophyll} {density of sample} {Depth is defined as the vertical distance below surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectivly. Depth can be reported as an interval for subsurface samples.} {concentration of diether lipids; can include multiple types of diether lipids} {concentration of dissolved carbon dioxide} {concentration of dissolved hydrogen} {dissolved inorganic carbon concentration} {dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2} {concentration of dissolved oxygen} {The elevation of the sampling site as measured by the vertical distance from mean sea level.} {any other measurement performed or parameter collected, that is not listed here} {concentration of nitrate} {concentration of nitrite} {concentration of nitrogen (total)} {concentration of organic carbon} {concentration of organic matter} {concentration of organic nitrogen} {total count of any organism per gram or volume of sample,should include name of organism followed by count; can include multiple organism counts} {oxygenation status of sample} {type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types} {pH measurement} {concentration of phosphate} {concentration of phospholipid fatty acids; can include multiple values} {concentration of potassium} {pressure to which the sample is subject, in atmospheres} {Aerobic or anaerobic} {salinity measurement} {Method or device employed for collecting sample} {Processing applied to the sample during or after isolation} {Amount or size of sample (volume, mass or area) that was collected} {none} {none} {none} {volume (mL) or weight (g) of sample processed for DNA extraction} {concentration of silicate} {sodium concentration} {unique identifier assigned to a material sample used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples.} {concentration of sulfate} {concentration of sulfide} {temperature of the sample at time of sampling} {measurement of magnitude and direction of flow within a fluid} +#{text} {text} {text} {text} {controlled vacabulary} {{timestamp}} {{term}} {{term}} {{term}} {{term}:{term}:{text}} {{float} {float}} {{float} {unit}} {{float} m} {{float} {unit}} {{text};{float} {unit}} {{float} {unit}} {{float} {unit}} {{term}; {timestamp}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} m} {{text};{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{text};{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{text};{float} {unit}} {['', 'aerobic', 'anaerobic']} {{text};{interval}} {{float} {unit}} {{float} {unit}} {{text};{float} {unit}} {{float} {unit}} {{float} {unit}} {['', 'aerobe', 'anaerobe', 'facultative', 'microaerophilic', 'microanaerobe', 'obligate aerobe', 'obligate anaerobe']} {{float} {unit}} {{text}} {{text|term}} {{float} {unit}} {{none}} {{none}} {{none}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{text}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}} +*sample_name *description *sample_title *seq_methods *organism *collection_date *env_biome *env_feature *env_material *geo_loc_name *lat_lon alkalinity altitude ammonium biomass bromide calcium chem_administration chloride chlorophyll density depth diether_lipids diss_carb_dioxide diss_hydrogen diss_inorg_carb diss_org_nitro diss_oxygen elev misc_param nitrate nitrite nitro org_carb org_matter org_nitro organism_count oxy_stat_samp perturbation ph phosphate phosplipid_fatt_acid potassium pressure rel_to_oxygen salinity samp_collect_device samp_mat_process samp_size samp_store_dur samp_store_loc samp_store_temp samp_vol_we_dna_ext silicate sodium source_material_id sulfate sulfide temp water_current |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/biosample.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biosample.xml Fri May 19 05:26:45 2017 -0400 |
| [ |
| @@ -0,0 +1,33 @@ +<BioSampleAttributes> + <Attribute> + <Name>EDTA inhibitor tested</Name> + <HarmonizedName>edta_inhibitor_tested</HarmonizedName> + <Description>Was carbapenemase activity tested in the presence of EDTA? If carbapenemase activity was tested in the presence of EDTA, the response should be "yes", otherwise "no”.</Description> + <Format>['', 'yes', 'no', 'missing', 'not applicable', 'not collected']</Format> + <Synonym>edta inhibitor tested</Synonym> + <Package use="mandatory">Beta-lactamase.1.0</Package> + </Attribute> + <Attribute> + <Name>FAO classification</Name> + <HarmonizedName>fao_class</HarmonizedName> + <Description>soil classification from the FAO World Reference Database for Soil Resources</Description> + <Format>{term}</Format> + <Synonym>fao class</Synonym> + <Synonym>fao classification</Synonym> + <Synonym>soil taxonomic/fao classification</Synonym> + <Package use="optional" group_name="Soil">MIGS.ba.soil.4.0</Package> + <Package use="optional" group_name="Soil">MIGS.eu.soil.4.0</Package> + <Package use="optional" group_name="Soil">MIGS.vi.soil.4.0</Package> + <Package use="optional" group_name="Soil">MIMARKS.specimen.soil.4.0</Package> + <Package use="optional" group_name="Soil">MIMARKS.survey.soil.4.0</Package> + <Package use="optional" group_name="Soil">MIMS.me.soil.4.0</Package> + </Attribute> + <Attribute> + <Name>HIV status</Name> + <HarmonizedName>hiv_stat</HarmonizedName> + <Description>HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO]</Description> + <Format>{boolean};{boolean}</Format> + <Synonym>hiv stat</Synonym> + <Synonym>hiv status</Synonym> + </Attribute> +</BioSampleAttributes> |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/cd-test.constaxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd-test.constaxonomy Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,6 @@ +OTU Size Taxonomy +Otu0001 4 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100); +Otu1000 1 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100); +Otu1676 1 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100); +Otu2360 1 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100); +Otu2439 1 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100); |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/cd-test.count_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd-test.count_table Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,6 @@ +Representative_Sequence total +GQY1XT001C296C 4 +GQY1XT001AUA36 1 +GQY1XT001DLSKT 1 +GQY1XT001B3W8S 1 +GQY1XT001A4UXI 1 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/cd-test.database --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd-test.database Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,6 @@ +OTUNumber Abundance repSeqName repSeq OTUConTaxonomy +Otu0001 4 GQY1XT001C296C A-GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-A-T-A--CCG-G--CG-C-T-C-A-A-CT--GACG-CTC--A-TGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-CC-G-G-C-A-A-CGGT-GAA Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100); +Otu1000 1 GQY1XT001AUA36 G-GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-A-T-A--CCG-G--CT-T-C-C-T-A-CT--GACG-CTC--A-TGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-CC-G-G-C-A-A-CGGT-GAA Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100); +Otu1676 1 GQY1XT001DLSKT ..GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-C-T-A--CCG-G--CG-C-T-C-A-A-CT--GACG-CTC--A-TGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-CC-G-G-C-A-A-CGGT-GAA Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100); +Otu2360 1 GQY1XT001B3W8S A-GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-A-T-A--CCG-G--CG-C-T-C-A-A-CT--GACG-CTC--A-TGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-AC-C-G-C-A-A-GGTT-GAA Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100); +Otu2439 1 GQY1XT001A4UXI C-GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GC-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-A-T-A--CCG-G--CG-C-C-C-G-A-CT--GACG-CTG--A-GGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-CC-G-G-C-A-A-CGGT-GAA Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100); |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/cd-test.list --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd-test.list Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +label numOtus Otu0001 Otu1000 Otu1676 Otu2360 Otu2439 +unique 5 GQY1XT001C296C,GQY1XT001BOB1X,GQY1XT001AT26X,GQY1XT001DWCTO GQY1XT001AUA36 GQY1XT001DLSKT GQY1XT001B3W8S GQY1XT001A4UXI |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/cd-test.repfasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd-test.repfasta Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,10 @@ +>GQY1XT001C296C Otu0001|4 +A-GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-A-T-A--CCG-G--CG-C-T-C-A-A-CT--GACG-CTC--A-TGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-CC-G-G-C-A-A-CGGT-GAA +>GQY1XT001AUA36 Otu1000|1 +G-GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-A-T-A--CCG-G--CT-T-C-C-T-A-CT--GACG-CTC--A-TGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-CC-G-G-C-A-A-CGGT-GAA +>GQY1XT001DLSKT Otu1676|1 +..GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-C-T-A--CCG-G--CG-C-T-C-A-A-CT--GACG-CTC--A-TGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-CC-G-G-C-A-A-CGGT-GAA +>GQY1XT001B3W8S Otu2360|1 +A-GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-A-T-A--CCG-G--CG-C-T-C-A-A-CT--GACG-CTC--A-TGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-AC-C-G-C-A-A-GGTT-GAA +>GQY1XT001A4UXI Otu2439|1 +C-GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GC-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-A-T-A--CCG-G--CG-C-C-C-G-A-CT--GACG-CTG--A-GGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-CC-G-G-C-A-A-CGGT-GAA |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/cd-test.repname --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd-test.repname Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,5 @@ +GQY1XT001C296C GQY1XT001C296C,GQY1XT001BOB1X,GQY1XT001AT26X,GQY1XT001DWCTO +GQY1XT001AUA36 GQY1XT001AUA36 +GQY1XT001DLSKT GQY1XT001DLSKT +GQY1XT001B3W8S GQY1XT001B3W8S +GQY1XT001A4UXI GQY1XT001A4UXI |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/env.dist --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/env.dist Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,25 @@\n+24\n+group18 0 2.07679533239178 6.88145502389971 4.47292990349355 2.50815747366843 3.58036212296744 2.6591292750976 2.29553760953804 4.71171667874897 5.16305059040855 2.21426134242764 3.92961213866286 3.13399015473536 4.90270725079791 5.49476199174931 4.24083600731234 6.11441501785041 6.05615282291975 4.95222984315722 4.21090492925648 2.85939902504818 4.97193013540636 6.55517500441812 2.54101803759533\n+group15 2.07679533239178 0 6.90291144667953 4.64003084174476 3.72544116897342 4.23057909059422 3.32236571813861 2.52327233791657 5.13562550988481 5.1437583829781 2.50862666200143 4.72257599677909 3.43881324942989 4.85150831682718 5.50342943536056 3.52222099128756 5.87491943777315 5.49066317297654 4.27208092800677 3.15270231033824 1.74819033890028 4.12374288054719 6.15931692104792 3.35050234347791\n+group24 6.88145502389971 6.90291144667953 0 5.48014130249836 5.71422767011491 5.44458516207639 6.21128694887343 7.57897769844682 5.72787031540342 5.50347777475312 6.05215034685817 5.13756253132332 6.81750519634229 8.76568212120474 9.04444618731187 8.33992506606364 9.11412838063313 5.67503738892289 6.94693258686523 5.30131540387761 6.85740763239976 5.5325902108287 6.30781548936649 7.84284307315349\n+group27 4.47292990349355 4.64003084174476 5.48014130249836 0 3.48549610587919 3.96397362332123 3.14459815680532 5.59791469171996 2.25198909783448 5.18311849821211 4.54741248463763 3.71058624754798 2.69797588499755 7.8250450422056 7.61406607135237 7.13381545095109 8.44384430044265 6.71088081591996 6.35910146136893 5.18001442223706 5.2381960545819 4.7094220651569 6.46329094926891 5.88708881996361\n+group23 2.50815747366843 3.72544116897342 5.71422767011491 3.48549610587919 0 2.09064557523382 2.35007842477788 3.84437623072582 3.37982049066074 4.82948860655148 2.61344414995761 3.08212085298007 3.39826001248126 6.34083256759322 6.7804402439463 5.9882682085243 7.368182657586 6.29229240618139 5.93365009305124 4.74001147278235 4.16875045563175 5.19193126631916 6.60549692940372 3.75170839493609\n+group19 3.58036212296744 4.23057909059422 5.44458516207639 3.96397362332123 2.09064557523382 0 2.91550590841545 4.53693024483879 4.16796766816088 4.70318440048524 2.79541837375649 3.79457424274492 4.23335312544269 6.52562476479155 7.28216604836819 6.15919058556992 7.48332275942444 6.29601002300864 6.13547796850531 4.6792323698443 4.45343001677936 5.90808732531762 7.12563061433389 4.29741620103145\n+group22 2.6591292750976 3.32236571813861 6.21128694887343 3.14459815680532 2.35007842477788 2.91550590841545 0 3.03537232143609 3.19717141237262 4.78031309163852 2.41753325811849 3.59607995374352 2.12854912039549 5.46704031619679 5.33701156479808 4.96043060818422 6.44826304723108 6.36381765874823 5.33050747387333 4.28625407689455 3.30334570818273 4.94667231796753 6.31277712868333 3.58610710419189\n+group16 2.29553760953804 2.52327233791657 7.57897769844682 5.59791469171996 3.84437623072582 4.53693024483879 3.03537232143609 0 5.42581905199784 5.5382425777602 2.21628461900339 4.91569734557852 3.76898373844346 3.66958270784948 3.7596809535214 3.09087676998529 5.16423793264611 6.19348191138961 4.67007617153741 4.11204634372634 2.12921147954829 5.20716627366845 6.64769970583513 2.40407490833653\n+group28 4.71171667874897 5.13562550988481 5.72787031540342 2.25198909783448 3.37982049066074 4.16796766816088 3.19717141237262 5.42581905199784 0 4.78731905692567 4.50479586376459 3.38670838656427 3.20693742829686 7.42683056394166 7.34570046678601 7.1701579995315 7.98002716787638 6.41561622183692 6.2124182195955 5.39657010741707 5.54110800674231 5.1577675165935 6.8516874226519 6.10574081766257\n+group13 5.16305059040855 5.1437583829781 5.50347777475312 5.18311849821211 4.82948860655148 4.70318440048524 4.78031309163852 5.5382425777602 4.78731905692567 0 4.67746569480341 4.08051856974203 5.63341628143736 6.13993687315028 7.7127998868603 6.72017341542958 6.71492819699427 4.33113554849634 4.44684649984502 4.82408553908334 5.61768442520245 5.26230208160398 6.54992709860'..b' 4.64487610678987\n+group5 5.49476199174931 5.50342943536056 9.04444618731187 7.61406607135237 6.7804402439463 7.28216604836819 5.33701156479808 3.7596809535214 7.34570046678601 7.7127998868603 5.29902826407876 7.18535849292866 5.5528259214464 3.95581421039689 0 4.04435991796256 5.01228422881506 8.11947221764963 5.86295047339197 5.99126094814824 4.58960572590818 6.61131730349409 7.40381675001318 4.84021195384958\n+group6 4.24083600731234 3.52222099128756 8.33992506606364 7.13381545095109 5.9882682085243 6.15919058556992 4.96043060818422 3.09087676998529 7.1701579995315 6.72017341542958 4.05541661524461 6.60015854488732 5.28753056505203 2.89070054815662 4.04435991796256 0 3.64256798987379 6.01870458325898 4.26211882754801 3.82653767294834 2.5630508080946 5.89444500689165 6.82255468001791 4.23311465341886\n+group3 6.11441501785041 5.87491943777315 9.11412838063313 8.44384430044265 7.368182657586 7.48332275942444 6.44826304723108 5.16423793264611 7.98002716787638 6.71492819699427 6.11473384050956 7.50539564845393 6.86459352948227 2.00584491640009 5.01228422881506 3.64256798987379 0 6.60501226761683 3.94055918447939 5.63216883653706 5.30106624617202 6.83112869949915 6.80321310613232 6.05396442753773\n+group4 6.05615282291975 5.49066317297654 5.67503738892289 6.71088081591996 6.29229240618139 6.29601002300864 6.36381765874823 6.19348191138961 6.41561622183692 4.33113554849634 5.23487714375643 4.98323825896227 6.60873730627615 6.4169416509523 8.11947221764963 6.01870458325898 6.60501226761683 0 4.58594627180039 3.55328319122345 5.54504004833869 5.61499654775589 6.828621895957 7.2430575511398\n+group2 4.95222984315722 4.27208092800677 6.94693258686523 6.35910146136893 5.93365009305124 6.13547796850531 5.33050747387333 4.67007617153741 6.2124182195955 4.44684649984502 4.87089053925741 5.96071394777962 5.6314567316324 3.98054063154574 5.86295047339197 4.26211882754801 3.94055918447939 4.58594627180039 0 3.90515299381786 4.28027849695426 4.38635292373633 5.39036567068314 6.01887662312089\n+group9 4.21090492925648 3.15270231033824 5.30131540387761 5.18001442223706 4.74001147278235 4.6792323698443 4.28625407689455 4.11204634372634 5.39657010741707 4.82408553908334 3.21806378630338 4.63371782472599 4.5625504604801 5.12176871169235 5.99126094814824 3.82653767294834 5.63216883653706 3.55328319122345 3.90515299381786 0 2.65742337348713 3.85104238688071 5.57317463010724 5.08393769559955\n+group12 2.85939902504818 1.74819033890028 6.85740763239976 5.2381960545819 4.16875045563175 4.45343001677936 3.30334570818273 2.12921147954829 5.54110800674231 5.61768442520245 2.37451207574614 5.21021128432828 3.80862359775727 4.25495681827209 4.58960572590818 2.5630508080946 5.30106624617202 5.54504004833869 4.28027849695426 2.65742337348713 0 4.28103353313767 5.86614162833534 3.27887996130286\n+group10 4.97193013540636 4.12374288054719 5.5325902108287 4.7094220651569 5.19193126631916 5.90808732531762 4.94667231796753 5.20716627366845 5.1577675165935 5.26230208160398 5.0909474774308 5.3351470840398 4.74234966729958 6.42605641292207 6.61131730349409 5.89444500689165 6.83112869949915 5.61499654775589 4.38635292373633 3.85104238688071 4.28103353313767 0 3.33721452854301 5.88678552682047\n+group11 6.55517500441812 6.15931692104792 6.30781548936649 6.46329094926891 6.60549692940372 7.12563061433389 6.31277712868333 6.64769970583513 6.8516874226519 6.54992709860496 6.73970215554685 6.70375146848393 6.39367296383052 6.84353264931 7.40381675001318 6.82255468001791 6.80321310613232 6.828621895957 5.39036567068314 5.57317463010724 5.86614162833534 3.33721452854301 0 6.7434003020233\n+group21 2.54101803759533 3.35050234347791 7.84284307315349 5.88708881996361 3.75170839493609 4.29741620103145 3.58610710419189 2.40407490833653 6.10574081766257 6.42845550946653 3.03452592937357 5.02891238126826 4.14114063107224 4.64487610678987 4.84021195384958 4.23311465341886 6.05396442753773 7.2430575511398 6.01887662312089 5.08393769559955 3.27887996130286 5.88678552682047 6.7434003020233 0\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/example.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.biom Fri May 19 05:26:45 2017 -0400 |
| [ |
| @@ -0,0 +1,55 @@ +{ + "id":null, + "format": "Biological Observation Matrix 0.9.1-dev", + "format_url": "http://biom-format.org/documentation/format_versions/biom-1.0.html", + "type": "OTU table", + "generated_by": "QIIME revision 1.4.0-dev", + "date": "2011-12-19T19:00:00", + "rows":[ + {"id":"GG_OTU_1", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}}, + {"id":"GG_OTU_2", "metadata":{"taxonomy":["k__Bacteria", "p__Cyanobacteria", "c__Nostocophycideae", "o__Nostocales", "f__Nostocaceae", "g__Dolichospermum", "s__"]}}, + {"id":"GG_OTU_3", "metadata":{"taxonomy":["k__Archaea", "p__Euryarchaeota", "c__Methanomicrobia", "o__Methanosarcinales", "f__Methanosarcinaceae", "g__Methanosarcina", "s__"]}}, + {"id":"GG_OTU_4", "metadata":{"taxonomy":["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Halanaerobiales", "f__Halanaerobiaceae", "g__Halanaerobium", "s__Halanaerobiumsaccharolyticum"]}}, + {"id":"GG_OTU_5", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}} + ], + "columns":[ + {"id":"Sample1", "metadata":{ + "BarcodeSequence":"CGCTTATCGAGA", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample2", "metadata":{ + "BarcodeSequence":"CATACCAGTAGC", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample3", "metadata":{ + "BarcodeSequence":"CTCTCTACCTGT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample4", "metadata":{ + "BarcodeSequence":"CTCTCGGCCTGT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}}, + {"id":"Sample5", "metadata":{ + "BarcodeSequence":"CTCTCTACCAAT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}}, + {"id":"Sample6", "metadata":{ + "BarcodeSequence":"CTAACTACCAAT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}} + ], + "matrix_type": "dense", + "matrix_element_type": "int", + "shape": [5,6], + "data": [[0,0,1,0,0,0], + [5,1,0,2,3,1], + [0,0,1,4,2,0], + [2,1,1,0,0,1], + [0,1,1,0,0,0]] +} |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/example.constaxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.constaxonomy Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,9 @@ +OTU Size Taxonomy +Otu1 34003 Bacteria(100);Bacteroidetes(100);Bacteroidia(99);Bacteroidales(99);Porphyromonadaceae(90);unclassified(87); +Otu2 11218 Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified; +Otu3 3343 Bacteria(100);Bacteroidetes(100);Bacteroidia"(100);Bacteroidales(100);Bacteroidaceae(100);Bacteroides(100); +Otu4 2223 Bacteria(100);Bacteroidetes(100);Bacteroidia"(100);Bacteroidales(100);Rikenellaceae"(100);Alistipes(100); +Otu5 623 Bacteria(100);Firmicutes(72);unclassified(53);unclassified(53);unclassified(53);unclassified(53); +Otu6 48 Bacteria(100);Actinobacteria(94);Actinobacteria(94);Coriobacteriales(71);Coriobacteriaceae(71);unclassified; +Otu7 4 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified; +Otu8 2 Bacteria(100);TM7(100);TM7_class_incertae_sedis(100);TM7_order_incertae_sedis(100);TM7_family_incertae_sedis(100);TM7_genus_incertae_sedis(100); |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/final.tx.1.cons.taxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/final.tx.1.cons.taxonomy Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,63 @@ +OTU Size Taxonomy +1 29357 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100); +2 2223 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Rikenellaceae"(100);Alistipes(100); +3 3211 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);unclassified(100);unclassified(100); +4 4646 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);unclassified(100);unclassified(100); +5 4462 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100); +6 445 Bacteria(100);"Bacteroidetes"(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100); +7 1194 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Lachnospiraceae"(100);unclassified(100); +8 467 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Oscillibacter(100); +9 417 Bacteria(100);"Firmicutes"(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100); +10 1571 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Barnesiella(100); +11 365 Bacteria(100);"Firmicutes"(100);"Erysipelotrichi"(100);"Erysipelotrichales"(100);Erysipelotrichaceae(100);Turicibacter(100); +12 3851 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);"Lactobacillales"(100);Lactobacillaceae(100);Lactobacillus(100); +13 46 Bacteria(100);"Tenericutes"(100);Mollicutes(100);Anaeroplasmatales(100);Anaeroplasmataceae(100);Anaeroplasma(100); +14 832 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);unclassified(100); +15 74 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);Clostridiaceae(100);unclassified(100); +16 80 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Papillibacter(100); +17 24 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Anaerotruncus(100); +18 26 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Butyricicoccus(100); +19 150 Bacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100); +20 6 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);unclassified(100);unclassified(100);unclassified(100); +21 10 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Lachnospiraceae"(100);Dorea(100); +22 10 Bacteria(100);"Actinobacteria"(100);Actinobacteria(100);Bifidobacteriales(100);Bifidobacteriaceae(100);Bifidobacterium(100); +23 13 Bacteria(100);"Actinobacteria"(100);Actinobacteria(100);Coriobacteriales(100);Coriobacteriaceae(100);unclassified(100); +24 99 Bacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Pseudomonas(100); +25 2 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);"Lactobacillales"(100);"Carnobacteriaceae"(100);Atopostipes(100); +26 17 Bacteria(100);"Actinobacteria"(100);Actinobacteria(100);Coriobacteriales(100);Coriobacteriaceae(100);Enterorhabdus(100); +27 641 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);"Lactobacillales"(100);Streptococcaceae(100);Streptococcus(100); +28 1 Bacteria(100);"Actinobacteria"(100);Actinobacteria(100);Actinomycetales(100);Corynebacteriaceae(100);Corynebacterium(100); +29 2 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);Clostridiaceae(100);Sarcina(100); +30 32 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);Incertae_Sedis_XIV(100);Blautia(100); +31 10 Bacteria(100);"Firmicutes"(100);"Erysipelotrichi"(100);"Erysipelotrichales"(100);Erysipelotrichaceae(100);Coprobacillus(100); +32 2 Bacteria(100);TM7(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100); +33 13 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Ruminococcus(100); +34 14 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Lachnospiraceae"(100);Johnsonella(100); +35 19 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);"Lactobacillales"(100);unclassified(100);unclassified(100); +36 12 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);"Lactobacillales"(100);Lactobacillaceae(100);unclassified(100); +37 52 Bacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Cronobacter(100); +38 10 Bacteria(100);"Firmicutes"(100);"Erysipelotrichi"(100);"Erysipelotrichales"(100);Erysipelotrichaceae(100);Holdemania(100); +39 5 Bacteria(100);"Actinobacteria"(100);Actinobacteria(100);Coriobacteriales(100);Coriobacteriaceae(100);Olsenella(100); +40 3 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Eubacteriaceae"(100);Eubacterium(100); +41 2 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);Incertae_Sedis_XIII(100);unclassified(100); +42 324 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);Clostridiaceae(100);Clostridium(100); +43 7 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);unclassified(100);unclassified(100);unclassified(100); +44 1 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Acetivibrio(100); +45 6 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);Incertae_Sedis_XIII(100);Anaerovorax(100); +46 1912 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);Bacillales(100);"Staphylococcaceae"(100);Staphylococcus(100); +47 469 Bacteria(100);"Deinococcus-Thermus"(100);Deinococci(100);Deinococcales(100);Deinococcaceae(100);Deinococcus(100); +48 448 Bacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);Pseudomonadales(100);Moraxellaceae(100);Acinetobacter(100); +49 286 Bacteria(100);"Actinobacteria"(100);Actinobacteria(100);Actinomycetales(100);Propionibacteriaceae(100);Propionibacterium(100); +50 295 Bacteria(100);"Proteobacteria"(100);Betaproteobacteria(100);Neisseriales(100);Neisseriaceae(100);Neisseria(100); +51 108 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);Bacillales(100);"Listeriaceae"(100);Listeria(100); +52 67 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);"Lactobacillales"(100);"Enterococcaceae"(100);Enterococcus(100); +53 58 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);Bacillales(100);Bacillaceae(100);Bacillus(100); +54 51 Bacteria(100);"Proteobacteria"(100);Epsilonproteobacteria(100);Campylobacterales(100);Helicobacteraceae(100);Helicobacter(100); +55 54 Bacteria(100);"Actinobacteria"(100);Actinobacteria(100);Actinomycetales(100);Actinomycetaceae(100);Actinomyces(100); +56 22 Bacteria(100);"Proteobacteria"(100);Alphaproteobacteria(100);Rhodobacterales(100);Rhodobacteraceae(100);unclassified(100); +57 29 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);Bacillales(100);unclassified(100);unclassified(100); +58 3 Bacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);unclassified(100); +59 1 Bacteria(100);"Actinobacteria"(100);Actinobacteria(100);Actinomycetales(100);unclassified(100);unclassified(100); +60 3 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);Bacillales(100);"Staphylococcaceae"(100);unclassified(100); +61 1 Bacteria(100);"Proteobacteria"(100);Alphaproteobacteria(100);Rhodobacterales(100);Rhodobacteraceae(100);Rhodobacter(100); +62 1 Bacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);unclassified(100); |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/final.tx.1.subsample.1.pick.shared --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/final.tx.1.subsample.1.pick.shared Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,10 @@ +label Group numOtus Otu01 Otu02 Otu03 Otu04 Otu05 Otu06 Otu07 Otu08 Otu09 Otu10 Otu11 Otu12 Otu13 Otu14 Otu15 Otu16 Otu17 Otu18 Otu19 Otu20 Otu21 Otu22 Otu23 Otu24 Otu25 Otu26 Otu27 Otu28 Otu29 Otu30 Otu31 Otu32 Otu33 Otu34 Otu35 Otu36 Otu37 Otu38 Otu39 Otu40 Otu41 Otu42 Otu43 Otu45 +1 F003D000 44 1934 191 396 970 156 59 294 74 61 149 40 68 33 143 56 24 9 5 5 4 2 2 2 1 2 2 2 1 2 3 1 1 1 0 0 0 0 0 0 0 0 0 0 0 +1 F003D002 44 2599 394 68 717 85 48 216 85 189 53 1 83 5 121 0 18 0 2 1 0 0 0 0 0 0 2 2 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +1 F003D006 44 3090 123 87 390 295 14 139 56 27 69 1 313 1 76 0 0 0 1 2 0 2 0 0 0 0 0 1 0 0 2 0 0 0 2 0 2 0 0 0 0 0 0 0 0 +1 F003D008 44 2203 288 64 621 713 22 226 59 22 21 1 318 1 88 0 7 6 4 1 2 3 0 1 0 0 2 1 0 0 2 2 1 2 8 2 1 1 0 0 0 0 0 0 0 +1 F003D142 44 3054 101 381 158 366 32 21 7 6 208 34 258 0 34 2 3 0 0 13 0 0 1 1 0 0 1 0 0 0 1 3 0 0 0 1 1 0 2 2 2 0 0 0 0 +1 F003D144 44 2649 32 503 119 162 44 14 8 10 215 86 786 0 24 3 5 0 1 12 0 0 3 2 0 0 2 0 0 0 5 0 0 1 0 3 1 0 0 1 0 2 0 0 0 +1 F003D146 44 2197 160 444 270 374 38 43 80 10 189 30 691 2 116 1 1 5 4 17 0 0 0 1 0 0 2 0 0 0 4 0 0 5 1 1 3 0 0 0 0 0 3 1 0 +1 F003D148 44 2284 285 460 317 232 33 31 3 25 235 101 574 0 37 5 8 2 2 44 0 0 0 1 0 0 1 1 0 0 2 2 0 2 1 0 0 0 0 1 1 0 0 0 3 +1 F003D150 44 2709 236 391 390 326 60 43 23 9 171 21 178 0 64 1 8 1 3 31 0 1 4 5 0 0 2 0 0 0 2 1 0 2 0 2 0 1 4 0 0 0 2 0 2 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/makesra.project --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/makesra.project Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,12 @@ +USERNAME userName +Last yourLastName +First yourFirstName +EMAIL yourEmail@mail.com +CENTER your University or Center Name +TYPE institute +WEBSITE www.yourWebsite.org +ProjectName yourProjectName +ProjectTitle Your Project Title +Description Your project description +Grant id=yourGrantID, agency=yourGrantAgency, title=yourGrantTitle + |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/metadata --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metadata Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,12 @@ +group dpw description +F003D000 0 "F003D000 description" +F003D002 2 "F003D002 description" +F003D004 4 "F003D004 description" +F003D006 6 "F003D006 description" +F003D008 8 "F003D008 galaxy rocks" +F003D142 142 "F003D142 description" +F003D144 144 "F003D144 description" +F003D146 146 "F003D146 description" +F003D148 148 "F003D148 description" +F003D150 150 "F003D150 description" +MOCK.GQY1XT001 12 "MOCK.GQY1XT001 description" |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/mock.flow --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mock.flow Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,108 @@\n+450\n+GQY1XT001ASWK1 450 0.99 0.00 1.01 0.00 0.00 1.06 0.00 1.00 1.07 0.02 0.00 2.06 1.04 0.02 0.00 1.04 0.00 2.18 2.93 0.98 0.98 0.01 0.97 0.00 0.01 2.08 0.00 0.00 1.91 0.02 1.98 0.00 2.88 0.00 0.01 1.00 0.08 1.03 0.00 1.01 2.86 0.01 0.98 0.02 0.08 1.10 1.98 1.05 1.94 0.01 0.05 1.01 0.05 0.00 2.04 1.97 0.01 0.00 1.01 1.00 1.02 1.09 1.01 0.02 0.95 0.00 3.73 0.03 0.04 1.05 0.08 1.98 1.01 0.05 0.00 1.97 0.04 1.88 0.00 0.08 1.02 0.05 0.01 1.02 0.07 0.02 1.01 0.06 2.05 2.20 0.97 1.03 0.14 0.08 1.02 0.07 2.91 0.00 0.97 1.02 0.03 0.00 0.97 0.07 1.00 0.00 0.04 1.02 0.98 0.00 0.02 1.05 0.05 0.01 2.02 0.07 0.02 1.12 3.02 0.05 0.01 1.08 0.04 4.00 1.11 0.11 1.10 0.00 0.10 2.12 0.00 0.12 1.07 0.06 5.69 2.01 0.05 0.86 1.16 0.19 0.00 1.04 0.07 0.96 0.03 0.15 0.87 0.10 1.04 0.90 0.13 0.98 0.09 0.15 1.01 0.13 0.06 1.02 0.12 0.01 2.09 0.10 1.03 0.02 0.13 1.04 0.11 0.05 0.96 0.11 1.03 1.04 3.02 1.04 1.09 0.11 1.18 0.15 0.12 0.97 1.01 0.01 0.08 1.03 0.08 0.08 1.06 2.07 0.07 0.97 1.05 0.12 1.05 1.07 1.98 0.02 0.12 0.99 0.08 3.00 0.94 1.01 0.08 0.13 0.95 0.15 1.03 0.06 0.99 1.93 0.03 0.05 1.02 0.13 2.00 0.08 0.97 0.05 0.08 1.04 2.88 0.11 0.06 1.05 0.14 1.04 0.05 0.11 1.00 0.06 3.80 1.06 0.12 0.08 1.14 0.07 0.04 1.00 0.96 0.08 2.96 0.04 0.99 1.00 1.03 0.03 0.02 1.03 0.06 0.03 1.93 0.04 1.05 0.06 1.05 0.10 0.11 0.91 0.09 1.07 0.11 0.07 1.01 1.02 1.09 0.07 1.04 0.06 0.10 1.02 0.05 1.00 1.00 0.90 0.10 3.04 0.07 0.02 1.07 0.94 0.12 0.08 2.06 2.03 1.02 1.03 0.06 0.06 1.01 0.02 0.08 1.02 0.09 0.01 1.07 0.13 1.03 0.03 0.03 1.13 0.02 0.03 2.06 0.08 2.06 0.07 0.95 1.06 0.04 0.03 0.91 0.13 0.13 2.18 0.10 0.00 0.96 0.00 0.99 4.03 1.92 0.06 1.03 0.12 1.02 0.02 0.10 0.97 0.11 0.02 1.01 0.96 1.01 0.09 0.05 1.04 0.06 1.02 0.05 0.06 0.97 0.98 0.10 0.07 1.01 0.10 1.08 0.06 0.93 1.01 0.07 0.11 1.09 0.05 0.11 1.34 0.10 0.10 1.07 0.03 0.00 1.10 0.02 0.08 3.11 0.09 1.06 0.09 0.04 1.05 1.95 1.05 0.13 0.12 0.89 0.06 1.04 0.97 1.03 0.10 0.02 0.81 1.88 0.10 0.09 1.03 0.93 1.13 0.10 0.11 1.11 0.04 0.09 0.97 0.00 0.11 2.02 0.10 2.01 0.86 0.15 0.14 1.15 0.10 0.09 0.94 0.09 0.07 0.81 1.14 1.16 0.06 1.95 0.10 0.99 0.10 1.10 0.11 1.13 1.15 0.12 0.12 2.77 0.10 0.05 1.09 0.96 0.02 0.96 0.14 1.22 1.01 0.13 0.83 0.05 0.83 0.10 0.09 2.94 2.18 0.19 0.14 1.13 0.12 0.01 1.01 0.12 1.16 3.10 0.00 \n+GQY1XT001EJF0G 450 1.02 0.00 1.06 0.00 0.00 0.97 0.00 0.99 1.07 0.00 0.00 2.11 1.00 0.00 0.02 1.02 0.00 2.13 3.07 1.01 0.94 0.00 1.02 0.00 0.01 2.13 0.00 0.00 2.01 0.08 1.97 0.00 2.98 2.06 0.02 0.91 3.01 0.15 0.95 0.04 0.23 1.00 0.05 0.00 1.87 0.08 1.04 0.01 2.15 0.00 0.02 0.94 0.10 0.00 1.08 1.10 0.00 2.02 1.08 1.04 1.07 1.18 1.08 0.03 1.03 0.04 3.99 0.01 0.05 0.91 0.22 1.82 0.90 0.14 0.00 2.17 0.13 1.06 0.00 0.21 0.92 0.15 0.83 0.03 0.15 0.97 1.09 0.00 2.04 1.29 0.13 0.02 2.15 0.13 0.01 0.89 0.39 0.00 0.97 1.08 2.76 0.00 0.12 1.04 0.46 0.00 0.87 0.15 0.98 0.00 0.12 1.03 0.11 0.00 0.95 2.00 0.01 0.06 1.24 0.21 0.00 1.01 1.96 1.10 0.06 1.04 0.33 0.12 0.92 0.15 0.05 2.81 1.12 0.09 2.07 0.39 0.11 1.06 0.24 0.01 0.98 1.09 2.69 0.01 0.10 1.05 3.08 0.03 0.02 1.08 1.26 0.03 0.01 1.04 2.09 0.01 0.96 1.08 0.19 0.85 1.05 0.13 0.03 1.04 0.12 0.83 0.04 0.08 1.04 0.15 1.03 0.05 0.16 1.01 0.12 0.04 0.99 0.10 0.83 1.08 2.81 1.03 1.12 0.10 1.30 0.11 0.12 1.00 0.10 0.05 0.91 1.11 1.01 0.10 0.11 1.90 0.10 0.84 0.89 0.29 0.93 1.10 1.86 0.11 0.12 1.00 0.20 2.70 0.98 1.08 0.08 0.25 1.13 0.09 1.05 0.08 1.01 1.83 0.03 0.04 1.08 0.17 2.12 0.06 1.03 0.11 0.17 1.02 2.00 0.10 0.93 1.00 0.24 1.00 0.11 0.11 0.95 0.99 2.75 0.11 0.15 0.98 1.21 1.00 0.12 0.05 0.97 0.08 2.93 0.05 1.00 0.91 1.18 0.03 0.10 1.04 0.12 0.04 1.89 0.07 0.91 0.07 1.12 0.11 0.13 0.99 0.07 0.94 0.10 0.10 0.91 1.02 1.11 0.09 1.07 0.20 0.08 0.92 0.08 1.01 0.92 0.93 0.11 3.00 0.17 0.07 0.89 1.10 0.11 0.08 1.95 1.93 1.01 1.01 0.10 0.09 1.04 0.05 0.08 0.96 0.09 0.02 1.08 0.10 1.08 0.00 0.07 0.99 0.04 0.04 1.84 0.07 2.05 0.05 1.05 1.11 0.12 0.12 0.90 0.08 0.08 2.08 0.09 0.05 1.11 0.06 1.01 2.06 0.08 0.76 0.07 1.06 1.93 0.05 0.95 0.12 1.09 '..b'5 1.10 0.03 0.02 1.06 0.04 0.97 0.00 0.09 1.04 0.96 0.03 1.02 0.05 0.99 0.01 0.09 0.97 0.09 1.16 0.03 1.02 0.04 0.01 1.01 0.05 1.05 0.03 1.00 0.05 1.02 0.00 0.11 0.93 1.00 0.03 1.12 0.02 1.07 1.00 0.09 1.05 3.10 1.04 0.04 1.91 0.96 0.04 0.08 2.00 0.06 0.05 2.03 1.02 0.04 1.01 1.03 0.98 0.10 0.10 2.01 0.09 1.05 0.05 0.06 1.05 0.10 0.08 1.07 0.06 1.03 1.06 2.93 1.12 1.01 0.05 0.90 0.10 0.10 0.96 0.13 0.00 1.02 1.04 0.98 0.07 0.07 2.02 0.12 0.89 1.13 0.01 0.95 1.03 1.93 0.09 0.08 0.96 0.02 2.97 1.00 1.08 0.09 0.00 1.02 0.11 1.08 0.03 0.94 1.97 0.03 0.03 0.98 0.01 2.09 0.08 1.09 0.08 0.11 1.03 2.01 0.07 1.07 0.96 0.12 0.98 0.10 0.07 1.08 1.11 3.09 0.09 0.04 0.94 1.02 1.07 0.16 0.08 1.07 0.05 2.94 0.05 0.90 1.02 0.85 0.01 0.11 1.02 0.10 0.04 0.96 0.00 2.16 0.06 1.03 0.08 0.04 1.00 0.09 1.03 0.07 0.03 1.09 1.06 1.19 0.06 1.03 0.06 0.11 0.96 0.06 0.99 2.08 0.08 0.12 2.96 0.01 0.05 0.99 0.76 0.08 0.05 2.03 2.02 1.01 0.97 0.02 0.03 1.02 0.00 0.04 1.09 0.05 0.02 1.11 0.10 1.07 0.03 0.00 1.07 0.02 0.00 2.07 0.10 2.08 0.03 0.83 1.07 0.06 0.01 1.06 0.08 0.04 1.97 0.04 0.02 1.15 0.01 1.07 2.00 0.01 0.91 0.07 0.81 2.06 0.00 1.10 0.10 0.88 0.03 0.10 1.09 0.07 0.04 1.07 0.93 1.13 0.09 0.02 1.02 0.10 1.03 0.11 0.02 1.07 0.96 0.06 0.07 1.05 0.06 0.97 0.14 0.84 1.05 0.06 0.03 0.90 0.02 0.04 1.11 0.11 0.03 1.07 0.00 0.11 1.04 0.11 0.07 3.16 0.04 0.99 0.06 0.01 1.05 2.02 1.17 0.08 0.06 0.82 0.00 1.28 1.16 1.05 0.08 0.05 0.74 2.10 0.11 0.13 1.08 0.76 0.98 0.12 0.10 1.14 0.06 0.10 1.06 0.10 0.05 1.99 0.07 2.06 1.04 0.11 0.00 1.02 0.02 0.11 1.04 0.11 0.06 0.99 0.99 1.13 0.13 1.95 0.11 1.06 0.01 1.01 0.13 0.86 0.91 0.19 0.00 2.96 0.06 0.07 1.00 1.01 0.07 1.15 0.00 1.16 0.09 0.06 2.03 0.11 1.02 0.16 0.78 1.10 0.02 0.09 1.87 \n+GQY1XT001AWPWA 450 1.01 0.00 1.03 0.00 0.00 1.01 0.00 1.02 1.03 0.06 0.00 2.13 1.04 0.00 0.00 1.06 0.04 2.10 3.04 1.04 1.01 0.00 1.00 0.00 0.00 2.21 0.00 0.00 2.07 0.00 1.97 0.00 2.78 2.24 0.00 0.89 2.91 0.04 0.98 0.00 0.02 1.10 1.91 1.08 2.11 0.00 0.05 0.93 0.03 0.07 2.05 1.95 0.13 0.00 0.97 0.99 1.05 1.11 0.96 0.05 1.00 0.03 3.80 0.01 0.06 1.03 0.11 2.03 1.06 0.03 0.13 1.92 0.03 1.00 0.10 0.98 0.00 0.00 1.04 1.11 0.03 0.00 0.96 0.11 2.03 2.12 0.94 1.06 0.13 0.06 1.05 0.00 3.15 0.12 0.86 0.89 0.10 0.00 0.93 0.07 0.95 0.00 0.04 1.13 1.13 0.04 0.00 2.00 0.06 0.00 1.06 0.11 0.07 1.00 2.89 0.10 0.00 1.01 0.05 4.05 0.01 0.06 1.95 0.05 0.04 1.15 0.08 0.03 1.95 0.11 5.45 1.82 0.13 1.04 1.06 0.43 0.06 1.01 1.97 0.05 0.91 1.19 0.30 0.88 0.12 0.14 1.02 1.02 0.03 0.00 1.06 0.08 1.01 0.03 1.11 0.00 0.13 1.02 0.12 0.00 1.02 0.13 0.99 1.02 2.89 1.06 1.96 1.05 0.30 0.09 1.15 1.06 0.98 0.06 0.10 1.98 0.16 0.94 0.89 0.17 0.99 1.10 1.90 0.03 0.12 1.02 0.19 2.83 0.92 1.07 0.06 0.24 1.06 0.07 1.05 0.05 1.04 1.90 0.09 0.08 0.97 0.15 1.93 0.05 1.02 0.04 0.18 1.07 1.99 0.13 0.91 1.00 0.13 0.95 0.18 0.06 1.03 0.11 3.39 0.10 0.14 0.85 1.28 1.01 0.02 0.05 0.95 0.07 2.97 0.02 1.07 0.93 1.18 0.00 0.11 1.09 0.10 0.00 1.10 0.03 2.02 0.05 1.01 0.08 0.17 0.86 0.08 0.90 0.13 0.06 1.01 1.09 1.03 0.08 1.03 0.10 0.09 0.93 0.09 0.91 0.95 1.00 0.09 1.90 0.08 1.89 0.11 1.06 0.08 0.05 1.90 1.88 0.05 0.12 1.01 0.11 0.18 0.99 0.10 0.07 0.90 0.01 0.10 1.08 0.09 0.04 1.14 0.07 0.96 0.07 0.00 1.01 0.08 0.07 1.76 0.03 1.89 0.04 0.96 1.06 0.11 0.11 1.08 0.10 0.10 1.93 0.09 0.04 1.02 0.03 1.00 3.69 1.80 0.06 0.98 0.11 1.02 0.05 0.07 0.98 0.10 0.00 0.93 1.12 1.11 0.03 0.11 0.96 0.07 0.93 0.10 0.00 1.08 0.97 0.06 0.04 1.02 0.05 0.92 0.03 1.04 1.08 0.09 0.06 1.06 0.01 0.02 0.99 0.16 0.10 1.09 0.07 0.13 1.08 0.09 0.09 2.85 0.10 1.01 0.05 0.13 0.97 1.89 0.98 0.15 0.06 0.99 0.01 1.04 1.13 1.12 0.02 0.05 0.87 1.79 0.06 0.09 1.10 1.00 1.04 0.18 0.10 0.95 0.06 0.09 1.04 0.06 0.08 2.31 0.03 2.00 1.21 0.04 0.09 0.92 0.00 0.12 0.93 0.10 0.00 0.99 1.13 1.05 0.03 2.09 0.01 1.09 0.02 0.84 0.08 1.06 0.03 2.04 0.09 1.87 0.01 0.17 1.01 1.13 0.03 1.02 0.00 0.94 0.09 0.07 2.12 0.06 1.06 0.08 0.90 0.10 0.09 1.12 0.11 1.07 1.01 0.18 0.08 1.97 0.00 0.27 1.04 0.03 1.08 3.12 0.15 1.06 0.00 0.10 1.85 \n' |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/mouse.design --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mouse.design Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,10 @@ +group dpw +F003D000 0 +F003D142 142 +F003D144 144 +F003D146 146 +F003D148 148 +F003D150 150 +F003D002 2 +F003D006 6 +F003D008 8 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/output.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.fa Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,12 @@ +> seq1 This is the description of my first sequence in sample 1. +AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCACGACGTAGATGCTAGCTGACTCGATGC +> seq2 This is a description of my second sequence in sample 1. +CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGCATCGTCAGTTACTGCATGCTCG +> seq1 This is the description of my first and only sequence in sample 2. +AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCACGACGTAGATGCTAGCTGACTCGATGC +> seq1 This is the description of my first sequence in sample 3. +AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCACGACGTAGATGCTAGCTGACTCGATGC +> seq2 This is a description of my second sequence in sample 3. +CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGCATCGTCAGTTACTGCATGCTCG +> seq3 This is a description of my third sequence in sample 3. +CGATCGATCGTACGTCGACTAGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCACGACGTAGATGCTAGCTGACTCGATGCGATCGTAGCTACGTCGTACGTAGCATCGTCAGTTACTGCATGCTCG |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/sample1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1.fa Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +> seq1 This is the description of my first sequence in sample 1. +AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCACGACGTAGATGCTAGCTGACTCGATGC +> seq2 This is a description of my second sequence in sample 1. +CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGCATCGTCAGTTACTGCATGCTCG |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/sample2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample2.fa Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +> seq1 This is the description of my first and only sequence in sample 2. +AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCACGACGTAGATGCTAGCTGACTCGATGC |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/sample3.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample3.fa Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,6 @@ +> seq1 This is the description of my first sequence in sample 3. +AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCACGACGTAGATGCTAGCTGACTCGATGC +> seq2 This is a description of my second sequence in sample 3. +CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGCATCGTCAGTTACTGCATGCTCG +> seq3 This is a description of my third sequence in sample 3. +CGATCGATCGTACGTCGACTAGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCACGACGTAGATGCTAGCTGACTCGATGCGATCGTAGCTACGTCGTACGTAGCATCGTCAGTTACTGCATGCTCG |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/silva.ss.map.head --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/silva.ss.map.head Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,10 @@ +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/testflow.flow --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testflow.flow Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +450 +GQY1XT001A8C6I 450 1.04 0.00 1.01 0.00 0.00 1.00 0.00 1.01 0.00 2.35 2.09 0.98 1.01 0.03 0.01 0.99 0.99 0.09 3.04 1.01 1.00 0.00 1.01 0.00 0.00 1.12 0.00 0.00 2.01 0.00 2.06 0.00 3.02 0.00 0.00 1.02 0.06 1.01 0.00 1.00 3.88 2.05 0.00 0.00 0.94 0.04 0.97 0.00 2.08 0.00 0.00 0.98 0.09 0.00 0.99 1.05 0.00 1.03 2.03 1.02 1.01 1.17 1.08 0.04 1.03 0.01 3.84 0.03 0.03 1.00 0.10 1.89 0.02 0.00 1.03 2.01 1.04 0.00 0.97 0.11 0.08 1.94 0.04 0.00 2.93 0.03 0.99 0.00 0.10 1.02 0.94 0.94 0.09 0.08 1.02 0.92 2.06 1.06 0.00 1.02 0.09 0.05 1.00 0.08 1.12 1.08 1.00 1.03 0.05 0.05 1.02 0.04 1.01 1.05 1.92 0.06 0.03 2.01 0.11 1.09 0.00 0.10 1.04 0.04 0.02 2.05 0.08 0.05 1.02 0.13 1.02 0.10 0.11 0.93 0.06 2.04 1.96 0.02 0.03 1.00 0.11 0.09 2.91 0.09 0.04 2.03 1.06 0.04 0.00 1.04 0.10 1.04 0.02 0.13 1.07 0.06 0.91 2.05 0.07 0.05 2.07 0.07 0.05 1.12 0.05 0.84 1.01 0.09 0.08 1.03 0.07 0.07 1.01 0.08 1.09 1.02 3.03 1.11 0.07 2.74 0.12 0.11 1.03 0.99 1.14 0.08 0.07 2.10 0.05 0.97 1.02 0.06 1.10 1.03 1.93 0.06 0.05 0.88 0.03 2.95 0.99 1.05 0.11 0.01 0.94 0.08 1.04 0.13 0.94 2.07 0.07 0.03 1.02 0.00 2.10 0.07 0.97 0.14 0.00 1.02 2.97 0.02 0.08 1.03 0.11 0.06 0.96 0.05 1.20 0.97 2.80 0.10 0.03 1.02 0.97 1.03 0.03 0.10 1.07 0.00 2.96 0.04 1.01 2.97 0.05 0.03 1.04 0.02 0.08 1.01 0.05 0.05 1.04 0.00 0.10 1.03 0.07 1.93 1.03 1.03 1.08 0.03 1.02 0.09 0.09 1.10 0.04 0.97 0.99 0.11 0.06 0.91 1.81 0.09 0.00 1.05 1.03 0.09 2.99 0.00 0.02 0.86 0.00 1.96 0.10 0.90 0.09 1.76 0.09 0.03 1.06 0.11 1.11 0.10 0.00 1.12 0.00 0.02 1.99 0.04 1.96 0.03 0.90 1.07 0.07 0.05 2.03 0.06 0.03 1.08 0.02 0.00 1.06 0.09 1.12 2.02 0.82 0.99 0.00 0.04 1.94 0.02 1.88 0.09 0.95 0.05 1.93 0.06 0.06 1.05 1.00 0.05 0.04 0.99 0.00 0.01 1.02 0.04 0.94 0.04 0.97 0.10 1.04 0.09 1.08 1.18 0.99 1.10 0.04 0.06 1.10 0.00 0.00 1.05 0.06 0.07 3.03 0.09 0.99 0.06 0.00 1.02 1.09 0.07 1.11 0.00 0.09 0.81 0.05 0.03 1.07 0.00 1.02 1.05 0.95 0.01 0.03 0.87 1.01 1.15 1.04 0.00 0.01 1.72 0.02 2.14 0.10 0.00 2.20 0.04 1.08 0.05 0.95 1.06 1.92 0.05 0.93 0.01 2.63 0.07 0.97 0.09 1.25 0.10 1.08 0.08 0.09 1.03 0.12 0.84 1.02 0.06 0.13 0.90 1.09 0.08 0.08 1.02 1.13 0.05 0.93 0.06 1.01 0.97 0.02 1.02 0.10 1.00 1.09 0.04 0.90 0.08 0.13 1.03 2.99 0.03 0.02 1.01 0.05 1.05 2.35 0.05 1.24 0.03 0.10 1.01 0.10 1.06 0.11 1.78 +GQY1XT001BPRBN 450 1.04 0.00 1.03 0.00 0.00 0.98 0.00 1.00 0.00 2.33 1.06 1.02 1.10 0.00 0.00 1.01 1.11 0.00 2.92 1.03 1.02 0.00 0.93 0.00 0.02 2.05 0.01 0.00 1.94 0.01 1.99 0.00 2.90 0.00 0.00 0.93 0.13 0.88 0.00 0.98 3.72 1.08 0.00 1.04 0.16 0.00 1.94 0.00 1.99 0.01 0.06 0.95 0.13 0.00 0.97 2.04 0.04 0.00 2.06 1.11 1.09 1.04 1.03 0.03 1.02 0.05 4.03 0.01 0.06 1.02 0.13 1.93 0.02 0.05 1.08 4.05 1.09 0.91 1.03 0.11 1.98 3.07 0.01 1.00 0.14 0.11 0.85 1.03 1.96 0.99 0.03 0.90 0.13 0.15 0.95 0.11 1.00 1.17 0.97 2.07 0.07 0.06 1.03 0.09 0.00 1.09 1.00 2.02 0.06 1.97 2.98 1.06 1.03 0.11 0.10 2.03 0.07 1.90 0.00 0.08 1.02 0.10 0.05 2.00 0.04 0.96 3.83 0.12 0.02 0.94 1.15 0.00 0.04 1.05 1.97 0.04 1.03 1.03 0.06 1.06 1.01 1.08 3.05 0.07 0.11 1.09 2.02 1.05 2.95 1.00 1.11 0.10 0.07 0.91 0.13 1.02 0.04 0.06 1.03 1.00 0.90 0.02 0.12 2.05 0.11 0.94 0.99 0.03 0.94 1.12 2.00 0.11 0.07 1.03 0.05 3.10 1.05 1.12 0.07 0.00 1.02 0.10 1.01 0.07 1.00 2.05 0.12 1.01 0.11 0.12 2.01 0.07 0.94 0.00 0.07 0.98 1.98 0.00 1.03 1.01 0.05 0.00 0.93 0.09 1.01 0.04 3.95 0.10 0.10 0.97 1.05 1.05 0.03 0.12 1.00 0.12 3.00 0.05 1.11 1.03 0.10 0.00 1.05 0.09 1.07 0.00 2.08 0.03 1.02 0.06 0.96 0.06 0.14 1.00 0.15 0.98 0.08 0.09 0.98 1.10 1.00 0.07 1.06 0.12 0.14 0.92 0.08 2.12 0.06 3.08 0.02 2.12 0.04 0.11 3.18 0.12 0.02 1.04 0.04 1.06 0.04 0.96 0.05 1.04 0.03 2.17 2.05 0.96 0.13 0.01 1.99 0.08 2.15 0.09 0.92 1.02 0.02 0.11 2.03 0.06 0.12 1.04 1.07 0.03 1.00 0.13 0.11 2.08 0.99 0.05 0.07 0.95 1.92 0.04 2.01 0.07 0.98 0.03 1.98 0.12 1.01 0.09 0.04 1.11 0.14 0.93 0.14 0.12 1.08 1.02 0.07 0.08 0.97 0.11 1.04 0.09 0.99 0.10 0.09 1.08 0.05 0.02 1.01 0.97 0.07 0.11 1.06 0.01 0.10 1.04 0.05 0.03 2.00 0.05 2.01 0.07 0.01 1.00 2.01 1.01 0.07 0.12 1.03 0.04 1.00 0.07 2.01 0.08 0.08 1.06 2.12 0.00 0.13 0.95 0.12 2.38 0.12 1.96 0.08 0.00 1.85 0.10 2.13 0.06 0.00 1.19 0.06 0.02 2.03 0.07 0.96 0.02 0.88 0.06 3.89 0.07 0.97 1.06 1.89 0.06 1.95 0.02 1.82 0.02 1.13 0.03 1.10 0.09 0.06 2.14 0.18 1.06 1.06 0.00 1.03 0.04 0.06 2.11 2.90 0.79 0.92 1.12 0.12 0.04 0.93 0.02 1.21 0.95 0.05 2.94 0.07 0.84 0.10 0.14 1.05 0.13 0.11 1.15 1.05 1.05 0.14 0.11 1.02 0.11 0.93 0.10 1.09 0.04 0.00 0.99 0.16 2.99 2.08 2.06 0.15 1.02 0.07 0.06 4.11 0.03 0.16 2.23 0.14 1.06 0.00 0.95 0.17 0.10 2.04 1.00 |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/toymothur.design --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/toymothur.design Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +forest tardis +pasture tardis +pasture dalek |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/toymothur.design2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/toymothur.design2 Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +forest tardis +pasture dalek |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/treetest.deunique.tre --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/treetest.deunique.tre Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +(((a:0,b:0,c:0):0.5,(d:0,e:0):0.3):0.25,f:0.25):0.5; |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/treetest.groups --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/treetest.groups Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,6 @@ +a green +b green +c green +d orange +e orange +f orange |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/treetest.names --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/treetest.names Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +a a,b,c +d d,e +f f |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/treetest.tre --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/treetest.tre Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +((a:0.5,d:0.3):0.25,f:0.25):0.5; \ No newline at end of file |
| b |
| diff -r 000000000000 -r 870f2a438139 test-data/veg.dist --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/veg.dist Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,25 @@\n+24\n+group18 0 0.531002122667858 0.668066081456845 0.562124668311531 0.3747077813648 0.509473807708101 0.623441897868918 0.533760972316003 0.841820910455228 0.345334659061175 0.544980977465613 0.387906855391038 0.631889119284077 0.360369716481462 0.495569929879871 0.338230884557721 0.527747996119875 0.46940182727116 0.572409158546537 0.658356940509915 0.468803827751196 0.624899560429172 0.445852306473965 0.556086425651643\n+group15 0.531002122667858 0 0.359778297016791 0.405560971081094 0.365209673840692 0.456075749605471 0.357951698566990 0.397667376920489 0.522541392379812 0.60638464347191 0.48037557590249 0.378418761774833 0.337611485751577 0.671739130434783 0.717861205915813 0.635512156237545 0.757850272278487 0.684397366160893 0.820626944245034 0.776103945014594 0.679419902681042 0.764456383429945 0.471627356163032 0.760728080850839\n+group24 0.668066081456845 0.359778297016791 0 0.493494677463379 0.502030649266258 0.509231821290175 0.50100504976222 0.590762326930444 0.573666487726319 0.757674655787863 0.653360627772091 0.434689236988378 0.336909757263505 0.793106938610254 0.856175256640914 0.744137292184681 0.83821186778176 0.830987488829312 0.83725508577857 0.759051704257184 0.689453763842811 0.78428294394681 0.567737261531031 0.727272727272727\n+group27 0.562124668311531 0.405560971081094 0.493494677463379 0 0.428611098255195 0.487819025522041 0.465522369035986 0.568393032270116 0.302780246286657 0.754373626373627 0.746791469651645 0.495783259540375 0.500159329903947 0.77929167212542 0.873218985388874 0.749693459050357 0.80902359221629 0.841379965785972 0.758192367410313 0.741589782845171 0.625361639704983 0.70965400435519 0.632291885091214 0.54560014236142\n+group23 0.3747077813648 0.365209673840692 0.502030649266258 0.428611098255195 0 0.360624235718861 0.481270602337428 0.409431221365516 0.697951879101213 0.622147127631921 0.564580791354366 0.287701365077311 0.425861695209191 0.639083780437474 0.729525454839929 0.625248311481923 0.712879825495866 0.711791887728906 0.724986879144997 0.669388904533934 0.538476172358033 0.662547573180473 0.471028037383178 0.495122079839688\n+group19 0.509473807708101 0.456075749605471 0.509231821290175 0.487819025522041 0.360624235718861 0 0.47264827514003 0.449673125625773 0.643173412512372 0.573924437650142 0.63319420574515 0.395377631035906 0.431129869389152 0.695857026807473 0.789820495341968 0.568402976531196 0.530275619878684 0.517760385310054 0.538922155688623 0.539314268896846 0.428855622420053 0.505990964447063 0.329349338004224 0.531589448015961\n+group22 0.623441897868918 0.357951698566990 0.50100504976222 0.465522369035986 0.481270602337428 0.47264827514003 0 0.267803106717773 0.598566633402885 0.69487361209544 0.535760932030719 0.462702018749640 0.382298106172113 0.745988552125364 0.861145064293746 0.724916160609081 0.802615164256341 0.801531425047536 0.83214644589104 0.772508176966776 0.70517511761631 0.787532847973119 0.581221922731357 0.677116737663332\n+group16 0.533760972316003 0.397667376920489 0.590762326930444 0.568393032270116 0.409431221365516 0.449673125625773 0.267803106717773 0 0.701535990362414 0.551494144215115 0.482635012046777 0.373779728755815 0.430605761857816 0.659614382490881 0.718478913197665 0.650987864807943 0.683795276397356 0.646264782232478 0.735420178184445 0.818586585827965 0.634216589861751 0.765659822656361 0.517282479141836 0.747455911343173\n+group28 0.841820910455228 0.522541392379812 0.573666487726319 0.302780246286657 0.697951879101213 0.643173412512372 0.598566633402885 0.701535990362414 0 0.860012230114305 0.82396672731999 0.696356043704593 0.608614963860129 0.896020179372198 0.953959215457244 0.9014440433213 0.9234484979528 0.938116913005677 0.905321324457207 0.868666952421774 0.854316702819956 0.901660445359763 0.754406370224568 0.724877304998332\n+group13 0.345334659061175 0.60638464347191 0.757674655787863 0.754373626373627 0.622147127631921 0.573924437650142 0.69487361209544 0.551494144215115 0.860012230114305 0 0.5547564'..b'9 0.86008579145263 0.323744637900580 0 0.398453833811446 0.563443208895949 0.537750556792873 0.725759700794764 0.901458342917606 0.780864053688773 0.850419084461638 0.556379750493714 0.888831597401258\n+group6 0.338230884557721 0.635512156237545 0.744137292184681 0.749693459050357 0.625248311481923 0.568402976531196 0.724916160609081 0.650987864807943 0.9014440433213 0.351567272898162 0.622747338353674 0.543911776469916 0.734387197501951 0.175471345902557 0.398453833811446 0 0.451762651100795 0.466509988249118 0.555275398861018 0.722312633832977 0.576246207195492 0.656792557980023 0.407794761777063 0.672014090541248\n+group3 0.527747996119875 0.757850272278487 0.83821186778176 0.80902359221629 0.712879825495866 0.530275619878684 0.802615164256341 0.683795276397356 0.9234484979528 0.496547756041427 0.783666100254885 0.669047897880314 0.816868430229662 0.515448702689836 0.563443208895949 0.451762651100795 0 0.359268929503916 0.209920283436670 0.388581148863785 0.264185101779485 0.341337757596926 0.300259669263359 0.750777302759425\n+group4 0.46940182727116 0.684397366160893 0.830987488829312 0.841379965785972 0.711791887728906 0.517760385310054 0.801531425047536 0.646264782232478 0.938116913005677 0.388174807197943 0.67347429120615 0.677185443802873 0.840013416065739 0.560172148132405 0.537750556792873 0.466509988249118 0.359268929503916 0 0.484114532261228 0.622234006652847 0.487074231539852 0.577606177606177 0.321596600394597 0.764130434782609\n+group2 0.572409158546537 0.820626944245034 0.83725508577857 0.758192367410313 0.724986879144997 0.538922155688623 0.83214644589104 0.735420178184445 0.905321324457207 0.596869061623382 0.859248929176213 0.695153896529142 0.817908907547258 0.646577681901937 0.725759700794764 0.555275398861018 0.209920283436670 0.484114532261228 0 0.233028585612046 0.184614740719039 0.145672877846791 0.420959606845713 0.677966101694915\n+group9 0.658356940509915 0.776103945014594 0.759051704257184 0.741589782845171 0.669388904533934 0.539314268896846 0.772508176966776 0.818586585827965 0.868666952421774 0.729252973406388 0.828249694002448 0.698248620855873 0.788424259207976 0.83184352597575 0.901458342917606 0.722312633832977 0.388581148863785 0.622234006652847 0.233028585612046 0 0.227722772277228 0.111727966689799 0.514525993883792 0.595256346665464\n+group12 0.468803827751196 0.679419902681042 0.689453763842811 0.625361639704983 0.538476172358033 0.428855622420053 0.70517511761631 0.634216589861751 0.854316702819956 0.590238621498489 0.750707371556218 0.518242618672176 0.70625642943982 0.699166591988529 0.780864053688773 0.576246207195492 0.264185101779485 0.487074231539852 0.184614740719039 0.227722772277228 0 0.179336829499938 0.368810178817056 0.560213727907933\n+group10 0.624899560429172 0.764456383429945 0.78428294394681 0.70965400435519 0.662547573180473 0.505990964447063 0.787532847973119 0.765659822656361 0.901660445359763 0.716043877642022 0.830408783452603 0.67063492063492 0.784595481217946 0.769745293466224 0.850419084461638 0.656792557980023 0.341337757596926 0.577606177606177 0.145672877846791 0.111727966689799 0.179336829499938 0 0.50435780791633 0.614787397309741\n+group11 0.445852306473965 0.471627356163032 0.567737261531031 0.632291885091214 0.471028037383178 0.329349338004224 0.581221922731357 0.517282479141836 0.754406370224568 0.427280771201043 0.674327728932078 0.446171234812094 0.617593040115998 0.526223291092406 0.556379750493714 0.407794761777063 0.300259669263359 0.321596600394597 0.420959606845713 0.514525993883792 0.368810178817056 0.50435780791633 0 0.671336257723692\n+group21 0.556086425651643 0.760728080850839 0.727272727272727 0.54560014236142 0.495122079839688 0.531589448015961 0.677116737663332 0.747455911343173 0.724877304998332 0.72127723067741 0.80964495077978 0.63204311611955 0.746623195156032 0.793334979017526 0.888831597401258 0.672014090541248 0.750777302759425 0.764130434782609 0.677966101694915 0.595256346665464 0.560213727907933 0.614787397309741 0.671336257723692 0\n' |
| b |
| diff -r 000000000000 -r 870f2a438139 tool-data/mothur_aligndb.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mothur_aligndb.loc.sample Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,19 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters): +# +# Reference Alignments: http://www.mothur.org/wiki/Alignment_database +# +#<dbname> <file_base> +# +#greengenes /project/db/galaxy/mothur/core_set_aligned.imputed.fasta +#silva archaea /project/db/galaxy/mothur/Silva.archaea/silva.archaea.fasta +#silva bacteria /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.fasta +#silva eukarya /project/db/galaxy/mothur/silva.eukarya.fasta +#silva archaea nogap /project/db/galaxy/mothur/Silva.archaea/nogap.archaea.fasta +#silva bacteria nogap /project/db/galaxy/mothur/silva.bacteria/nogap.bacteria.fasta +#silva eukarya nogap /project/db/galaxy/mothur/nogap.eukarya.fasta +#FungiLSU_train_1400bp_8506_mod.fasta /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.fasta +#trainset6_032010.rdp.fasta /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.fasta +#trainset7_112011.pds.fasta /project/db/galaxy/mothur/RDP/trainset7_112011.pds.fasta +#trainset7_112011.rdp.fasta /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.fasta |
| b |
| diff -r 000000000000 -r 870f2a438139 tool-data/mothur_lookup.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mothur_lookup.loc.sample Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,11 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters): +# +# lookup files from: http://www.mothur.org/wiki/Lookup_files +# +#<name> <file_base> +# +#GS20 /project/db/galaxy/mothur/lookup/LookUp_GS20.pat +#GSFLX /project/db/galaxy/mothur/lookup/LookUp_GSFLX.pat +#Titanium /project/db/galaxy/mothur/lookup/LookUp_Titanium.pat |
| b |
| diff -r 000000000000 -r 870f2a438139 tool-data/mothur_map.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mothur_map.loc.sample Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,10 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters): +# +# Secondary structure maps: http://www.mothur.org/wiki/Secondary_structure_map +# +#<name> <file_base> +# +#greengenes /project/db/galaxy/mothur/gg.ss.map +#silva /project/db/galaxy/mothur/silva.ss.map |
| b |
| diff -r 000000000000 -r 870f2a438139 tool-data/mothur_taxonomy.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mothur_taxonomy.loc.sample Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,24 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters): +# +# Silva reference files: http://www.mothur.org/wiki/Silva_reference_files +# +#<taxonomyname> <file_base> +# +#archaea.gg /project/db/galaxy/mothur/Silva.archaea/silva.archaea.gg.tax +#archaea.silva /project/db/galaxy/mothur/Silva.archaea/silva.archaea.silva.tax +#archaea.rdp /project/db/galaxy/mothur/Silva.archaea/silva.archaea.rdp.tax +#archaea.ncbi /project/db/galaxy/mothur/Silva.archaea/silva.archaea.ncbi.tax +#bacteria.gg /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.gg.tax +#bacteria.silva /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.silva.tax +#bacteria.ncbi /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.ncbi.tax +#bacteria.rdp /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp.tax +#bacteria.rdp6 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp6.tax +#eukarya.silva /project/db/galaxy/mothur/silva.eukarya.silva.tax +#eukarya.ncbi /project/db/galaxy/mothur/silva.eukarya.ncbi.tax +#trainset6_032010.rdp.tax /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.tax +#trainset7_112011.pds.tax /project/db/galaxy/mothur/RDP/trainset7_112011.pds.tax +#trainset7_112011.rdp.tax /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.tax +#FungiLSU_train_1400bp_8506_mod.tax /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.tax +# |
| b |
| diff -r 000000000000 -r 870f2a438139 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri May 19 05:26:45 2017 -0400 |
| b |
| @@ -0,0 +1,18 @@ +<tables> + <table name="mothur_aligndb" comment_char="#" allow_duplicate_entries="False"> + <columns>name, value</columns> + <file path="tool-data/mothur_aligndb.loc" /> + </table> + <table name="mothur_lookup" comment_char="#" allow_duplicate_entries="False"> + <columns>name, value</columns> + <file path="tool-data/mothur_lookup.loc" /> + </table> + <table name="mothur_map" comment_char="#" allow_duplicate_entries="False"> + <columns>name, value</columns> + <file path="tool-data/mothur_map.loc" /> + </table> + <table name="mothur_taxonomy" comment_char="#" allow_duplicate_entries="False"> + <columns>name, value</columns> + <file path="tool-data/mothur_taxonomy.loc" /> + </table> +</tables> \ No newline at end of file |
| b |
| diff -r 000000000000 -r 870f2a438139 tools.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools.yaml Fri May 19 05:26:45 2017 -0400 |
| b |
| b'@@ -0,0 +1,802 @@\n+---\n+# This is a sample file to be used as a reference for populating a list of\n+# tools that you wish to install into Galaxy from a Tool Shed via the\n+# `install_tool_shed_tools.py` script.\n+#\n+# For each tool you want to install, you must provide the following keys:\n+# * name: this is is the name of the tool to install\n+# * owner: owner of the Tool Shed repository from where the tools is being\n+# installed\n+# Further, you need to provide **one** of the following two keys:\n+# * tool_panel_section_id: ID of the tool panel section where you want the\n+# tool to be installed. The section ID can be found\n+# in Galaxy\'s `shed_tool_conf.xml` config file. Note\n+# that the specified section must exist in this file.\n+# Otherwise, the tool will be installed outside any\n+# section.\n+# * tool_panel_section_label: Display label of a tool panel section where\n+# you want the tool to be installed. If it does not\n+# exist, this section will be created on the target\n+# Galaxy instance (note that this is different than\n+# when using the ID).\n+# Multi-word labels need to be placed in quotes.\n+# Each label will have a corresponding ID created;\n+# the ID will be an all lowercase version of the\n+# label, with multiple words joined with\n+# underscores (e.g., \'BED tools\' -> \'bed_tools\').\n+#\n+# Tou can also specify the following optional keys to further define the\n+# installation properties:\n+# * tool_shed_url: the URL of the Tool Shed from where the tool should be\n+# installed. (default: https://toolshed.g2.bx.psu.edu)\n+# * revisions: a list of revisions of the tool, all of which will attempt to\n+# be installed. (default: latest)\n+# * install_tool_dependencies: True or False - whether to install tool\n+# dependencies or not. (default: True)\n+# * install_repository_dependencies: True or False - whether to install repo\n+# dependencies or not. (default: True)\n+\n+\n+# pip install ephemeris -U\n+# shed_install -t tools.yaml -a <galaxy admin API key> -g <galaxy instance>\n+# (the latter two can also be configure inside the yaml with following two lines)\n+#api_key: admin\n+#galaxy_instance: http://localhost:8080/\n+\n+tools:\n+- name: mothur_align_check\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_align_seqs\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_amova\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_anosim\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_bin_seqs\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_chimera_bellerophon\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_chimera_ccode\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_labe'..b'true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_sffinfo\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_shhh_flows\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_shhh_seqs\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_sort_seqs\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_split_abund\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_split_groups\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_sub_sample\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_summary_qual\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_summary_seqs\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_summary_shared\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_summary_single\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_summary_tax\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_tree_shared\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_trim_flows\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_trim_seqs\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_unifrac_unweighted\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_unifrac_weighted\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_unique_seqs\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_venn\n+ install_resolver_dependencies: true\n+ install_tool_dependencies: true\n+ owner: iuc\n+ tool_panel_section_label: "Mothur"\n+ tool_shed_url: https://toolshed.g2.bx.psu.edu\n' |
