| Next changeset 1:918d141a166b (2017-12-03) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 2da91121887cc148ff398ddc2f56142490a8e22f |
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added:
orthofinder_only_groups.xml test-data/inputs/blastfa/Species0.fa test-data/inputs/blastfa/Species1.fa test-data/inputs/blastfa/Species2.fa test-data/inputs/blastfa/Species3.fa test-data/inputs/blastids/SequenceIDs.txt test-data/inputs/blastids/SpeciesIDs.txt test-data/inputs/blastout/Blast0_0.txt test-data/inputs/blastout/Blast0_1.txt test-data/inputs/blastout/Blast0_2.txt test-data/inputs/blastout/Blast0_3.txt test-data/inputs/blastout/Blast1_0.txt test-data/inputs/blastout/Blast1_1.txt test-data/inputs/blastout/Blast1_2.txt test-data/inputs/blastout/Blast1_3.txt test-data/inputs/blastout/Blast2_0.txt test-data/inputs/blastout/Blast2_1.txt test-data/inputs/blastout/Blast2_2.txt test-data/inputs/blastout/Blast2_3.txt test-data/inputs/blastout/Blast3_0.txt test-data/inputs/blastout/Blast3_1.txt test-data/inputs/blastout/Blast3_2.txt test-data/inputs/blastout/Blast3_3.txt test-data/inputs/proteomes/Mycoplasma_agalactiae.faa test-data/inputs/proteomes/Mycoplasma_gallisepticum.faa test-data/inputs/proteomes/Mycoplasma_genitalium.faa test-data/inputs/proteomes/Mycoplasma_hyopneumoniae.faa test-data/results/Orthogroups.csv test-data/results/Orthogroups.txt test-data/results/Orthogroups_SpeciesOverlaps.csv test-data/results/Orthogroups_UnassignedGenes.csv test-data/results/Statistics_Overall.csv test-data/results/Statistics_PerSpecies.csv test-data/results_fromblast/Orthogroups.csv test-data/results_fromblast/Orthogroups.txt test-data/results_fromblast/Orthogroups_SpeciesOverlaps.csv test-data/results_fromblast/Orthogroups_UnassignedGenes.csv test-data/results_fromblast/Statistics_Overall.csv test-data/results_fromblast/Statistics_PerSpecies.csv |
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| diff -r 000000000000 -r bfb20dbe1309 orthofinder_only_groups.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/orthofinder_only_groups.xml Tue Oct 24 06:40:40 2017 -0400 |
| [ |
| b'@@ -0,0 +1,294 @@\n+<tool name="OrthoFinder OnlyGroups" id="orthofinder_onlygroups" version="1.1.4">\n+ <description>finds orthogroups in a set of proteomes</description> \n+ <requirements>\n+ <requirement type="package" version="1.1.4">orthofinder</requirement>\n+ </requirements>\n+ <command>\n+ <![CDATA[\n+ ## prepare inputs\n+ #if $init.start=="fasta":\n+ #set $infiles = ""\n+ #for $input in $init.input_fasta\n+ ln -s \'$input\' \'$input.element_identifier\' &&\n+ #set $infiles = $infiles + str($input.element_identifier) + ","\n+ #end for\n+ #set $infiles = $infiles[:-1]\n+ #elif $init.start=="blast":\n+ #set $infilesbl = ""\n+ #for $input in $init.input_blast_out\n+ ln -s \'$input\' \'$input.element_identifier\' &&\n+ #set $infilesbl = $infilesbl + str($input.element_identifier) + ","\n+ #end for\n+ #set $infilesbl = $infilesbl[:-1]\n+ \n+ #set $infilesfa = ""\n+ #for $input in $init.input_blast_fa\n+ ln -s \'$input\' \'$input.element_identifier\' &&\n+ #set $infilesfa = $infilesfa + str($input.element_identifier) + ","\n+ #end for\n+ #set $infilesfa = $infilesfa[:-1]\n+\n+ ln -s $init.specIDs $init.specIDs.element_identifier &&\n+ ln -s $init.seqIDs $init.seqIDs.element_identifier &&\n+ #end if\n+\n+ ## start Orthofinder\n+ orthofinder\n+ #if $init.start=="fasta":\n+ -f .\n+ #elif $init.start=="blast":\n+ -b .\n+ #end if\n+\n+ -I $I -og -t \\${GALAXY_SLOTS:-1} -a \\${GALAXY_SLOTS:-1} &&\n+\n+ #if $init.start=="fasta":\n+ mv Results_* results\n+ #if $init.keepblastout=="yes":\n+ && mkdir -p results/WorkingDirectory/blast results/WorkingDirectory/fa &&\n+ mv results/WorkingDirectory/Blast* results/WorkingDirectory/blast/ &&\n+ mv results/WorkingDirectory/*.fa results/WorkingDirectory/fa/\n+ #end if\n+ #elif $init.start=="blast":\n+ mkdir results &&\n+ mv *.csv results/ &&\n+ mv Orthogroups.txt results/\n+ #end if\n+ \n+ ]]> \n+ </command>\n+ <inputs>\n+ <!-- Control where Orthofinder starts -->\n+ <conditional name="init">\n+ <param name="start" type="select" label="Orthofinder starting point" help="OrthoFinder_OnlyGroups works in 2 steps. Choose \'From fasta proteomes\' to run OrthoFinder_OnlyGroups from scratch and \'From blast results\' if you have all the blast results from a previous OrthoFinder_OnlyGroups run.">\n+ <option value="fasta" selected="true">From fasta proteomes</option>\n+ <option value="blast">From blast results</option>\n+ </param>\n+\n+ <when value="fasta">\n+ <param name="input_fasta" type="data" format="fasta" multiple="true" label="Select input fasta proteomes" help="One fasta file per species; species and sequences names in the results will remain the same than in the input files."/>\n+ <param name="keepblastout" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Do you want to get the blast results ?" help="Used to re-run OrthoFinder_OnlyGroups from pre-computed blast results"/> \n+ </when>\n+\n+ <when value="blast">\n+ <param name="input_blast_out" type="data_collection" collection_type="list" format="txt" label="Select the pre-computed blast files" help="blastX_Y.txt files from the blast output files of a previous OrthoFinder_OnlyGroups run." />\n+ <param name="input_blast_fa" type="data_collection" collection_type="list" format="fasta" label="Select the fasta files" help="= SpeciesX.fa files from the blast output files of a previous OrthoFinder_OnlyGroups run." />\n+ <param name="specIDs"'..b'"/>\n+ <element name="Blast2_0.txt" value="inputs/blastout/Blast2_0.txt"/>\n+ <element name="Blast2_1.txt" value="inputs/blastout/Blast2_1.txt"/>\n+ <element name="Blast2_2.txt" value="inputs/blastout/Blast2_2.txt"/>\n+ <element name="Blast2_3.txt" value="inputs/blastout/Blast2_3.txt"/>\n+ <element name="Blast3_0.txt" value="inputs/blastout/Blast3_0.txt"/>\n+ <element name="Blast3_1.txt" value="inputs/blastout/Blast3_1.txt"/>\n+ <element name="Blast3_2.txt" value="inputs/blastout/Blast3_2.txt"/>\n+ <element name="Blast3_3.txt" value="inputs/blastout/Blast3_3.txt"/>\n+ </collection>\n+ </param>\n+ <param name="input_blast_fa">\n+ <collection type="list">\n+ <element name="Species0.fa" value="inputs/blastfa/Species0.fa"/>\n+ <element name="Species1.fa" value="inputs/blastfa/Species1.fa"/>\n+ <element name="Species2.fa" value="inputs/blastfa/Species2.fa"/>\n+ <element name="Species3.fa" value="inputs/blastfa/Species3.fa"/>\n+ </collection>\n+ </param>\n+ <param name="specIDs" ftype="txt" value="inputs/blastids/SpeciesIDs.txt"/>\n+ <param name="seqIDs" ftype="txt" value="inputs/blastids/SequenceIDs.txt"/>\n+ </conditional>\n+ <param name="inflation" value="1.5" />\n+ <output name="orthogroups1" value="results_fromblast/Orthogroups.txt"/>\n+ <output name="orthogroups2" value="results_fromblast/Orthogroups.csv"/>\n+ <output name="specs_overlap" value="results_fromblast/Orthogroups_SpeciesOverlaps.csv"/>\n+ <output name="unassigned_genes" value="results_fromblast/Orthogroups_UnassignedGenes.csv"/>\n+ <output name="stat_overall" value="results_fromblast/Statistics_Overall.csv" lines_diff="2"/>\n+ <output name="stat_specs" value="results_fromblast/Statistics_PerSpecies.csv"/>\n+ </test>\n+ </tests> \n+ <help>\n+======================\n+OrthoFinder OnlyGroups\n+======================\n+\n+Full readme at https://github.com/davidemms/OrthoFinder/blob/master/README.md\n+Summary sketch at https://github.com/davidemms/OrthoFinder/blob/master/OrthoFinder-options.pdf\n+\n+OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format (Emms, D.M. and Kelly, S., 2015).\n+\n+.. class:: infomark\n+\n+This galaxy tool implements the first part of the Orthofinder program, e.g. the clustering of orthogroups of genes.\n+\n+If you have already ran OrthoFinder, the tool allows to re-run the analysis from the pre-computed blast-results.\n+\n+-----------\n+Input files\n+-----------\n+ - When using "from fasta" option (e.g Orthofinder from scratch) : the input files are a set of proteomes in fasta format (on file per species). Choose this option if you have no OrthoFinder results yet.\n+ - When using "from blast results" option : the input files are all the following files from of a previous OrthoFinder run (these files appear only if you have chosen to keep them while launching a previous run):\n+ - A dataset collection / multiple datasets for the blast outputs\n+ - A dataset collection / multiple datasets for .fa files\n+ - The SpeciesIDs.txt file\n+ - The SequencesIDs.txt file\n+\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1186/s13059-015-0721-2</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastfa/Species0.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastfa/Species0.fa Tue Oct 24 06:40:40 2017 -0400 |
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| b'@@ -0,0 +1,5439 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| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastfa/Species1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastfa/Species1.fa Tue Oct 24 06:40:40 2017 -0400 |
| b |
| b'@@ -0,0 +1,5395 @@\n+>1_0\n+MIISFINNKGGVLKTTLATNICGVFSKFFPKSRSVIVDLDGQGNVSATFGQHPERLKNTLIDIFRGEKDI\n+DDCVLNVFPSIDILPSNHELSFVDMDVARKEYKLSVIKNLIEKLEEMYDFVFLDTPPAMSTIVSVSMHIS\n+DMIVIPFEPDQYSILGLLRVIDTIETFRERNEDLKVLVVPTKVNARTRLHNDVLNIVKTKLSKKNIPLSK\n+NIVSFTTKSSASVGYEKLPIVLINQRSKYQEEYIEITKEIINLLKDNKNNEK\n+>1_1\n+MKNKKAKKKERRFTDLSADLDEEVEKIDPEYEDFKEIKIEKNKDNQVIDKNDPFFYSESFEEARIQLIKD\n+KKVEVKKEEEKVQETTVKNKISEAKKEEAKDVYIDSSLEIASQEPLTKGMHFYTNSRIIRKVRECAKNKG\n+LSISRLITMILDKSIKEE\n+>1_2\n+MKTKLKRFLEEISVHFNEANSELLDAFVHSIDFVFEENDNIYIYFESPYFFNEFKNKLNHLINVENAVVF\n+NDYLSLEWKKIIKENKRVNLLNKKEADTLKEKLATLKKQEKYKINPLSKGIKEKYNFGNYLVFEFNKEAV\n+YLAKQIANKTTHSNWNPIIIEGKPGYGKSHLLQAIANERQKLFPEEKICVLSSDDFGSEFLKSVIAPDPT\n+HIESFKSKYKDYDLLMIDDVQIISNRPKTNETFFTIFNSLVDQKKTIVITLDCKIEEIQDKLTARMISRF\n+QKGINVRINQPNKNEIIQIFKQKFKENNLEKYMDDHVIEEISDFDEGDIRKIEGSVSTLVFMNQMYGSTK\n+TKDQILKSFIEKVTNRKNLILSKDPKYVFDKIKYHFNVSEDVLKSSKRKKEIVQARHICMYVLKNVYNKN\n+LSQIGKLLRKDHTTVRHGIDKVEEELENDPNLKSFLDLFKN\n+>1_3\n+MRVNIFERYQSFSVKNTDKFEKASVLTRMTTDINFIHQSIQSGRTAIRGMSVFLFSLVLMFVTS\n+>1_4\n+MPVIIGGILLVYRFVIGNYKKLFKQYDQLNNLAKESIAGARVVKSYHQQDNEIQKFNRVAGFIYKNFTKI\n+ERITALISPIVLFCIYALAIAIAWIGTNNIVDGKLDIGSLASVFAYAFQMLINLLLLSVVYVTIITAKPS\n+KDRIIEVLTEKIDIKDKKYAIDTVSDYEVEYKDVSFKYVDTNPHHNLEKINIKIKKGQTIGIIGSTGSGK\n+TSIVNLLTRLYECNEGQVLLNNIQLNNYSIKALRDAIAIVPQKSILYSGTIKDNILMGGNYSDEEVEKAI\n+TQAQAAEFINKLPNKLDSIVEQKWN\n+>1_5\n+MSHKKERNAQKKKYFKELLRFIWKNKKWHLLIAFFLIIISSITLVLVNNFIKDLIDDYIAPLLREKSTGK\n+PLDFSGLIKYLSIIGLIFILGVLSNIISGQIMAKATHATLFKLRNNMYVHMQGLPIKYFDTTKHGDIMSY\n+YTNDVDTVRNLIVQIIPQSFQALVQIVVIFVFMLQISIVLTLITVLLLLPMLIFFGFFGKKTRVNFVANQ\n+VEIANLNGVIQEYIETQMISNLFNYSDQVIHKFKLANNKQAAIMKKANVLASIVFPVIFNYSNVMYIVVA\n+IASVFLFESYQNKPILGQQITLRVIVSFVALVRAFVGPLANISENVNFFARSKAGAERIYTMLDEKLEEN\n+KGKIILDYIEKYENGNWRIANKWTKQIGWVINGEIKPFQGKVEFKNVNFSYDGKKQVLKNINISGYPGEK\n+IALIGKTGSGKTTIANLISRFYNVSDGEIYFDDIPISSVDINSIRKTVGMVLQSTELFSGSIRDNIAYGN\n+KEAKLEDIIEAAKLANAHDFIMALPNEYDTYITNNGEGLSQGQKQLLTIARVSSMNPTIMVLDEATSNID\n+SRTEKVIKESMDKLMQNQTTFAIAHRLSTIKNFNQILVIQEGEIVERGNHEQLMAKKGLYESFYHSSFSD\n+EMS\n+>1_6\n+MKRTYQPNKRKRAKTHGFRARMATASGRAVLAARKRKGRHILTVSDEAR\n+>1_7\n+MKRENSLKKITNFLELVKSKNKYYSNNYVIYAEKNRENKIKIGISVSKKLFAKAVIRNKIKREVRSFFDD\n+FTDWSKSLNILIKINNVNYLTNSYYLAKKEEFFDTYKKVVQKFKTI\n+>1_8\n+MNKVHSEIKTQSFNPFWNAATLKEKSRIDPNLKKALSYLWKFLKICVFLFLTVIGLWGCTQTYSEPWTVS\n+NPRIGVGLEIGYNYGVTGDYRYDLTSSNIGPYFSFANYQLSYGPFLAWFVWPASQIILPILYQTRVPLTQ\n+GIDYGLNTILAILILLFIIRLITIGITLNSTLNTERMGEVQGKIAEINAKYKNATDTQSKKMKQIEVMHI\n+YKKHKIKPAALFVQGFVTIPIFLIVYKMVSLTRPIKATILFGIWDLSVTPGTEIISDISRNWVYIFFVLL\n+VVPMQIVSQWLPQFWATRRNRNAKTTSQKGLEQLKKTRRIQWILIFVFALFPVITPSAVGLYWFLNSIFT\n+ILQSYITHVFIVKRRQRTKTISRLDQILNRELD\n+>1_9\n+MINKINKFFKNNEFSPSKQRGQNFLIDQNIINNVVEAVSKINPSKVLEIGPGLGAISEQLIKRFADNYYA\n+IELDKKLFHHLNERLLKDHILHADALEIDWKSIFDNLGDNPTMVGNLPYNISSKLIKKFILSTYRCAIIM\n+VQKEMGLRLLAKINSKDYSAFSALCQYSLSVSKIIEINETAFIPQPKVRSTLLFLEKKDIAFNEGYEKFL\n+KLIFLSRRKTILNNLKNNYDPKLIIQSLVSLGFKKTSRAQELSPTQLFSLYESLSKLC\n+>1_10\n+MVLKKHPELKSYHLPNCLAYMNHYRSYAKVNFYLKIKEYCPKVKKHKLESKLVLVKDLYDDLYLEKWNQT\n+KIKYFDQNNNSLTFSDDILVRTKKFLEDKLNQTFEFKAKVIKRIPTLSGLGSAPSNAAVLINWIYQEFGI\n+LNPVSYYEIATELGSDIPFFLSLHDCAIIKNFGDQVEQSILDGYETEKIIFNKQKPSTKKIFELLDYSQI\n+KKENLNDLEQPFFSLFPELLPSFNQLKNDSNHVVLAGAGSCFVVFRKLNEI\n+>1_11\n+MVFKKIKTQIDHALKQLNLPTDVEYLIQQTKNIQFGDFSSNVAMVLSKRQNKNPQEIAKQIIEQLNPNEF\n+EKITFSKPGFINFFLSNQDKLVVLKRLQETNYSVEKLPKEEQESINIEFVSANPTGFLHLGHVRNAYTGD\n+VLSNILRAVGHNVTKEYWINDLGNQVSLFALSTIIRYLQELGINKYELPDDSYHGKEPIFVAEEMIKDFG\n+NKYQDIKIEDNKIVDSKIANELTQYCTNKMLHFIKQDLESIGVKMDVWTSEKVVYQSNTLTELLNNQLKD\n+HIYEQDGAVWLRTTDGGDDKDRVIIKENKQPTYYGTDIANHYLKHKRGFDRLINVWGADHFGHILRTAYA\n+AELTGIKKGKFVVVLIEMVKLLKDNKEIKFSKRLGNAISIPDMLEFLSKDASRWFMLNQSWTSGIRIDVD\n+LTNKKDSSNPVYYVQYAHARIHKLLTKAEHIDLNKVNLSLLNSDVERTMVNYLASFEHYVHNVATTYEVN\n+KLLNFVYTLTQSFHSWYNSHEILNQKDEIKQTRLLLAKAIKNLINYLLSLFGIEAVEQM\n+>1_12\n+MRNRVRDKQNQNTRKKQVNNKRWIMWVLLLLLIILGVSAYFVINKFPPPKNDVPDSERTNDSQVTTPGTR\n+NETIPLNEQYKKVGDLRLMSWNTLNFGSRSEPTSNKFMNIIRTIQLSDADVVGLSEINYDDQLLAQRLND\n+ALGSSWSYTFSGKNFNENYPRSKESILILYKNQVVQPEVSKAINPNNIYTRPLWYTKFKIIGFDYSFITF\n+FGHFDAPGVNANNGETSAAGFSRQGSQEIKEAQAIATVFSDLKTQYPDTDIIGAADTNIRETN'..b'\n+MKYKLYDTHCHVNIEQLFPKHDELLKAFDQENIYINVVGTTLEDSILANDITKKYNNCSACIAVHPNDVQ\n+QHNLKEVRTTFEQMLSTPNNKIVGIGECGLDFYYTDQYKAIQYQFLDMHLELANKYKKPLMLHIRNAHKE\n+LVEYLNNKEILVPIIFHCFSQDIETYKLLEQLPTKIVRFYSIPGVVTFKNAKALQEVIPLIKNEQLLVET\n+DAPFLTPHPFRGKENNSLYLKYTIEKIAELKNVSVDQIKQLTFDNAYNLFKPKIKD\n+>1_755\n+MINKIMKKYETIYALATAPYNSAIHVIRLSGPDAFEIINKICDKQITKEGYRIQNARIVDNDQIIDDVLL\n+MKFVAPKSFTGEDSIEINCHGGLFVINKIMALLNKHGAHLARRGEFSKRSYINKKIDLNQATAIHDLIFA\n+KNNLSHSASIKALSGEFSKDIKNIQQEIFRLIGLVEIAIDYPEYEDEKKELTEEFKNLTNIRQKLQRIVN\n+KSLKLKQISEGIKIAIVGEPNAGKSSLLNALLNEQKAIVTNIPGTTRDTVEGQIVLNDELIINLIDTAGI\n+RKSSDQIEQIGINKSFKTIDKSDLVIYLIDLNKYQNYDKTNIYKYLINKKKQFVLVGNKVDEVDPTLNTG\n+EIQIKISAKNNDISDLIKYLEETSLAIFNDENKQDSIFQEEWQINLLQTALYNINLILNDPNQYHDLVIQ\n+HLNEANNSLLKVLSEYEDYNLIDEIFKNFCLGK\n+>1_756\n+MNLTNKYIPILLFENKGCYLKKYLEEYLINIVCTEANKPCKKCVWCSKIINNGYYDLIHVYPHNNVIRKQ\n+EIIDIQNKFNNTALESRGIKIYIIHQIEKANKESLNSLLKFLGEPKDNTIGILTTRKPYGVLDTIVSRCV\n+RYSTNSYEEKVEFKNKYKPKELELIKIMFYSYDDILQYESTKDIFKLLELIHLLELNNKKFDQIIKIRDL\n+FEKIDYYEISLVLNYLIFTGDFKRKSKLIPILNNLNLNLSKNAILISIID\n+>1_757\n+MKKGVFIVIEGVDGSGKSSFLKRMMNEHTMINSQPIIYSREPGGCDTSEAVRELIMKLSNSDPLTEALLF\n+CASRNEHLKKKILPALNENKIAICDRFVVSSWIYQGLIKNAGYEKVKKINEYVTDGLEPDLTILFDVDPE\n+IAAKRISERSTMNHLDAYTKERINKIRNAYLERLKDNKKAKIINASLDLDTVYDQVVNIITLFVKNHELN\n+>1_758\n+MLDKNLLKTNSKEIREQLKSRSFNLDWYDEFLRLEKQLSTLLRTIEKLNEQKNINAKKAATTESDAQRKK\n+LIQEGGLLRAELEKNEAKYNEIKEDFDYIYQRIPNLPTEDVPIGKDEKENVEMFKSRKPTFFDFKPLPHY\n+ELATKLEMIGLDVASKITGSRFSIYKKDGARLMRAIQQFCLYVNADKYEEYLPPVIVNKDSYYGSGQFPK\n+FVEDVFKLEGTNYYLASTAEVQLVNLHRNEILKEADLPKYYTASTACFRSEAGSAGKDTKGLIRQHQFYK\n+TELVKIVHPSTSKQEHEAMAKDAEKILELLELPYRRMVLCTGDMGFSATKTYDLEVWIPSENKYREISSI\n+SNCGDFQARRANIKFKDAISKKNLYVHTLNASALAHDRLFVAIVENYQQKDGSIKIPKALVKYFGKEYIK\n+>1_759\n+MNPNDKNNIKELLNKTVVKEASITKELETSFMEYAMSVIVSRALPESRDGLKPVHRRVLYGAYTSGLTHD\n+KPYRKSAQIVGHVMGKYHPHSDSAIYETMVRMAQPFSLRYMLIDGHGNFGSIDGDSAAAMRYTEARLSKI\n+SAEMLRNIDKDTVDFVDNYDASEQEPIVLPSLFPNLLANGSSGIAVGMATNIPPHNLSELIGGIKHLLVN\n+ENATIEELKEFIKGPDFPTAAEILGETGINEYFNTGRGSVSVRAKSEIEELANNKSNIVITQIPYMVNKA\n+NLINKIAELVKTEQIQGIADLRDESNREGIRIVIETKRDVIPEVLLNQLYKSTQLQTNFSVAMLALVNNQ\n+PKVLNLKEALQIYIDHQFDILLRKTNFELKKAKASAHIVEGLVIATNNIDDVIETIKNAKDNEDAKNTLM\n+TKYELSDLQAKAILDMRLRSLSGLERENLQKELAKLKELIKDLEEILQNKERRIKIISDQLDEIDHKFGD\n+ERRTKICYGLNSTIDNEQLIPVETVVITRSSKGYLKRIPISAYKVQHRGGVGVKGMNTYEDDDVESLIVC\n+STHSDLLFFTNYGKVYRIRAHQVPLGSRISKGIPAINLISIEKDEKLMSLLSINDYDSGYFFFSTKKGLV\n+KRVKASEFSRIQNNGKIAIKLTENDSLFKVIKTAGDEEIYIGVSSGLLVRFKEDVVRSMGRTAQGVIGVK\n+FKNPNDEVIGLSSSHEGSLLLAVCEKGVGKMTDREEYRMTNRGSKGVITIKVTPKTGNIINTQLVNGNEE\n+LLMISSTGKIVRVPLAEVSEQGRNTSGVKLISLNEKETLQSVAIFDVEQDDSQQVGSDNPDTELSSDDSN\n+QDQDKE\n+>1_760\n+MNNTKKDQYSSQSIKVLEGLSAVRKRPGMYIGSTDQKGLHHMIWEIIDNSVDEMMAGYGTTVKLTLKDNY\n+LVEVEDDGRGIPVDIHEKTNKSTVETVLTILHAGGKFDSDTYSMSGGLHGVGASVVNALSSSFKVWVNRD\n+YKIHYIEFKDGGVPLKPLEIIGTDSKKQGTRIQFVPDFSIMEQFEYDETIIADRIEQLAFLNKGIKFIFN\n+DERTDKKTKQEWLYEGGIKQYVENLNASKEPIIPQIIYGEKKTKVTLPKRNLEVTMLLEVAFQYTNGYYN\n+STYSFCNNIHTNQGGTHEEGFKNALYKIINRYALEKKFIKETDGKISKEDLSEGLTAIISIKHSEPQYQG\n+QTKDRLGNTEVREFTNSVVSELLERFFLENPEEAAKITAKAVSAMFSRKRSEAALESARKSPFESASLPG\n+KLADCTTKDMEISELYIVEGDSAGGSAKSGRDRFYQAILPLRGKVLNVEKANHEKIFKNEEIRTLITAIG\n+AGVNPEFSLDKIRYNKIIIMTDADVDGAHIRILLLTFFFRHMFPLIEKGHVYIAQPPLYRVSYNKQNKYI\n+YSDAQLEEWKNQNPNVRYELQRYKGLGEMDDVQLWETTMDPEKRTLLKVSINDAANADKTFSLLMGDEVS\n+PRRDFIEKNAKSVKNIDF\n+>1_761\n+MTLYELLEVDQNATLSEIKSSYKRLAKKYHPDVNKNGHDKFVQINNAYSILSDEVQREKYDFMLDHENSK\n+TFEFSADGLTYEYSGVEVWHENFTKNVSLTQQWDFNPSNYYYEEYNLYHKFDKISIDGLGAFLDFDISCA\n+FYELDTSFSLPNNLVKRLINRPDVIRYDISENELIEYLKHRYDFSSWLLLKKYFNIEAIIEVTQEEIDSQ\n+KIINIPIKIKVINLNRSFEIWHEELRNYAFIVPENTKTGDISEFFGKGNVALGWQGDLIVRFKVVPSVEK\n+RLKIFSSMLNNEKSSLWFLVPSENNKNPNTKIFNYKTYQFNN\n+>1_762\n+MKFFTSKSSFLEAIKFSSNFSSDNNFEQLLKNLYIKIDNKECKIYSSNGQVSSIYKIEDDIDVEEEGEVI\n+VNAKKLITIIQSIVSDNFTLAKLDNQLIIRAGKMQTSLNLEEDVSYPEIEIDDSNFSVIDVDSFLFAKSI\n+KKVIHSTSFQTTKNSISSAINFQKEADDMNIWITGSDAIKLSSCYYKVNDTEDALKAKFNFSVNALSLSY\n+VAAFLKDKDQLLLKISKKSDKVVLTNNKFVLYLRVENEPFPEFKKILNANKVVSSFVVDKDLISNNLHAL\n+TGVLSLSDQGKNNADANFEILKNTLRISTNSFDIASYNSEFDISEFQGEVKDINLNPFYLQEHIKMFESK\n+DIEFKLLLQSAISGCILKVCEKNNDQFKLKFVQVLAPSSTN\n+\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastfa/Species2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastfa/Species2.fa Tue Oct 24 06:40:40 2017 -0400 |
| b |
| b'@@ -0,0 +1,3212 @@\n+>2_0\n+MKILINKSELNKILKKMNNVIISNNKIKPHHSYFLIEAKEKEINFYANNEYFSVKCNLNKNIDILEQGSL\n+IVKGKIFNDLINGIKEEIITIQEKDQTLLVKTKKTSINLNTINVNEFPRIRFNEKNDLSEFNQFKINYSL\n+LVKGIKKIFHSVSNNREISSKFNGVNFNGSNGKEIFLEASDTYKLSVFEIKQETEPFDFILESNLLSFIN\n+SFNPEEDKSIVFYYRKDNKDSFSTEMLISMDNFMISYTSVNEKFPEVNYFFEFEPETKIVVQKNELKDAL\n+QRIQTLAQNERTFLCDMQINSSELKIRAIVNNIGNSLEEISCLKFEGYKLNISFNPSSLLDHIESFESNE\n+INFDFQGNSKYFLITSKSEPELKQILVPSR\n+>2_1\n+MNLYDLLELPTTASIKEIKIAYKRLAKRYHPDVNKLGSQTFVEINNAYSILSDPNQKEKYDSMLKVNDFQ\n+NRIKNLDISVRWHENFMEELELRKNWEFDFFSSDEDFFYSPFTKNKYASFLDKDVSLAFFQLYSKGKIDH\n+QLEKSLLKRRDVKEACQQNKNFIEVIKEQYNYFGWIEAKRYFNINVELELTQREIRDRDVVNLPLKIKVI\n+NNDFPNQLWYEIYKNYSFRLSWDIKNGEIAEFFNKGNRALGWKGDLIVRMKVVNKVNKRLRIFSSFFEND\n+KSKLWFLVPNDKQSNPNKGVFNYKTQHFID\n+>2_2\n+MEENNKANIYDSSSIKVLEGLEAVRKRPGMYIGSTGEEGLHHMIWEIVDNSIDEAMGGFASFVKLTLEDN\n+FVTRVEDDGRGIPVDIHPKTNRSTVETVFTVLHAGGKFDNDSYKVSGGLHGVGASVVNALSSSFKVWVFR\n+QNKKYFLSFSDGGKVIGDLVQEGNSEKEHGTIVEFVPDFSVMEKSDYKQTVIVSRLQQLAFLNKGIRIDF\n+VDNRKQNPQSFSWKYDGGLVEYIHHLNNEKEPLFNEVIADEKTETVKAVNRDENYTVKVEVAFQYNKTYN\n+QSIFSFCNNINTTEGGTHVEGFRNALVKIINRFAVENKFLKDSDEKINRDDVCEGLTAIISIKHPNPQYE\n+GQTKKKLGNTEVRPLVNSVVSEIFERFMLENPQEANAIIRKTLLAQEARRRSQEARELTRRKSPFDSGSL\n+PGKLADCTTRDPSISELYIVEGDSAGGTAKTGRDRYFQAILPLRGKILNVEKSNFEQIFNNAEISALVMA\n+IGCGIKPDFELEKLRYSKIVIMTDADVDGAHIRTLLLTFFFRFMYPLVEQGNIFIAQPPLYKVSYSHKDL\n+YMHTDVQLEQWKSQNPNVKFGLQRYKGLGEMDALQLWETTMDPKVRTLLKVTVEDASIADKAFSLLMGDE\n+VPPRREFIEKNARSVKNIDI\n+>2_3\n+MAKQQDQVDKIRENLDNSTVKSISLANELERSFMEYAMSVIVARALPDARDGLKPVHRRVLYGAYIGGMH\n+HDRPFKKSARIVGDVMSKFHPHGDMAIYDTMSRMAQDFSLRYLLIDGHGNFGSIDGDRPAAQRYTEARLS\n+KLAAELLKDIDKDTVDFIANYDGEEKEPTVLPAAFPNLLANGSSGIAVGMSTSIPSHNLSELIAGLIMLI\n+DNPQCTFQELLTVIKGPDFPTGANIIYTKGIESYFETGKGNVVIRSKVEIEQLQTRSALVVTEIPYMVNK\n+TTLIEKIVELVKAEEISGIADIRDESSREGIRLVIEVKRDTVPEVLLNQLFKSTRLQVRFPVNMLALVKG\n+APVLLNMKQALEVYLDHQIDVLVRKTKFVLNKQQERYHILSGLLIAALNIDEVVAIIKKSANNQEAINTL\n+NTKFKLDEIQAKAVLDMRLRSLSVLEVNKLQTEQKELKDSIEFCKKVLADQKLQLKIIKEELQKINDQFG\n+DERRSEILYDISEEIDDESLIKVENVVITMSTNGYLKRIGVDAYNLQHRGGVGVKGLTTYVDDSISQLLV\n+CSTHSDLLFFTDKGKVYRIRAHQIPYGFRTNKGIPAVNLIKIEKDERICSLLSVNNYDDGYFFFCTKNGI\n+VKRTSLNEFINILSNGKRAISFDDNDTLYSVIKTHGNDEIFIGSTNGFVVRFHENQLRVLSRTARGVFGI\n+SLNKGEFVNGLSTSSNGSLLLSVGQNGIGKLTSIDKYRLTKRNAKGVKTLRVTDRTGPVVTTTTVFGNED\n+LLMISSAGKIVRTSLQELSEQGKNTSGVKLIRLKDNERLERVTIFKEELEDKEMQLEDVGSKQITQ\n+>2_4\n+MLDPNKLRNNYDFFKKKLLERNVNEQLLNQFIQTDKLMRKNLQQLELANQKQSLLAKQVAKQKDNKKLLA\n+ESKELKQKIENLNNAYKDSQNISQDLLLNFPNIAHESVPVGKNESANLELLKEGRKPVFDFKPLPHRELC\n+EKLNLVAFDKATKISGTRFVAYTDKAAKLLRAITNLMIDLNKSKYQEWNLPVVINELSLRSTGQLPKFKD\n+DVFKLENTRYYLSPTLEVQLINLHANEIFNEEDLPKYYTATGINFRQEAGSAGKQTKGTIRLHQFQKTEL\n+VKFCKPENAINELEAMVRDAEQILKALKLPFRRLLLCTGDMGFSAEKTYDLEVWMAASNEYREVSSCSSC\n+GDFQARRAMIRYKDINNGKNSYVATLNGTALSIDRIFAAILENFQTKDGKILIPQALKKYLDFDTIK\n+>2_5\n+MNKGVFVVIEGVDGAGKTALIEGFKKLYPTKFLNYQLTYTREPGGTLLAEKIRQLLLNETMEPLTEAYLF\n+AAARTEHISKLIKPAIEKEQLVISDRFVFSSFAYQGLSKKIGIDTVKQINHHALRNMMPNFTFILDCNFK\n+EALQRMQKRGNDNLLDEFIKGKNDFDTVRSYYLSLVDKKNCFLINGDNKQEHLEKFIELLTRCLQQPTHY\n+>2_6\n+MLTTTHALLIIQRKGSFLKPFLDNYLTSIVCENKNGCKKCINCLEILNNKYNSLYWFDQINPFKRENALQ\n+LARIFNRERTSVNNKNIYLIEEIEKLSSNSINSLLRLVEDSPINSYGIFTTKNESLILSTFLSRVQKVVL\n+KKASKVPFKVSKNDQEIITSFFTVDEQIEAIENGSFNRFKIILDACLNKKTGTEQIYHAWQIFRDFSNSE\n+IAQLITLIINKTENIDKKSILFNCLKVLPYNPPKSTLFANLVSW\n+>2_7\n+MKSEINIFALATAPFNSALHIIRFSGPDVYEILNKITNKKITRKGMQIQRTWIVDENNKRIDDVLLFKFV\n+SPNSYTGEDLIEISCHGNMLIVNEICALLLKKGGVYAKPGEFTQRSFLNGKMSLQQASAVNKLILSPNLL\n+VKDIVLNNLAGEMDQQLEQIAQQVNQLVMQMEVNIDYPEYLDEQVELSTLNNKVKLIIEKLKRIIENSKQ\n+LKKLHDPFKIAIIGETNVGKSSLLNALLNQDKAIVSNIKGSTRDVVEGDFNLNGYLIKILDTAGIRKHKS\n+GLEKAGIKKSFESIKQANLVIYLLDATHPKKDLELISFFKKNKKDFFVFYNKKDLITNKFENSISAKQKD\n+IKELVDLLTKYINEFYKKIDQKIYLIENWQQILIEKIKEQLEQFLKQQKKYLFFDVLVTHLREAQQDILK\n+LLGKDVGFDLVNEIFNNFCLGK\n+>2_8\n+MEYFDAHCHLNCEPLLSEIEKSIANFKLINLKANVVGTDLDNSKIAVELAKKYPDLLKATIGIHPNDVHL\n+VDFKKTKKQLNELLINNRNFISCIGEYGFDYHYTTEFIELQNKFFEMQFEIAETNKLVHMLHIRDAHEKI\n+YEILTRLKPTQPVIFHCFSQDINIAKKLLSLKDLNIDIFFSIPGIVTFKNAQALHEALKIIPSELLLSET\n+DSPWLTPSPFRGKVNWPEYVVHTVSTVAEIKKIEIAEMKRIIVKNAKKLFWH\n+>2_9\n+MDVRTERLNELFFVYHKNLKNQSKSKYSRAVNYLKRRGFNLQDF'..b'KDFNSFFENLSPLLCGNIPYSITSPIINKFLESKLRSFVLMTQKEFANRLLA\n+KVNSSDYSAFGAFCQYYLTITTVFKIDRHAFKPKPKVDSTLILLEKNKSVSYDFKFGLFLKQCFNQRRKM\n+LINNLKHFFAVDYLLNIIQKQNLKTSIRAQELSPCQLFNLYQNICNGKN\n+>2_468\n+MPIKLAQTNKEIKTTFNPFWSAAVVNEKNNWKNFKKFSAIFIKVIKVFIFIFLTIVGLWGCTQTLAQPWT\n+GTNQVLGSGLEIGYKFGTTGDYRYDLISNNFGPYFTFSDYTLAYGPFYGWFVWPAAQIVLPIMYATRVPL\n+GSGVELGFNMILSLIVLLLLVRLITIVITLNSTLALEKMNEVQGKLAEINAKYKGAIDLQSKRNRQLEIM\n+SLYKKHNIKSSAAFVQVFVTLPIFLIIYRIVTTLRPIKAIILFNFWDLSKVPLTEIFSNFTTTGWPFIIF\n+LVIVLPVQFLSQKLPQVWASKRNENAKAHSQKSIEQLNKTKKMQLIFYFVFAAITAFSAAGVGVYWFLNA\n+LFTLLQSYLTHVFIVKRREKRKQNYSKLDLILERE\n+>2_469\n+MLNSRFPVSVKKSHSLRERKVFTTILQSKTRFFGTFINAYFIKNNHSTWRVAISIAKTKYKLAVQRNLIK\n+RQIRSIFQQISNNLEPWDILVIVNKGFIELTFKEKQKLFLQLLKRIKEVDAYQTSANK\n+>2_470\n+MKRTYQPSKLKRAKTHGFMARMATAQGRKVLRQRRFKNRAQLTVSSER\n+>2_471\n+MKKGNKTVWNECIDILDNVKSPSFSANFDDYFKKSKSKPPKKNKKVLNNIKKAELKLKKKANKKQKANTL\n+YIPPFAQQAKGIVITINKMWKNVHNDDSKQEISILSDVSLQIAYGEIVIILGSSGSGKTTLLNLIGGYDS\n+ISLGSCIVANCPLEKCTSEQLLTYRKNNLGYVYQRYNLIELLSAYDNIAISQNLIPKYQRRLDIEELAEK\n+LDIKEILYKFPYEMSGGQKQRVAIARAIIKEPKLLLCDEPTGALDSNSAENIINLLQTINKTYKQTILMV\n+THDVSLTRIANRIIKISDGKIVSNQLVRPLV\n+>2_472\n+MFSFFKQIFKSLKKFFFLLFGIIFVLFSIIFLETSIVQLSNNLVSTYTTLVSKTNSSDIVAPAILKEANP\n+VYIASLTNDSGYFSKIKIDDKKINYLFPYQENDFGSDSGQSNGSGDNQNKTIPRKGDVNEKDKLFLARKR\n+GILKAYGEANIAEKRIYKGLAVSFNNTDSFNGSDISDSITNRHIISDPQNLIYDASGNLLGYFADGLIKE\n+TISLRAGIARFPGDKGKSTGTQVKITQKQQTNNDPQKDSTVNSLYKTNNKDKVWFKSDETKADNTDISAN\n+YLFTGGNEAANWFPNLYANIPIDLEIDPGSQFWKDVNPFKEIVEEFQTQKESKDNQSFTLTFNLDISKLN\n+KLDNEQLKWLETNAKTIANNSSFGDWDLENKLKQLKKFELKINKDWLKKKVESEKDTILNSLPGFSDSDK\n+DTIFKTQNGMMVRNNNLSFQPSSNNLQLVQNQNSQASNGIADPNFSNVQTAYNKIHQSNNTPEKTLDAVY\n+AAVLDQWRSIFQEDLVKKTVDLLEKYRDHFLKATAFNNIDYSKQNIAIANNVSSAESASFLVSNKDEQRY\n+NDLSLIDGVDLKSWLFKPEQNESNPLDTIYGGQDANNGFLQKIDYEFKPSTSSGGMTASLKNTQALSPKS\n+TKFPIYPKLANIIAQAQLPEATNIPTTALDALKQWTNLDANGFNNLKEEDKRKAANNYLALLSYFTPAFQ\n+DPNELIETNRQMLEIPITVKNGVNPLILPTDQQNLVVQTPEAHGAVVSQQWLFRHNKEILPQEGEYAWKT\n+ALQTPNNFPNWLNDLPDRYKFSINGLTFAILGIGESVETGYPVLSLQSPLPNTQDEALIFVNDQAYRSIL\n+FAVPAANQENYYAFKSTDLKQHTDQDPVQFIANRLEGYLDVPRSDLAFNVKDISKFNYLTTARNYFPDLV\n+QSYLAIVSTVIAIFLIILALYLIILLIKSFIKKNQTEFSIIRAGGFSTTKFIVGMSVFAGIVAIVSSFLG\n+VLFAFLLEGQVKGIINRYWFIALPENSFNWLSFFGSFFITFFVFEFISWIAFKQLFSKPVNVLIDQGNET\n+KFSVLLHLLKHKSHTMSPLTKFRVSLIVSRFSRLFTYVGLSSVALLLIGIAGTIPQKFSAAQTSTSLNRN\n+FNYKLNLQTPTEQSGWYAIQPYSHFGVTDNNNGIKTLYNESVQANSQNEHPYKPSNLKLKNRQDQPIKAA\n+DGTELELGNLLLPSYGGAQQLNTDENFFRHASLSKWIIDFPIRVGGSNINPWEIVEKSIPKQITQLLSAS\n+SDQFLISVLTDDFFNNLNANGFLIRNPRTNQIQLDASRVLTTIDVFNPGGVKFNDSFLSFMLKVYGDFEL\n+AKQDSKLNFGIVPVDPAIEETYTYVEGPFGFQEDNLDENSPYTLTGINPESSFVNLIDGSGNSLRNLISS\n+DQEMNVIVNAGFQYANNINIGDYVYIKPKNTATRYSEKFLKAPLNNSTVAFKVVGVSTDAFGQELYINQH\n+IANNLLKLSGNQGRGIIRDVIKKTNGQSQSSDEYEIDYVKPNGYVPFNGVFSKELKPSLLNKALVLNSII\n+GVWGNFTDFGNNFQNLVRNKLDKVITSILPTDPEIINKLAQEKQIINTTSMNYESLRKELVNKYKTEWNS\n+VNLLSQNASSIFGNNIIAPVLNIDAAGTSAQIIRNNAEVLFNTVNQVDAFLLGTIIPFIFITCVVLGISM\n+LEEMKRIFISLKAIGYRDVQNLISLLTFFIPAFVLALLISIGVLAGVLIGIQAVVFNVAQVFLTNVFEFL\n+PYMVGIVLFGVTIFVIGSYFWIKLRSAELKEGF\n+>2_473\n+MVLKTKENKKFDIYLKSSDFAVSKKASKLIKKLNKKHPKRKSLNSFEAKKYDIYFKEVCKAVTNGINNQL\n+ICNHINLKILPGEFVVILGKSGSGKTSLLSLISALDRPTSGDSFVCGTNTICCSDAKLTALRNKNVGYIF\n+QQYGLLRDLDVDDNIKLALPLKKRFNNNLEELLERLELKEHRHKKVHKLSGGQQQRVAIARALIKEPKIL\n+FGDEPTGAVNIDISKKILQFFVEYNRDKGTTIVIVTHNEKIVELAKRVIKIHDGKIIVDYLNQNPKTIEQ\n+INWV\n+>2_474\n+MEQFNAFKSLLKKHYEKTIGFHDKYIKDINRFVFKNNVLLILLENEFARNSLNDNSEIIHLAESLYEGIK\n+SVNFVNEQDFFFNLAKLEENSRDTLYQNSGLSKNYTFQNFVISEGNKRAYEAGVRLAETQDNEFSPLFIY\n+GETGLGKTHLLQAIGNEKFRNFPNARVKYVVSSDFAQEVVDAFYQRDKGIEKLKKNYENLDLVLIDDTQI\n+FGRKEKTLEILFNIFNNLVLNKKQIVLVSDKAPDELIDIDARMISRFKSGLLLKIEKHNLSSLCEILTVK\n+LKEKDPNIQITNEARHDAAQISGNDVRALNGIATKLLFFAKTSKQNLINTENLKEILFEEFEKFHKKSFD\n+PYLLIENVCRRFNVPMDSVLSENRKAELVRVRDVCNYLLRQKYNMQFQQIGKIFKRSHSSVLMAVKRVAK\n+MIENDSSLRDVITSLVI\n+>2_475\n+MIISFVNNKGGVLKTTMATNVAGSLVKLCPERRKVILDLDGQGNVSASFGQNPERLNNTLIDILLKVPKF\n+SGSNNFIEIDDCLLSVYEGLDILPCNFELNFADIDISRKKYKASDIAEIVKQLAKRYEFVLLDTPPNMAT\n+LVSTAMSLSDVIVIPFEPDQYSMLGLMRIVETIDTFKEKNTNLKTILVPTKVNVRTRLHNEVIDLAKTKA\n+KKNNVAFSKNFVSLTSKSSAAVGYEKLPISLVSSPSKKYLNEYLEITKEILNLANYNVH\n+\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastfa/Species3.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastfa/Species3.fa Tue Oct 24 06:40:40 2017 -0400 |
| b |
| b'@@ -0,0 +1,4765 @@\n+>3_0\n+MQTNKNNLKVRTQQIRQQIENLLNDRMLYNNFFSTIYVLNETETEIIIDFTDLIAKQEVISRWVDTVEKA\n+IKNLEISKILTFNNTNNYTINSKESQNFSIKNKYCSFNINNVLNKFTFRNFIKSSYNFQIFSIYDAIVAN\n+SRLNYSPIFISGPSGIGKTHFINAIGNLLVEKQKKVFYINDYKFISCVSSWMQNGQNEKISEFLNWLSQV\n+DAFLFDDIQGLANKQQTSIVALEILNRFIEEDKTVIITSDKSPSLLGGFEERFITRFSSGLHIKLNKPKK\n+EDFLRIFKHKLVEEKLEKHIWTNDAFEFLSKHFRNSIRELEGALKSIVFYIQTNKNKFENEIYFDKKKMF\n+EIFVEKYEIEQTITPDLIIEVVSKYYGVSILDIKSEKRGKNIVHARDIAIWLIKNILDLTHNSVGTFFNN\n+RRHSTIISTLKKIDTLKQSNNNELEIALNHIYKQLNWSFKQRK\n+>3_1\n+MKFTIEKKIIEWQIERMQSAILNNINSPLSSFFLKLTRSGLFIISTNSELSYKVFINKKDLIEIHDVGSC\n+LIDGVFLRDVIRKSDKQLSFHLIGSELKVFWEDALFSKTTRDSSFFPEINFEQKGIKLTVNAKNFKRAIK\n+NTAFATTNNPSQPILSAINLRSEAGFLHFSATDTSRFASEKIEISNKSRINISVSAKNLKDFIPPELDKD\n+IELNIESSKISYIYDNLTIQSRIFTIEYKDISNILPKDSEILYSLTINKRDILDLIDKTTIITPGKDNVI\n+NLSLSKNALKGYISQYDSGQSNVQTKNVLDFRFNPRFASDFRFDPELAQVNINYRYLKDAISVFDKVIDI\n+HINEKMNKMLIVSPEKPEICQLVGLVLV\n+>3_2\n+MSKKSKNSSIEFDAIVVGGGHAGIEAVYALLKKKLKVVLITLDKKKLASMPCNPAIGGPAKGIITREIDA\n+LGGVQGKFSDLAMIQIKYLNESKGPAVLAIRAQIDKEKYSKLILKDLKKQENLLIIEDLVSELLVEKNRV\n+FGLKTAKKQVFFSKTVIITTGTYMDSKVLRGSLAIPSGPDGQQTSNLLSNNLKRLGFELQRLKTGTPPRI\n+FTSSIDFSKVEKEVLPVYNINFSFQSKHKIKKQISCYLTYTTAKTHDIINKNLGKSSMYSGLISGVGPRY\n+CPSIEDKIVRFSEKPRHQIFFEPETKKQDIMYINGLSTSMPEDVQLEMVKTIPGLENAKIAKFGYAIEYD\n+ALNPLELKKSLETKKVKGLFMAGQINGTSGYEEAAAQGLVAGINAGQFVLGKKPVEILRNDGYIGVLIDD\n+LVTKGTKEPYRMLTSRAEYRLILRNDNADIRMAKYALKSGLISKKEYLKIKAKYAKIDRKILELSKEFVS\n+PKDELAKKYNLEKRISKLKLISWPNVNFKDILPDFEFGYELTVMARLKGYIQKQNSEAQKMIRLEKLLIP\n+GDLNYEKVANLSSEALDKFQKVRPKTIGEASRISGVNPADIQMLLFHIKVLKMQKVSKI\n+>3_3\n+MKISIISFGSSPREWLGLYKKEINKIKQFKYQIEFINLSEHSQENIELKKMLETKDILQKIPKNSSCYLF\n+TERGKTVTSKEFSQLLNFSNICFIIGGSYGVDEKLIAKSRPDIGFLSFGKLTFAHKIFKLIVLEQIYRGF\n+SIKFNRKYHHAD\n+>3_4\n+MKRKNYEKIIQNIENHDNIFIFHHIRPDGDCLGAQQGFGYAIAKRFPKKKVFFIGDNENIFNFLNFHFDN\n+ENLIQDEFFQNSLAITVDTADIKRIKKLDFFLNSNFKTRIKIDHHPDIFEEIYNEKWVDPTFSAASEMIG\n+YLLMEENWEINSEISKFIYLGILTDSGRFLFPSTTSRTFQVAAFLMKFNFDFAKLNWFLSNRTEQEVAFC\n+AEVLANYKKKDKVLWYFVSKEIQNKFKLRNDQLSAVNILANIGDARIWLFLIEMENGIRVRIRSNGPKVN\n+EIASEYGGGGHEYAAGINLEKSEKTKEISQEIIEKLVIQVKEFEQNE\n+>3_5\n+MSNIKIKEIIKLIENHDTIVIFHHIRPDGDCIGAQLGLKNLILDNFKNKKVFAVGNHKGSFSFLNAKTDS\n+IPDKLILKNSLAIIVDANFKNRIESVFLFDQFKFKTILRIDHHPNEDDFEQIYRWVDPSYVATCEQIADL\n+AYKAKWKISRKSATFIYLGIYTDSGRFLYKNTSARTHFLTGILFRTGFNFALIHEKLNQKKLSDIDFDSY\n+IFSVKKIYKNVIFYTLSMEEQKKLNKNPSNSVRPNLLANIENFRIWLCLVQEKENSWRVEFRSSGPNVQK\n+VAQNWGGGGHLNASGAIIESLDKLDLLIKDCQAEYESWFSQLK\n+>3_6\n+MEGINITNFLKYLFAYYYIDTGEREVYRTWVQKILWFTHWKFYRMYQIPFFSENFQSYKYGPISWTVLQT\n+QFFGIESFKNSQYNIDEILDFHQNNLVDEFKNRLKEDFLNDFNEDFGETFDENQIKGDLDLRWSCFVFVF\n+EKLKKFRPKDLINLSHSQKSFKIAAKNPHSKVIFNETILDDEEISILES\n+>3_7\n+MSFFRKIREKIFGTKQEKPANLDKYVAGLTKSRLSFFKQIVQLQKKHIKIDENFFEELEEILIMSDISPN\n+FVRTIIDSLKAEVRHHNLNNPDLIPEIIMDKMYTIYSNRSVVNTNLNIKDGRINVFLISGVNGSGKTTSI\n+AKVARKFIIEGKKVLIIAADTFRAAAVEQLEIWANRVGALILKPEANEKDPGSVVFRGLDFAIKEKTDLV\n+LIDTAGRLQNNVNLMQELKKINKIISQKVPNAPHESLLVIDATTGQNGVSQAANFAKITPVSGIILTKMD\n+GTSKGGIIFSIKDQLDISVKLVGLGEAMDDLQPFDLDLFIFAITKEVKNQYQV\n+>3_8\n+MAKISFFALGGQDENGKNCYILEIDDNIFIINSGAKIPLDSSVGVDTIIADFTYLEENQHKIRGVFITDA\n+KNESFSALPWLIMKLKKIKIYSSFFTKALIIERIHKYRLSESAFEVIPITSELKINEKISVSPFPVAGSM\n+PGTIGFCFHTEDGGIVFMANYVVGNLGVYGETNFELIKKISQNPKGILMFISDSGKSNLPGKAINKLFAK\n+NFLENFFLKADKNSRIVVSAYDEEMVSIQEIIDLSIKFNRQITAYGKKYDKLYDMIYKLDKLTTNKLKKL\n+PTFFDYKYANKQKNSVILITSSPERICYRFNRILENDDVYFKLKKSDYVIMLTPPINGMEQLYAKVLDQI\n+AKSTTSIVDISESDFGLARPYKEDISEMIQLLKPKYFLPIQGLYRYLIVASNIAVANKVKRQNIIVLQNK\n+RSANFIDGSLFSRKKISKGEEEIYVSGFGIGDVCFRVLKERDALSRNGLIIVSFLFDPIEKKIFSTPEIT\n+TYGILSRENREAYYDIIRKIIFNNFSNIKKINDKILKELQQKSQKNIKRKLLRIFDKEPSVSVLIHNIYP\n+EVKKMKKMLWKQAENELKTGVVYLEFAADWCNDCKMQEPVNEELSKYFKDRSDVKLIKVDAEESKLFRQK\n+GTKYEVLFVPTHFIFKDGQILFKQFNYVPAEVLIEKIEKALNS\n+>3_9\n+MPKLDSKKEKYLKQIVENFIKTGESIGSLNLKQSYGIKKSPSYLRAIMNQLEKEGFLEKSHSSSGRIPTL\n+QGFQYYAEFLSFDENENLANKLKDLFARRRINIENTISEAVKLISESVGTTLIATTNNENERLMSINLTQ\n+ISQNEGIIVVVSSSGNVENKKITFSEQIPRQDVKIAIRLFQERLINTPLLEISSKLAILKQELEKQIKHS\n+DELLHHFMEKIFNFQVQNKSNIYNKNSLILDKEISRAKLVDLLYIIEKKSIWEMLEDRTTKDDDTLKISI\n+KSPEVSFISKKFEKFLPIKEISMVGAAKKINYSAARTGIKLLEDFLSNKSKIRKG\n+>3_10\n+MVFG'..b'FSMLIFYFSD\n+IIKWIIYEILYLKTNWAINLTLEKTAKKIL\n+>3_666\n+MPRLTNMKISFVAIFISIAVIMLIIGVRLAPFAILPNFRLSIIGLPIKITGFIFGPIVGFLTGLLADLIT\n+FLFIPGVYSWYYTLHLSLAGFIPGIFFWFFVIKGKKWFEKKSILTRLDQKIFEQKQKIFDFTYYRIANNQ\n+KDENLERKMKQKLLFLQKKVKRVESWQEEKSLLNFYWIASNLILISIVVTTIYVVMFSSSIDFSQSRFIS\n+SKLSFLILTLFGTVSMIIFLLLARFINFFRKNERYLTIAPIVVFSALHEPIASIIGARGDVQSGALNNFD\n+TAFLSHIIVSPVKIWINLSVIYFTAKAVVPLVYKKFSYSIT\n+>3_667\n+MTNLHQEKRKKLLFHNIKNKYWNYFSLELEANQGSFIYSSDKNFFNEFKKILEDENSYNGFILENNEPYE\n+YQKNTCFSDFLTKKFFEKNKNKLVIEVLLSLWRIEPFKIKTNTTRRYIQYLSIKNVENFLKMFENELNYL\n+LENRAQAFKFIEKIAKIKEEYQILNKNFYNLYLKTELKPNIEQEKLNEKLKLSIPYPETKFENLKFSQTY\n+AQIALQTIKNDIKNVINHHNSLINSFDSDPYKIKIFITGYNCFLDLIKRSDNFRWLSSLQIYEIYFKFEQ\n+WLIKLLNQKALENILGTQNFFNNTFAEEFWGFWKQNSQQKILEERNKKAQKHFKVKKINSFHKENPYYQN\n+LKTNSKTLLRANILWQHEVIKMEKKLRNKNFQNSFFIKRIWVSSIENKLKKLKEKISKVEYENHFIFLKD\n+ALSDLKNFFYLKNLKKIDVFLKKNQFFIFCFDNKINFDILYKKYGVLTNDDLFFLETKKMQMGNYSRFLF\n+DEYSFLLETNYKQKLFQHFFNNGENSAQLFIYSRRTIKPIRDFSIIFIENGTLVEYIREIDLPLTPKTSF\n+GKFFYQNGTFERTNLPLLETQLYKQLQNEVFQNNSGGIKNNFESFINSWIPIKEFKLEFDSENKKYSLKK\n+DILVIDL\n+>3_668\n+MKNKYDFKLVEEKRNEKWQKKGFFIAPKQTKKPFSIISPPPNVTGQLHLGHSWNAFIQDSLVRYHKLQGF\n+DVLLLPSVDHAGIATQVKVEEDLAKKGIKKSDLKREEFIKKCYHWKEKQYLKIKEQWDKLGICYDFSKER\n+FTLDQDAQIAVSDFFIKLWEKNLIYRGQKAINWDIKLQTAISNIEVINKPVEQKMYYLKYFLENSNEFLT\n+VATTRIETISSDVALAINPKDKRYLHLVGKKVVHPLTKKLIIIIADSNVSSDFGSGIMKVSAHSILDFEI\n+MEKHNLESKDCIDNYGNLNHEVPEFQGQNRFFARDLIAKKLEKEGFLAKIETVISNVGFSQRSDEIVEIL\n+KKPQWFVKMDELAKSLISHLNSKDKIKFYPKNFEKNLRKWFEKIHDWTISRQLWWGHRIPVWCKNDEFKV\n+QIDSPGQGWIQDEDVLDTWFSSGISAFAFLGWPQNFDLIKSYFPTSLLVTGWDILFFWVARMYFSSLFIM\n+KQKPFEKVLLHGLIRDEIGRKMSKSLGNGLDPMEIIEKYGSDTLRQALIFNSSPGKDIKFNIEKLNTAWN\n+LNNKIWNIAKYIADLDTFFAKPDLIDLWMENKIYILKRQIVKNIKKYNFSVIGTEINNFIYGDFSSRYIE\n+LIKTRKNGFYARKLLRKVLIILHPFLPFLTDFLMEKIFKMEILEQKMPRIRQFKENQKVENILEIIDNLR\n+TYREKFQISKKIILEYCIINDKFSNAEIDIINKLTFGKWLENKELVIKTKNFEIAIKVPEELKKEQKGRE\n+LKEIQFLKSEILRAEKILTNKGFLEKAPREKIDLERTKLEKLKEKLVFYEKK\n+>3_669\n+MKKLKIYKNLNYFLPSFVFLGGAFFVLVSCGSTHFGLNISRESQTGIENAKKLKKIVNSPNLIELSPENN\n+EKIYEDKDAKFFLFDLNSAVNGGKNLELMPEFTTKFSPKTEITYLNFINRYYNTRQLQQKKKSLNQDSNS\n+IYIPHVDEKFKDFWYVFMIPTSIGFSALELNGKKTVIDREKTKLPSTLIPYSSVEVKILKKGIISADKKN\n+YLQINVNQMINSFAFREKKSNEPNSSEINVFGFQDNKAYPNYKLIFDSLDSSKKIIKFKLHRKNDNLHEE\n+RSAKNKLNSYISVMNFIYKAKEYKQNLNPDDFFEKNTEQKDKNSEYPFVRFYTQTFIVPFEGKEEVFDSD\n+FSILIEKSE\n+>3_670\n+MKNKITPCIWSLISNTHLRKAESLEILIRALLLNNEEINQNFKNKWLKIYKNKNWKPIGDLNEHLKLAAQ\n+LGVTKTDILTPGQQKINILAKLVNSGIIKIREYISIILFNLVSFINYEYRHIFKMTLELLKKQNNSPVSV\n+DEIFQNFNFGEPVCAEFNIKLLRYNLKQKDHIFYILISGVFFEVLSSRGKNQQYNINFFKIKLYDHWYSR\n+IDELIKRCNNQLESYNFEKASLIRLDSEKWSNYLTQNSQANYDYIVDVLMQKESNNLDEKNDNTINFKAS\n+INHLENQVQKNLENSLQETQINQDISTTISNNPEKVDIELEAILENSQENKVDLSELPANFNDKDQAESH\n+QISLENADLTSTNSVEKLEIEEKIQEKQSDIRIISNNLEQNCCPEQNVVEKEIEKTYEDNIEKNSFYSNF\n+YQDQFERDFNKISEPSGEKNLQDNAQSEICAAEKCCNHIQLEKENLEHIDSSKQEKVVKINSNYLNKGEK\n+NNSNTNKKVPSLPLLYQAKQEMQREISKYPISKSVNSKEHYYNYFIHKINKLFNFSLENMLNKTNFKQNF\n+FNILDFHKKNHEIILKPKKTIIKSGKNLLLISPSANLIYSKIKNELCKTEISEKNYEIVTFFDDYNPESF\n+IGYNDFVLGSKEKLNFIPGPFARILHKAYWNPEKKYCLILENIDNDAAKITLAPLKPLFIRGENGESLLG\n+ISQFDLSFYIFSHPEEKNFIPGNLTIIGTVNSNLDRDFVDLYPDFLENWEIKYLERDNLYSHITKYQICD\n+TGLSWKHFSEKLNSLLESENLNNKWFLPNQIETKILENPRIFVDKVLFSLWNFTSPEKRKIIFRSNSYSV\n+MVKEFLETKGSKRLNIFKFDYEKIKNI\n+>3_671\n+MKNRKIRPKAFDYFQSQNNQNKKTFKFKGFFKFLKIFFYTIIFGISLTGCIQSMVVKTSYNPGEALEFYN\n+SKEEITPNYTIFRESKNKDLPGIDIVTKNNNFLVSADNKKVNQEKILNALRKQIKNENAEFGEFSSLIMF\n+QKGENEFEYLKGDKNNEFIFFSSSENSIEQKTNWTEIKIPSPKYFSLKSDKQYFEKLRDVKSLPINTYSF\n+DKSSSENAAISEKIDSYFFNLDNKIPPVNRSYAIFARDVFQVIYNKLILLPQFSQGKLEKAIAEFEQKSG\n+KDVSPETEKILSGYANLVKKLVFPTNFSRIDIQNKTYSWNNNDESAAKNIAFQNKIPAFPIVSWAESWKL\n+GPFYAIFVYPLSKIILWVTASQSLYEWSGWITILSILAVVVFTKIISFIFRFKTIFGQNKQMELQLKKAK\n+IDAKYENYKKNKVMQQRHRQEIVDLYKKNNFSPFSPFSQILVTMPIFIAVWRALQGIPSFKVTYFLGLEL\n+AATSYQKLFEGYWIYLPIIIVTVLVQALQQIIPKILNKKKSNRIMNVQENETLKKQQKTQRIVSIIFIFF\n+GVIFQASLQIYWIIGGIWEILQTLGIFYLQKSNFYREKMRPWLERKKWV\n+>3_672\n+MQKIRSIKKNWEFQAIINKKNQIVTNYLIFYYVKSDFFEIGISVPKKFANAVKRNYYKRQIKNALYILWK\n+KGEIFLNFRVVLIARKNFLPLSFETKYQKLAKIFKELKRNEK\n+>3_673\n+MKRTYQPNKRKHLKTHGFRARMSTADGRKILAARRAKGRKRLTVSDK\n+\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastids/SequenceIDs.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastids/SequenceIDs.txt Tue Oct 24 06:40:40 2017 -0400 |
| [ |
| b'@@ -0,0 +1,2733 @@\n+0_0: gi|290752267|emb|CBH40238.1| Chromosomal replication initiator protein DnaA [Mycoplasma agalactiae]\n+0_1: gi|290752268|emb|CBH40239.1| DNA polymerase III, beta chain [Mycoplasma agalactiae]\n+0_2: gi|290752269|emb|CBH40240.1| Esterase/lipase [Mycoplasma agalactiae]\n+0_3: gi|290752270|emb|CBH40241.1| Esterase/lipase [Mycoplasma agalactiae]\n+0_4: gi|290752271|emb|CBH40242.1| NADH dependent flavin oxidoreductase [Mycoplasma agalactiae]\n+0_5: gi|290752272|emb|CBH40243.1| Lipoate protein ligase A [Mycoplasma agalactiae]\n+0_6: gi|290752273|emb|CBH40244.1| Lipoate protein ligase A [Mycoplasma agalactiae]\n+0_7: gi|290752274|emb|CBH40245.1| Conserved hypothetical protein [Mycoplasma agalactiae]\n+0_8: gi|290752275|emb|CBH40246.1| Glycine cleavage system H protein [Mycoplasma agalactiae]\n+0_9: gi|290752276|emb|CBH40247.1| Conserved hypothetical protein [Mycoplasma agalactiae]\n+0_10: gi|290752277|emb|CBH40248.1| Hypothetical protein MAGa0130 [Mycoplasma agalactiae]\n+0_11: gi|290752278|emb|CBH40249.1| Conserved hypothetical protein, predicted lipoprotein, P48 [Mycoplasma agalactiae]\n+0_12: gi|290752279|emb|CBH40250.1| Hypothetical protein MAGa0150 [Mycoplasma agalactiae]\n+0_13: gi|290752280|emb|CBH40251.1| ABC transporter, ATP binding protein, P59 [Mycoplasma agalactiae]\n+0_14: gi|290752281|emb|CBH40252.1| Sugar ABC transporter Permease [Mycoplasma agalactiae]\n+0_15: gi|290752282|emb|CBH40253.1| Sugar ABC transporter permease protein [Mycoplasma agalactiae]\n+0_16: gi|290752283|emb|CBH40254.1| Deoxyguanosine kinase [Mycoplasma agalactiae]\n+0_17: gi|290752284|emb|CBH40255.1| Deoxyguanosine kinase [Mycoplasma agalactiae]\n+0_18: gi|290752285|emb|CBH40256.1| Conserved hypothetical protein, predicted lipoprotein [Mycoplasma agalactiae]\n+0_19: gi|290752286|emb|CBH40257.1| Hypothetical protein, predicted lipoprotein, DUF285 family [Mycoplasma agalactiae]\n+0_20: gi|290752287|emb|CBH40258.1| Conserved hypothetical protein, DUF285 family [Mycoplasma agalactiae]\n+0_21: gi|290752288|emb|CBH40259.1| Transposase [Mycoplasma agalactiae]\n+0_22: gi|290752289|emb|CBH40260.1| Hypothetical protein, predicted lipoprotein, DUF285 family [Mycoplasma agalactiae]\n+0_23: gi|290752290|emb|CBH40261.1| Conserved hypothetical protein YeiN [Mycoplasma agalactiae]\n+0_24: gi|290752291|emb|CBH40262.1| Conserved hypothetical protein YeiC [Mycoplasma agalactiae]\n+0_25: gi|290752292|emb|CBH40263.1| Hydrolase of the HAD superfamily [Mycoplasma agalactiae]\n+0_26: gi|290752293|emb|CBH40264.1| Conserved hypothetical protein [Mycoplasma agalactiae]\n+0_27: gi|290752294|emb|CBH40265.1| Hypothetical ABC transporter, ATP binding protein [Mycoplasma agalactiae]\n+0_28: gi|290752295|emb|CBH40266.1| Hypothetical protein MAGa0310 [Mycoplasma agalactiae]\n+0_29: gi|290752296|emb|CBH40267.1| Hypothetical protein MAGa0320 [Mycoplasma agalactiae]\n+0_30: gi|290752297|emb|CBH40268.1| Hypothetical protein MAGa0330 [Mycoplasma agalactiae]\n+0_31: gi|290752298|emb|CBH40269.1| Oligopeptide ABC transporter, ATP binding protein (OppF) [Mycoplasma agalactiae]\n+0_32: gi|290752299|emb|CBH40270.1| Oligopeptide ABC transporter, ATP binding protein (OppD) [Mycoplasma agalactiae]\n+0_33: gi|290752300|emb|CBH40271.1| Oligopeptide ABC transporter, permease protein(OppC) [Mycoplasma agalactiae]\n+0_34: gi|290752301|emb|CBH40272.1| Oligopeptide ABC transporter, permease protein(OppB) [Mycoplasma agalactiae]\n+0_35: gi|290752302|emb|CBH40273.1| Oligopeptide ABC transporter, substrate bindingprotein (OppA), predicted lipoprotein [Mycoplasma agalactiae]\n+0_36: gi|290752303|emb|CBH40274.1| Conserved hypothetical protein [Mycoplasma agalactiae]\n+0_37: gi|290752304|emb|CBH40275.1| Cysteinyl tRNA synthetase (Cysteine tRNA ligase) [Mycoplasma agalactiae]\n+0_38: gi|290752305|emb|CBH40276.1| tRNA/rRNA methyltransferase [Mycoplasma agalactiae]\n+0_39: gi|290752306|emb|CBH40277.1| Hypothetical protein MAGa0420 [Mycoplasma agalactiae]\n+0_40: gi|290752307|emb|CBH40278.1| 50S ribosomal protein L33 [Mycoplasma'..b'ae J]\n+3_632: gi|144227736|gb|AAZ44718.2| conserved hypothetical protein [Mycoplasma hyopneumoniae J]\n+3_633: gi|144227737|gb|ABO93485.1| hypothetical protein MHJ_0699 [Mycoplasma hyopneumoniae J]\n+3_634: gi|71852111|gb|AAZ44719.1| O-sialoglycoprotein endopeptidase [Mycoplasma hyopneumoniae J]\n+3_635: gi|71852112|gb|AAZ44720.1| transcription antitermination protein [Mycoplasma hyopneumoniae J]\n+3_636: gi|144227738|gb|AAZ44721.2| conserved hypothetical protein [Mycoplasma hyopneumoniae J]\n+3_637: gi|71852114|gb|AAZ44722.1| hypothetical protein MHJ_0639 [Mycoplasma hyopneumoniae J]\n+3_638: gi|71852115|gb|AAZ44723.1| putative tRNA/rRNA methyltransferase [Mycoplasma hyopneumoniae J]\n+3_639: gi|144227739|gb|AAZ44724.2| cysteinyl-tRNA synthetase [Mycoplasma hyopneumoniae J]\n+3_640: gi|144227740|gb|AAZ44725.2| conserved hypothetical protein [Mycoplasma hyopneumoniae J]\n+3_641: gi|71852118|gb|AAZ44726.1| putative hemolysin C [Mycoplasma hyopneumoniae J]\n+3_642: gi|71852119|gb|AAZ44727.1| replicative DNA helicase [Mycoplasma hyopneumoniae J]\n+3_643: gi|71852120|gb|AAZ44728.1| 50S ribosomal protein L9 [Mycoplasma hyopneumoniae J]\n+3_644: gi|71852121|gb|AAZ44729.1| conserved hypothetical protein [Mycoplasma hyopneumoniae J]\n+3_645: gi|71852122|gb|AAZ44730.1| leucyl-tRNA synthetase [Mycoplasma hyopneumoniae J]\n+3_646: gi|144227741|gb|AAZ44731.2| excinuclease ABC subunit B [Mycoplasma hyopneumoniae J]\n+3_647: gi|71852124|gb|AAZ44732.1| conserved hypothetical protein [Mycoplasma hyopneumoniae J]\n+3_648: gi|71852125|gb|AAZ44733.1| 30S ribosomal protein S9 [Mycoplasma hyopneumoniae J]\n+3_649: gi|71852126|gb|AAZ44734.1| 50S ribosomal protein L13 [Mycoplasma hyopneumoniae J]\n+3_650: gi|144227742|gb|AAZ44735.2| dimethyladenosine transferase [Mycoplasma hyopneumoniae J]\n+3_651: gi|144227743|gb|AAZ44736.2| conserved hypothetical protein [Mycoplasma hyopneumoniae J]\n+3_652: gi|144227744|gb|AAZ44737.2| ribose-phosphate pyrophosphokinase [Mycoplasma hyopneumoniae J]\n+3_653: gi|71852130|gb|AAZ44738.1| glucose inhibited division protein B [Mycoplasma hyopneumoniae J]\n+3_654: gi|71852131|gb|AAZ44739.1| putative prolipoprotein p65 [Mycoplasma hyopneumoniae J]\n+3_655: gi|71852132|gb|AAZ44740.1| putative ABC transporter ATP-binding protein P115-like protein [Mycoplasma hyopneumoniae J]\n+3_656: gi|71852133|gb|AAZ44741.1| 50S ribosomal protein L33 [Mycoplasma hyopneumoniae J]\n+3_657: gi|71852134|gb|AAZ44742.1| XAA-PRO aminopeptidase [Mycoplasma hyopneumoniae J]\n+3_658: gi|144227745|gb|AAZ44743.2| hypothetical protein MHJ_0660 [Mycoplasma hyopneumoniae J]\n+3_659: gi|144227746|gb|AAZ44744.2| conserved hypothetical protein [Mycoplasma hyopneumoniae J]\n+3_660: gi|144227747|gb|AAZ44745.2| hypothetical protein MHJ_0662 [Mycoplasma hyopneumoniae J]\n+3_661: gi|71852138|gb|AAZ44746.1| putative adhesin like-protein P146 [Mycoplasma hyopneumoniae J]\n+3_662: gi|71852139|gb|AAZ44747.1| putative ABC transporter ATP-binding - Pr1 [Mycoplasma hyopneumoniae J]\n+3_663: gi|71852141|gb|AAZ44749.1| hypothetical protein MHJ_0666 [Mycoplasma hyopneumoniae J]\n+3_664: gi|71852142|gb|AAZ44750.1| transcription elongation factor [Mycoplasma hyopneumoniae J]\n+3_665: gi|144227748|gb|AAZ44751.2| conserved hypothetical protein [Mycoplasma hyopneumoniae J]\n+3_666: gi|71852144|gb|AAZ44752.1| conserved hypothetical protein [Mycoplasma hyopneumoniae J]\n+3_667: gi|71852145|gb|AAZ44753.1| hypothetical protein MHJ_0670 [Mycoplasma hyopneumoniae J]\n+3_668: gi|71852146|gb|AAZ44754.1| valyl-tRNA synthetase [Mycoplasma hyopneumoniae J]\n+3_669: gi|144227749|gb|AAZ44755.2| hypothetical protein MHJ_0672 [Mycoplasma hyopneumoniae J]\n+3_670: gi|144227750|gb|AAZ44756.2| hypothetical protein MHJ_0673 [Mycoplasma hyopneumoniae J]\n+3_671: gi|71852149|gb|AAZ44757.1| conserved hypothetical protein [Mycoplasma hyopneumoniae J]\n+3_672: gi|71852150|gb|AAZ44758.1| ribonuclease P protein component [Mycoplasma hyopneumoniae J]\n+3_673: gi|71852151|gb|AAZ44759.1| 50S ribosomal protein L34 [Mycoplasma hyopneumoniae J]\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastids/SpeciesIDs.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastids/SpeciesIDs.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +0: Mycoplasma_agalactiae.faa +1: Mycoplasma_gallisepticum.faa +2: Mycoplasma_genitalium.faa +3: Mycoplasma_hyopneumoniae.faa |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastout/Blast0_0.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastout/Blast0_0.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
| b'@@ -0,0 +1,3999 @@\n+0_0\t0_0\t100.00\t466\t0\t0\t1\t466\t1\t466\t0.0\t 941\n+0_0\t0_720\t27.36\t106\t70\t3\t155\t258\t153\t253\t1e-07\t48.1\n+0_1\t0_1\t100.00\t369\t0\t0\t1\t369\t1\t369\t0.0\t 734\n+0_2\t0_2\t100.00\t261\t0\t0\t1\t261\t1\t261\t0.0\t 531\n+0_2\t0_499\t64.62\t260\t90\t1\t4\t261\t5\t264\t8e-121\t 345\n+0_2\t0_3\t57.03\t263\t111\t1\t1\t261\t1\t263\t3e-111\t 321\n+0_2\t0_223\t49.04\t261\t132\t1\t2\t261\t3\t263\t1e-88\t 263\n+0_2\t0_147\t38.40\t263\t158\t3\t2\t261\t5\t266\t1e-54\t 176\n+0_2\t0_718\t29.51\t122\t81\t3\t10\t130\t15\t132\t2e-08\t48.9\n+0_3\t0_3\t100.00\t272\t0\t0\t1\t272\t1\t272\t0.0\t 560\n+0_3\t0_499\t58.78\t262\t108\t0\t2\t263\t3\t264\t1e-118\t 340\n+0_3\t0_2\t57.03\t263\t111\t1\t1\t263\t1\t261\t4e-111\t 321\n+0_3\t0_223\t49.04\t261\t132\t1\t3\t263\t4\t263\t1e-89\t 266\n+0_3\t0_147\t37.02\t262\t163\t2\t3\t263\t6\t266\t2e-56\t 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552\n+0_809\t0_809\t100.00\t104\t0\t0\t1\t104\t1\t104\t2e-75\t 217\n+0_810\t0_810\t100.00\t147\t0\t0\t1\t147\t1\t147\t4e-104\t 293\n+0_811\t0_811\t100.00\t319\t0\t0\t1\t319\t1\t319\t0.0\t 653\n+0_812\t0_812\t100.00\t131\t0\t0\t1\t131\t1\t131\t1e-90\t 258\n+0_813\t0_813\t100.00\t902\t0\t0\t1\t902\t1\t902\t0.0\t1827\n+0_813\t0_453\t30.33\t755\t425\t21\t39\t730\t10\t726\t4e-80\t 275\n+0_814\t0_814\t100.00\t357\t0\t0\t1\t357\t1\t357\t0.0\t 722\n+0_814\t0_535\t29.70\t202\t133\t4\t139\t336\t18\t214\t1e-18\t79.7\n+0_814\t0_105\t26.58\t237\t150\t7\t134\t348\t51\t285\t3e-18\t80.1\n+0_814\t0_157\t30.91\t220\t133\t8\t120\t336\t3\t206\t5e-17\t74.7\n+0_814\t0_259\t26.17\t256\t126\t3\t139\t331\t21\t276\t5e-16\t72.8\n+0_814\t0_32\t28.26\t230\t145\t7\t139\t348\t113\t342\t5e-15\t70.9\n+0_814\t0_534\t25.34\t221\t141\t4\t142\t338\t25\t245\t1e-14\t68.9\n+0_814\t0_31\t29.37\t126\t83\t3\t229\t348\t251\t376\t4e-14\t68.2\n+0_814\t0_31\t27.91\t129\t80\t4\t120\t237\t37\t163\t8e-04\t35.8\n+0_814\t0_13\t23.74\t198\t139\t3\t128\t317\t10\t203\t2e-13\t66.6\n+0_814\t0_13\t24.08\t245\t152\t10\t120\t336\t263\t501\t1e-10\t57.8\n+0_814\t0_106\t32.56\t129\t73\t5\t235\t356\t605\t726\t3e-13\t65.9\n+0_814\t0_106\t32.26\t93\t62\t1\t119\t210\t9\t101\t9e-07\t45.4\n+0_814\t0_476\t24.00\t200\t140\t3\t120\t317\t4\t193\t6e-12\t59.7\n+0_814\t0_325\t29.05\t210\t131\t6\t139\t339\t371\t571\t4e-11\t58.9\n+0_814\t0_712\t26.47\t102\t74\t1\t238\t338\t193\t294\t6e-11\t58.2\n+0_814\t0_712\t38.46\t52\t29\t1\t142\t190\t28\t79\t7e-05\t39.3\n+0_814\t0_520\t30.10\t103\t71\t1\t238\t339\t454\t556\t7e-11\t58.5\n+0_814\t0_520\t34.48\t87\t51\t1\t137\t223\t58\t138\t4e-10\t56.2\n+0_814\t0_624\t25.54\t231\t120\t10\t120\t318\t1\t211\t3e-10\t56.2\n+0_814\t0_124\t30.68\t88\t55\t1\t139\t226\t26\t107\t5e-10\t55.5\n+0_814\t0_124\t30.34\t89\t61\t1\t257\t344\t229\t317\t2e-07\t47.4\n+0_814\t0_324\t25.55\t227\t146\t7\t121\t336\t365\t579\t2e-09\t53.5\n+0_814\t0_626\t28.70\t230\t136\t8\t121\t336\t370\t585\t1e-08\t51.6\n+0_814\t0_627\t27.81\t187\t118\t6\t121\t298\t354\t532\t1e-08\t51.2\n+0_814\t0_224\t28.09\t89\t63\t1\t252\t339\t204\t292\t4e-08\t49.3\n+0_814\t0_27\t32.84\t67\t44\t1\t251\t317\t105\t170\t3e-06\t43.1\n+0_815\t0_815\t100.00\t2723\t0\t0\t1\t2723\t1\t2723\t0.0\t5445\n+0_816\t0_816\t100.00\t675\t0\t0\t1\t675\t1\t675\t0.0\t1368\n+0_816\t0_210\t27.33\t150\t93\t6\t236\t380\t106\t244\t9e-08\t49.3\n+0_816\t0_217\t27.52\t109\t64\t2\t197\t305\t10\t103\t4e-05\t41.2\n+0_817\t0_817\t100.00\t286\t0\t0\t1\t286\t1\t286\t0.0\t 583\n+0_818\t0_818\t100.00\t188\t0\t0\t1\t188\t1\t188\t1e-134\t 374\n+0_819\t0_819\t100.00\t756\t0\t0\t1\t756\t1\t756\t0.0\t1533\n+0_819\t0_208\t34.65\t228\t116\t8\t314\t518\t279\t496\t1e-16\t78.6\n+0_819\t0_205\t42.86\t70\t40\t0\t671\t740\t43\t112\t8e-11\t56.6\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastout/Blast0_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastout/Blast0_1.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
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162\n+0_815\t1_20\t24.63\t402\t254\t10\t2337\t2715\t978\t1353\t3e-22\t 100\n+0_815\t1_20\t27.39\t157\t105\t4\t2570\t2721\t487\t639\t1e-04\t42.0\n+0_816\t1_25\t54.04\t483\t208\t3\t172\t645\t239\t716\t9e-165\t 491\n+0_816\t1_715\t28.99\t169\t102\t7\t235\t393\t100\t260\t1e-06\t45.8\n+0_816\t1_551\t28.72\t94\t58\t2\t230\t322\t40\t125\t2e-06\t45.1\n+0_817\t1_701\t34.39\t285\t172\t6\t3\t284\t10\t282\t4e-38\t 134\n+0_818\t1_700\t45.90\t183\t97\t1\t1\t181\t1\t183\t2e-53\t 167\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastout/Blast0_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastout/Blast0_2.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
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122\n+0_815\t2_63\t24.58\t419\t270\t12\t2307\t2715\t941\t1323\t1e-14\t74.7\n+0_815\t2_472\t21.66\t434\t299\t11\t1640\t2049\t723\t1139\t3e-14\t73.6\n+0_815\t2_472\t20.75\t482\t301\t15\t2289\t2722\t1334\t1782\t7e-09\t55.5\n+0_816\t2_461\t52.73\t550\t239\t7\t110\t647\t135\t675\t3e-168\t 498\n+0_816\t2_366\t23.98\t221\t137\t7\t191\t401\t4\t203\t2e-05\t41.2\n+0_817\t2_83\t33.33\t288\t179\t6\t3\t286\t8\t286\t1e-42\t 145\n+0_818\t2_82\t34.76\t164\t104\t2\t2\t162\t5\t168\t9e-32\t 110\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastout/Blast0_3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastout/Blast0_3.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
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518\n+0_815\t3_446\t24.27\t754\t488\t27\t556\t1258\t469\t1190\t3e-23\t 103\n+0_815\t3_446\t23.55\t310\t192\t10\t1\t309\t1\t266\t2e-07\t51.6\n+0_816\t3_202\t66.73\t532\t172\t3\t144\t674\t175\t702\t0.0\t 665\n+0_816\t3_414\t22.13\t253\t162\t8\t197\t439\t11\t238\t5e-05\t40.4\n+0_817\t3_201\t32.71\t269\t178\t2\t3\t271\t12\t277\t3e-45\t 152\n+0_818\t3_200\t43.78\t185\t102\t1\t1\t185\t1\t183\t2e-51\t 162\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastout/Blast1_0.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastout/Blast1_0.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
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272\n+1_755\t0_794\t37.78\t135\t80\t2\t218\t349\t168\t301\t7e-21\t89.7\n+1_755\t0_794\t35.54\t121\t75\t3\t224\t343\t6\t124\t1e-13\t67.4\n+1_755\t0_116\t36.67\t90\t56\t1\t224\t313\t6\t94\t4e-11\t58.9\n+1_755\t0_139\t28.12\t192\t111\t8\t205\t372\t1\t189\t2e-06\t43.1\n+1_755\t0_404\t30.48\t105\t55\t3\t221\t309\t2\t104\t5e-06\t43.1\n+1_755\t0_87\t38.03\t71\t37\t3\t218\t286\t123\t188\t1e-05\t42.0\n+1_755\t0_525\t29.21\t89\t60\t3\t224\t312\t160\t245\t6e-04\t36.6\n+1_756\t0_739\t34.21\t152\t87\t6\t59\t203\t60\t205\t1e-11\t58.5\n+1_756\t0_743\t41.51\t53\t31\t0\t90\t142\t119\t171\t8e-06\t41.6\n+1_757\t0_740\t36.82\t201\t117\t6\t5\t197\t1\t199\t4e-36\t 124\n+1_758\t0_54\t42.76\t428\t228\t8\t1\t419\t1\t420\t1e-107\t 323\n+1_759\t0_591\t50.87\t804\t389\t4\t23\t822\t80\t881\t0.0\t 791\n+1_759\t0_174\t32.57\t786\t511\t12\t1\t779\t1\t774\t4e-125\t 396\n+1_760\t0_808\t52.38\t651\t300\t6\t2\t648\t11\t655\t0.0\t 671\n+1_760\t0_173\t47.72\t658\t315\t12\t1\t648\t1\t639\t0.0\t 550\n+1_761\t0_799\t48.33\t60\t29\t1\t4\t61\t7\t66\t1e-11\t59.7\n+1_762\t0_1\t28.95\t152\t95\t8\t56\t205\t58\t198\t5e-05\t39.7\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastout/Blast1_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastout/Blast1_1.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
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654\n+1_761\t1_348\t33.85\t130\t52\t4\t4\t128\t15\t115\t1e-14\t69.7\n+1_761\t1_298\t48.57\t70\t34\t1\t4\t71\t10\t79\t5e-14\t67.0\n+1_761\t1_298\t32.88\t73\t47\t1\t4\t74\t98\t170\t1e-05\t41.2\n+1_761\t1_150\t44.16\t77\t40\t2\t4\t78\t8\t83\t4e-13\t64.3\n+1_761\t1_155\t42.31\t78\t42\t2\t4\t79\t8\t84\t5e-13\t61.2\n+1_761\t1_75\t50.77\t65\t29\t2\t4\t65\t11\t75\t3e-12\t61.6\n+1_761\t1_300\t42.59\t54\t29\t1\t4\t55\t244\t297\t8e-08\t47.8\n+1_762\t1_762\t100.00\t391\t0\t0\t1\t391\t1\t391\t0.0\t 768\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastout/Blast1_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastout/Blast1_2.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
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358\n+1_696\t2_392\t36.89\t103\t48\t1\t1\t103\t159\t244\t4e-17\t76.6\n+1_696\t2_396\t28.57\t112\t64\t3\t1\t111\t3\t99\t2e-04\t37.0\n+1_696\t2_334\t35.06\t77\t32\t2\t1\t76\t1\t60\t2e-04\t37.0\n+1_697\t2_31\t45.41\t207\t108\t3\t6\t211\t7\t209\t2e-63\t 194\n+1_698\t2_80\t72.79\t136\t36\t1\t4\t139\t1\t135\t9e-67\t 198\n+1_699\t2_81\t62.78\t223\t83\t0\t3\t225\t2\t224\t1e-101\t 293\n+1_700\t2_82\t41.62\t185\t104\t3\t2\t183\t5\t188\t5e-44\t 142\n+1_701\t2_83\t37.86\t280\t164\t2\t4\t276\t2\t278\t1e-63\t 200\n+1_702\t2_61\t30.11\t641\t394\t17\t20\t621\t10\t635\t7e-70\t 238\n+1_712\t2_254\t50.41\t244\t114\t6\t16\t256\t2\t241\t1e-73\t 223\n+1_712\t2_352\t22.45\t147\t108\t4\t111\t253\t6\t150\t6e-04\t33.9\n+1_713\t2_255\t41.67\t432\t244\t3\t5\t435\t4\t428\t3e-117\t 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336\n+1_755\t2_334\t35.79\t95\t57\t2\t222\t313\t179\t272\t3e-12\t62.4\n+1_755\t2_334\t28.90\t173\t106\t4\t224\t382\t4\t173\t1e-11\t60.8\n+1_755\t2_392\t26.11\t180\t104\t7\t208\t378\t149\t308\t6e-08\t48.5\n+1_755\t2_447\t38.20\t89\t45\t5\t204\t291\t103\t182\t1e-06\t43.9\n+1_755\t2_21\t28.71\t101\t54\t3\t225\t309\t5\t103\t9e-05\t38.5\n+1_755\t2_396\t27.56\t127\t72\t3\t222\t332\t4\t126\t1e-04\t37.7\n+1_756\t2_6\t29.41\t255\t169\t8\t9\t260\t7\t253\t7e-20\t80.9\n+1_756\t2_426\t28.04\t107\t67\t3\t40\t142\t72\t172\t9e-04\t34.7\n+1_757\t2_5\t39.68\t189\t107\t5\t1\t185\t1\t186\t5e-41\t 136\n+1_758\t2_4\t49.29\t420\t210\t1\t1\t420\t1\t417\t4e-142\t 411\n+1_759\t2_3\t60.34\t817\t322\t2\t7\t823\t9\t823\t0.0\t1009\n+1_759\t2_203\t31.62\t718\t461\t10\t20\t727\t10\t707\t2e-120\t 381\n+1_760\t2_2\t64.55\t646\t228\t1\t3\t647\t4\t649\t0.0\t 887\n+1_760\t2_202\t45.37\t648\t330\t10\t6\t645\t2\t633\t0.0\t 536\n+1_761\t2_1\t45.99\t324\t155\t5\t1\t320\t1\t308\t6e-88\t 265\n+1_761\t2_16\t35.71\t84\t45\t2\t4\t79\t9\t91\t1e-10\t56.6\n+1_761\t2_199\t41.77\t79\t40\t4\t4\t77\t9\t86\t1e-09\t53.1\n+1_762\t2_0\t25.45\t330\t224\t8\t35\t354\t36\t353\t3e-16\t73.9\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastout/Blast1_3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastout/Blast1_3.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
| b'@@ -0,0 +1,1475 @@\n+1_2\t3_0\t26.35\t334\t218\t9\t124\t443\t115\t434\t3e-30\t 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137\n+1_746\t3_432\t29.49\t312\t181\t15\t259\t541\t284\t585\t1e-20\t91.3\n+1_747\t3_220\t21.96\t428\t305\t11\t22\t431\t46\t462\t6e-19\t84.3\n+1_749\t3_137\t43.23\t495\t238\t9\t3\t487\t2\t463\t1e-119\t 358\n+1_751\t3_96\t28.25\t315\t174\t12\t30\t333\t32\t305\t4e-21\t87.8\n+1_754\t3_651\t30.11\t269\t172\t5\t2\t263\t150\t409\t2e-28\t 107\n+1_755\t3_205\t40.44\t455\t244\t13\t10\t453\t4\t442\t8e-78\t 248\n+1_755\t3_66\t31.55\t206\t119\t5\t222\t412\t171\t369\t2e-22\t94.0\n+1_755\t3_66\t27.12\t118\t85\t1\t224\t341\t5\t121\t2e-10\t57.4\n+1_755\t3_152\t36.56\t93\t52\t3\t224\t313\t9\t97\t7e-07\t45.4\n+1_755\t3_85\t34.09\t132\t64\t8\t202\t317\t93\t217\t2e-06\t43.9\n+1_755\t3_442\t28.99\t169\t91\t10\t223\t371\t39\t198\t3e-04\t36.6\n+1_756\t3_253\t33.33\t90\t60\t0\t67\t156\t62\t151\t2e-08\t48.5\n+1_756\t3_249\t33.04\t115\t70\t4\t31\t143\t66\t175\t4e-07\t45.4\n+1_757\t3_252\t31.90\t210\t131\t6\t5\t207\t1\t205\t2e-25\t95.9\n+1_758\t3_244\t41.36\t411\t236\t4\t6\t414\t5\t412\t3e-102\t 309\n+1_759\t3_526\t45.27\t804\t434\t5\t23\t823\t51\t851\t0.0\t 704\n+1_759\t3_28\t33.70\t727\t452\t12\t13\t725\t1\t711\t6e-114\t 366\n+1_760\t3_107\t49.38\t640\t312\t5\t9\t644\t5\t636\t0.0\t 617\n+1_760\t3_29\t43.73\t638\t337\t8\t9\t640\t3\t624\t1e-179\t 524\n+1_761\t3_64\t43.28\t67\t30\t1\t3\t61\t6\t72\t8e-11\t57.0\n+1_762\t3_1\t23.73\t354\t210\t16\t24\t348\t23\t345\t9e-06\t42.0\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastout/Blast2_0.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastout/Blast2_0.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
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141\n+2_475\t0_652\t42.22\t45\t24\t1\t2\t46\t3\t45\t5e-05\t38.5\n+2_475\t0_472\t42.22\t45\t24\t1\t2\t46\t3\t45\t5e-05\t38.5\n+2_475\t0_294\t42.22\t45\t24\t1\t2\t46\t3\t45\t5e-05\t38.5\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastout/Blast2_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastout/Blast2_1.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
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182\n+2_475\t1_0\t60.30\t267\t96\t3\t1\t267\t1\t257\t2e-115\t 332\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastout/Blast2_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastout/Blast2_2.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
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879\n+2_475\t2_475\t100.00\t269\t0\t0\t1\t269\t1\t269\t0.0\t 541\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastout/Blast2_3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastout/Blast2_3.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
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121\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastout/Blast3_0.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastout/Blast3_0.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
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173\n+3_668\t0_383\t29.86\t211\t118\t6\t1\t199\t1\t193\t4e-16\t77.8\n+3_668\t0_383\t21.64\t402\t250\t15\t394\t746\t379\t764\t6e-14\t70.5\n+3_668\t0_196\t40.68\t59\t35\t0\t497\t555\t292\t350\t1e-06\t47.0\n+3_668\t0_196\t26.81\t138\t83\t4\t31\t168\t2\t121\t7e-06\t43.9\n+3_671\t0_58\t35.85\t463\t240\t12\t185\t607\t269\t714\t1e-66\t 228\n+3_671\t0_58\t41.25\t80\t46\t1\t4\t82\t2\t81\t4e-13\t67.4\n+3_672\t0_57\t44.55\t110\t58\t1\t1\t110\t1\t107\t7e-24\t85.9\n+3_673\t0_56\t79.55\t44\t9\t0\t3\t46\t4\t47\t3e-20\t72.8\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastout/Blast3_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastout/Blast3_1.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
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236\n+3_652\t1_24\t38.89\t54\t28\t1\t202\t250\t74\t127\t4e-04\t35.8\n+3_653\t1_677\t24.14\t145\t102\t3\t16\t154\t22\t164\t2e-06\t42.4\n+3_655\t1_172\t32.30\t997\t631\t13\t3\t976\t4\t979\t1e-150\t 471\n+3_655\t1_395\t34.44\t90\t53\t3\t879\t968\t140\t223\t0.001\t37.0\n+3_656\t1_468\t45.83\t48\t26\t0\t3\t50\t4\t51\t2e-10\t47.4\n+3_656\t1_682\t32.61\t46\t30\t1\t3\t48\t2\t46\t9e-04\t28.5\n+3_657\t1_467\t35.48\t341\t217\t3\t6\t345\t13\t351\t1e-66\t 212\n+3_657\t1_71\t27.74\t137\t85\t4\t185\t312\t72\t203\t2e-07\t46.2\n+3_664\t1_194\t41.18\t153\t88\t2\t8\t158\t6\t158\t2e-32\t 111\n+3_666\t1_589\t33.71\t89\t53\t2\t9\t96\t79\t162\t8e-07\t44.7\n+3_666\t1_594\t32.58\t89\t54\t2\t9\t96\t41\t124\t2e-06\t43.9\n+3_668\t1_598\t38.92\t848\t479\t12\t1\t816\t9\t849\t0.0\t 556\n+3_668\t1_333\t25.33\t679\t407\t19\t40\t633\t58\t721\t2e-41\t 158\n+3_668\t1_456\t21.89\t845\t501\t36\t5\t746\t2\t790\t5e-19\t87.0\n+3_668\t1_159\t27.10\t214\t121\t9\t347\t549\t181\t370\t2e-07\t49.3\n+3_668\t1_159\t31.48\t54\t37\t0\t36\t89\t19\t72\t9e-05\t40.4\n+3_671\t1_8\t29.15\t247\t156\t7\t351\t583\t113\t354\t3e-16\t75.9\n+3_672\t1_7\t37.88\t66\t38\t2\t1\t63\t1\t66\t7e-04\t32.0\n+3_673\t1_6\t76.60\t47\t11\t0\t1\t47\t1\t47\t4e-20\t72.4\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastout/Blast3_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastout/Blast3_2.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
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437\n+3_656\t2_330\t46.51\t43\t23\t0\t8\t50\t9\t51\t2e-08\t41.2\n+3_656\t2_53\t30.43\t46\t31\t1\t3\t48\t2\t46\t3e-04\t29.3\n+3_657\t2_329\t39.17\t337\t197\t4\t13\t344\t19\t352\t4e-69\t 218\n+3_657\t2_173\t27.61\t134\t89\t5\t185\t312\t72\t203\t2e-08\t48.9\n+3_664\t2_286\t42.68\t157\t86\t2\t7\t159\t4\t160\t1e-35\t 119\n+3_666\t2_97\t37.14\t70\t44\t0\t26\t95\t81\t150\t2e-08\t49.3\n+3_666\t2_317\t39.29\t56\t34\t0\t40\t95\t42\t97\t1e-05\t40.4\n+3_668\t2_338\t39.71\t836\t459\t17\t5\t817\t11\t824\t0.0\t 555\n+3_668\t2_351\t26.25\t701\t372\t22\t40\t633\t56\t718\t9e-40\t 152\n+3_668\t2_270\t21.77\t519\t269\t20\t242\t704\t310\t747\t4e-15\t73.6\n+3_668\t2_270\t25.81\t186\t118\t4\t5\t187\t2\t170\t2e-07\t48.9\n+3_668\t2_18\t22.22\t261\t145\t8\t320\t560\t128\t350\t1e-07\t48.9\n+3_671\t2_468\t26.94\t245\t165\t7\t351\t583\t115\t357\t1e-16\t76.6\n+3_672\t2_469\t25.23\t111\t77\t3\t1\t108\t10\t117\t1e-04\t33.5\n+3_673\t2_470\t65.96\t47\t16\t0\t1\t47\t1\t47\t4e-16\t61.2\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/blastout/Blast3_3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/blastout/Blast3_3.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
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132\n+3_661\t3_265\t32.95\t176\t100\t4\t738\t903\t541\t708\t1e-17\t83.6\n+3_661\t3_369\t26.72\t232\t153\t6\t6\t235\t21\t237\t4e-18\t85.1\n+3_661\t3_369\t28.19\t149\t84\t5\t1009\t1153\t718\t847\t2e-05\t43.5\n+3_661\t3_489\t28.09\t235\t151\t5\t3\t235\t2\t220\t7e-13\t68.2\n+3_661\t3_98\t24.83\t286\t182\t10\t15\t296\t31\t287\t2e-10\t59.7\n+3_661\t3_98\t25.55\t227\t136\t9\t1045\t1238\t864\t1090\t3e-04\t39.7\n+3_662\t3_662\t100.00\t284\t0\t0\t1\t284\t1\t284\t0.0\t 546\n+3_662\t3_622\t26.21\t206\t142\t5\t20\t217\t20\t223\t4e-07\t45.4\n+3_663\t3_663\t100.00\t204\t0\t0\t1\t204\t1\t204\t3e-144\t 400\n+3_664\t3_664\t100.00\t160\t0\t0\t1\t160\t1\t160\t3e-110\t 310\n+3_665\t3_665\t100.00\t520\t0\t0\t1\t520\t1\t520\t0.0\t1018\n+3_666\t3_666\t100.00\t321\t0\t0\t1\t321\t1\t321\t0.0\t 632\n+3_667\t3_667\t100.00\t637\t0\t0\t1\t637\t1\t637\t0.0\t1248\n+3_668\t3_668\t100.00\t822\t0\t0\t1\t822\t1\t822\t0.0\t1656\n+3_668\t3_27\t24.63\t735\t438\t16\t18\t657\t34\t747\t8e-50\t 184\n+3_668\t3_645\t22.37\t854\t418\t29\t6\t711\t3\t759\t3e-25\t 107\n+3_668\t3_404\t24.08\t191\t112\t7\t30\t220\t2\t159\t2e-06\t45.8\n+3_669\t3_669\t100.00\t359\t0\t0\t1\t359\t1\t359\t0.0\t 716\n+3_670\t3_670\t100.00\t867\t0\t0\t1\t867\t1\t867\t0.0\t1732\n+3_671\t3_671\t100.00\t609\t0\t0\t1\t609\t1\t609\t0.0\t1212\n+3_672\t3_672\t100.00\t112\t0\t0\t1\t112\t1\t112\t4e-75\t 217\n+3_673\t3_673\t100.00\t47\t0\t0\t1\t47\t1\t47\t1e-28\t94.0\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/proteomes/Mycoplasma_agalactiae.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/proteomes/Mycoplasma_agalactiae.faa Tue Oct 24 06:40:40 2017 -0400 |
| [ |
| b'@@ -0,0 +1,5438 @@\n+>gi|290752267|emb|CBH40238.1| Chromosomal replication initiator protein DnaA [Mycoplasma agalactiae]\n+MNINSPNDKEIALKSYTETFLDILRQELGDQMLYKNFFANFEIKDVSKIGHITIGTTNVTPNSQYVIRAY\n+ESSIQKSLDETFERKCTFSFVLLDSAVKKKVKRERKEAAIENIELSNREVDKTKTFENYVEGNFNKEAIR\n+IAKLIVEGEEDYNPIFIYGKSGIGKTHLLNAICNELLKKEVSVKYINANSFTRDISYFLQENDQRKLKQI\n+RNHFDNADIVMFDDFQSYGIGNKKATIELIFNILDSRINQKRTTIICSDRPIYSLQNSFDARLISRLSMG\n+LQLSIDEPQKADLLKILDYMIDINKMTPELWEDDAKNFIVKNYANSIRSLIGAVNRLRFYNSEIVKTNSR\n+YTLAIVNSILKDIQQVKEKVTPDVIIEYVAKYYKLSRSEILGKSRRKDVVLARHIAIWIVKKQLDLSLEQ\n+IGRFFGNRDHSTIINAVRKIEKETEQSDITFKRTISEISNEIFKKN\n+>gi|290752268|emb|CBH40239.1| DNA polymerase III, beta chain [Mycoplasma agalactiae]\n+MKIIINKNFLDDIIEVVSRFSDPISSLYGMRCIKITANHNFVKFEATNEITNIVKKIKVDDNKIIVEEDG\n+ELLVQANYFKNIIKKLNGFIEIKTYFNKMEIKQQDSVYTLTLNEISSFPQIDENINIKKFQINTEEFKKA\n+VKNVAFAASNGANLIYKCINFKSSGNKLNLAATDTFRLAYYTIKTNQILEDFDFSVNAKDVKELLPTDVP\n+KTVTMFYNSIKFGVEYDDTTITARITDLPYHNVEQLFNKAISETKHKITIEKSEFNNLLNKIWINSSADK\n+QNRIELKISNQEINVYTKIDELGDSNVRTAKFTLEGSPFVFDMNFNYLKDAISITEGETYILIDEKIQNI\n+VLFSKDNPNSKQIITPLRR\n+>gi|290752269|emb|CBH40240.1| Esterase/lipase [Mycoplasma agalactiae]\n+MKPIYKYNVVFKDNNNPNENIIFCHGLNSTADRFDIFKNYWTKSNYYSLQFPASNLTPVLDGDEPSVFCF\n+AKLLVEFVEKNNLKNVTLIGHSLGGGTISLAYQLRPDLFKKLVYLAPMNKPALALYDRYKKDYFPKDYEG\n+FLDLMRSLYYDISKFTSDPNWVKEQKENFDPYLYNNPDIVKLGTPDMNVFNAIEETLKIVKVPTLLILGE\n+KDGVILREECIDYFKKYVKDVETHWIPKTGHMMYLEDWDSFIKILEPFLDK\n+>gi|290752270|emb|CBH40241.1| Esterase/lipase [Mycoplasma agalactiae]\n+MNVIYKYDFVFKDNNNPDENIIFCHGFNSSPNSFKIFENYWTKSNYYALQFPGNNHTEIKEGDEATVECY\n+SDLLIKFIEDNKLKNIILIGHSMGGGTISLAYQKRPELFKKLIYLAPTNKSSQNVTEAFLRDYFPKTFDE\n+FIGFFKSLYYDVTKFTSNESWMRLVKNTFDPYDFNNPTIVGLGQYLISNYFHDKLELALQSVNVPALLIL\n+GEDDGVVDRDLCINYFKENVKGVQSLWMPKTGHMMFEEDWENFIKIVEEFINRSELASPKAL\n+>gi|290752271|emb|CBH40242.1| NADH dependent flavin oxidoreductase [Mycoplasma agalactiae]\n+MNKYEQLFRPFKLGNYSLKNRFVLSPMTLSLATKDGKVTIEEEKYSARRADCAPLLISGGTYFDDFGQLF\n+EYGYSAKSDDDIESLKKLAKAMKSKGNIAILQLAHAGKFSKASLKKYGYLYGPSYEKNHIPVEHEVFELS\n+ISQIKQIVKDYASATKRAIAAGFDGIEISMAQRLLIQTFFSSIVNKRNDEYSSDSFENRSRLCLEIVEEI\n+RKMINQYADENFIFGFRATPEETYGAELGYSIIDFIQLIEEIIKKGKINYLAIASWGHDIYLNKVRSENE\n+YKGQLVNKVIYDKFKGILPIISSGGINTPQKCLDALEYSDLVGLSSVFVADPEFVQKIENDQEDKINLNI\n+SFSQLKDLAIPESSFKGIVEMFGFCETIPTESLKTLEENSKS\n+>gi|290752272|emb|CBH40243.1| Lipoate protein ligase A [Mycoplasma agalactiae]\n+MILVEPIRNGKYIKDGAYYLATQIWALSHLKFDEIVAFPAVLDPYVQIGYFQNPEVEVNFKYLKEHNIPI\n+VRRDTGGGAIYIDSNQMGVCYLIPYKDNESILGNYEKFLEPAIKIIKELGAKNVVQSGKNDLTIDGFKVS\n+GAAMALIGDTIYGGNTYIYKIDYDAMSQVLKPNRKKIEAKGIKSVRQRIAPLSDYFNEPYKNMDIFEFKD\n+LVVKKLFNVDDLSNVKRYVLTENDWKQIDELVNAKYKNWDWNYGLSPRYEYNRDARLAIGTINFSLAVKG\n+QRIERIKISGDFFAKADINELEKSLVGIKMDYDELSNAIKQANLEKYFFNEISVDDVVRTILSEDDNE\n+>gi|290752273|emb|CBH40244.1| Lipoate protein ligase A [Mycoplasma agalactiae]\n+MILVEPIRNGKYVKDGAYWLAIQIWAMNHLRLNEKIVFPGIAAPHIQLGYFQNPEVEVNFKYLKDHNLEV\n+VRRNTGGGAIYIDDNSVNVCYLIPYDEKDNILGNYDKFYEPTIKMLKELGAKDVVQSGKNDLTIDGRKVS\n+GAAMMLNGDVIYGGNSLLYKVDYDAMVDSLKPNRKKIEAKGVKSIRQRVAPLSDYFDEPYRNLDIFEFKD\n+LVIKKLFGVDDLSKVKRYELTEEDWAQVDELVNTKYKNWDWNYGLSPRYEYNRDARLAIGTINFSLAVEG\n+QRIEKIKISGDFFAKKDITELEKALVGTKMTYENLVKAFKDADLQSYFFNEIKAEEVAKIILDEE\n+>gi|290752274|emb|CBH40245.1| Conserved hypothetical protein [Mycoplasma agalactiae]\n+MHTLNSVKELDSLINEADAIVIGIGSGMTSADGIGYSGQRFVQNFKDFIDEFKFLDMLQASVYHFDDIQN\n+YWAFHSRFMKLNYFDQPASESFLKLKEYLKGKNYHIITTNSDNSLEAADFEEDKIFYIQGKYNLLQCSKM\n+CHNTLYSNDKAVYEMIEKQKDMKVPLELIPRCPKCNNFLEVNKRLKGKGMVEDKRFFEEKKMYEDFIYRH\n+KGQKILFWEIGVGFSTPTLIKFPFWEMTKEFSNSKYVAMNNKSYRTPQEIRQRTYVWTDDIKQTINKLLE\n+VKNDFSRAN\n+>gi|290752275|emb|CBH40246.1| Glycine cleavage system H protein [Mycoplasma agalactiae]\n+MKKVVKYLVVEKLEGKDQFYLRFTPEMQDDIGTIGFIQYKNTDKKVLHKDDIFLNLEASKAILTLKMPFD\n+ATVVEINKEAMANPKLLSSPKDSENWVMILSDIDPKTLEQLEDF\n+>gi|290752276|emb|CBH40247.1| Conserved hypothetical protein [Mycoplasma agalactiae]\n+MKISILDHGLLTDQNNYEKAYKEVIELCQYVKDLNLYSFWISEQHNVNSLVISSPLILLDHLANSVSGIK\n+LGCGGIMLANYQAYNVAEQIQTLNLLHPERFIYGFGSNIGTKETIELLKPSLTSTEYQQKIIAVNEYLNN\n+KKKFDFKINPNINKPVDIVMLVTSEQSAIFAAQHKFKINYGWFLNPSK'..b'SILQNIDFNVLSNYLSEHLTTNYFEYKKSDLDYESNKEKVL\n+REKVALKTIRPKDGMMALIYGLFYNPGTNREFKANLIKMFNLSDKVSTIKVENGSGSVVTPDSDEEKLSF\n+SDFLAFFPALLSADQSKTIFKNQQINNDISYAKEHILKVMSAKGNSVGLHELDIKALEILKKFNIITNEI\n+TIDKKVIEKLNKVQSFIVQTTTSLDEKTKIVSETNKTLADLIYDFNSFDEGDESWKVWKGVIGSYGQASV\n+VNKFSLGAQAFDLLIPWINMLTYSNNATQKEALQFVNDFLKLSIDKSILEEINKLAQDENLPNFNSTNFG\n+LSIALHRPEQVTVFNESNGKFTNAKVEELASKNPKFRRYLSSQKRSLIELLGLIGASQQYSKYDKQPAET\n+GKIYAPNGIYYETIKKAVDRYFSTKEFWEIKDIVLLIARSMQINFPIELLGLSRIIINPVLRSMYPQLMT\n+SFLSTQKQSLGKINGNLAYIVSNRIGNFEEIIRDNSKKLELEAYFEQIWSNKDTSLVPLDYSEEITLALD\n+GARVNKIFNEQTKKVTIFGIDFLNLAGRVVNGIVEPKELKDIVFNDINSYYAKVNYAYLSKNNKAIYNGE\n+LPRNNVEMESLLNTIDDKYILDVNGIKFLIVGEDTTVDYIYPVIDENHLQVNTQNQALVYLNNYGFSRIM\n+AAYQGNVVKKNLLVVNGSKNSNEVVKRNITNIVDSSISDANKLKRVFSYDELDPINPERALRITTIEGMI\n+NVISSSIIALMSLFIIMVSVAIIFIIRRYIANKAKVFGILLAQGYRPIEIAISLLPFAMVTSLIGGILGY\n+SIGFRTQILLQNVFSNYWTLPKSAIPFDFFSLFFNVFIPFLGMSLLIIVVALISLRKSSIDLITGVDDAP\n+RGKLFNKIKKKFINKKNVKKRFSFTLAYSGFWKLASFGGSVLLTSIATMFGLANYKTFNNTINDTYKNRD\n+YRFKIDLESPTTEGKYYSLYNPSELKDLIYTPIGSLNEGNRETADYFKPGKSSIINPDNKANGNPGEFAP\n+HLLSQFSVNVTVDAGVAADPWLIAYNGMPDSQKAKIDKIRDLVGHQLEWTQSLDENGKLITDPNKPIIKV\n+DSNGLMSYEDASGKKYDFFKYYKSPNDKQGSFRLAHWDAANKEYIMKTIKTGDSGGRNEYRDFLVKAYQK\n+NDIVRMQHEKLLAEGKELINPITNWKESRSDSDFWLVDKSDLDRQWVNDYFIGFGGILFDKHYDETYTYI\n+SGSYNNISSKIYGYRKPEDIKSAKVKLIDKNGENLYDALYNFKIENNVYPLVVNDVFAKKHKLGIDDQID\n+FVISNRVDRYRQKLLEKIYANNPIKQADLKKQYDQNIKTKFRIVGINPTYINDELITTHSAANLLVGLPD\n+NESSFNGVLTQNANPVQVTESAGLYSPSGYWAGLDGFDVSSLDQGTVKKMFDEIFKVSDIPEKGGVLQSQ\n+HGFTKDEIAKFLDPKAEKFSDSLYESAKNSAKAHIEDFSRIYENKLFIALSNSIDSRDIEVGFVVQVGHT\n+IEQISIFIIVINFVISLIILIIMSSIIVSENERNIAIWSILGYSQKEKLMMFFGAFIPFLVAALIISIPI\n+VIAMINVFGSFLLSSSSIALLLSLKWWHVLITSGLMLIIFAVTSISVWISINKMKPVDLLKGK\n+>gi|290753083|emb|CBH41059.1| Cell division protein ftsH homolog [Mycoplasma agalactiae]\n+MENERKQKIAKIVLWTILSAVILLIITLLLWNRFKPQVRQGNFQDFVNDIVAASKSVDDNTYLAEVKIDG\n+VQDIAKYTFVENGIAKLREVSLGKGIVEKTFILPDKFTIGDKTYNIADLLKHPGADANVLSTQWSTVGLV\n+LEKPNTFARIALSVLPTLLWIIILFWLYRSMMKRSMNMIGAIGDEKNPAQKIKSDKTFKDVAGNKEAVEE\n+IKEIVDYLKNPKKYEIAGARMPHGILLGGPPGTGKTLLAKATAGEANVPFYFISASNFVEMFVGLGAKRV\n+RTVVDEARKNAPAIIFIDELDAIGRTRGSGIGGGHDEREQTLNQLLVEMDGMKDNNGILFFAATNRTDVL\n+DPALTRPGRFDRTITVGLPDVKEREEILNLHAKGKRVSPNVNLAQVAKRTPGYSGAQLENVINEAGLLAV\n+RRDSEIIERDDIDEAIDRVMAGPAKKNRVITKSELTMVAYHEAGHAVVGIKMPGANKVQKITIIPRGQAG\n+GYNLMTPEEEKYNLTKKELIAMITSFMGGRAAEEIIYGKENVSTGASDDLHKATKIARKMVTEWGMSDLG\n+PIQYEQDEGSPFLGRDYLKSAQFSAQVAHEIDIEVRNIITEAEKKAKEIIEENRELHELIKTALLEKETI\n+VAEEIEYIAKNMKLPSESKEEKAENVNLTIDDILDGKSEEKGETM\n+>gi|290753084|emb|CBH41060.1| Conserved hypothetical protein [Mycoplasma agalactiae]\n+MILLGVSGGPDSMYLLDLISSQRSDIVVATVNYNVRHDSAYDAEIVRKFCEDKDIIFECLEIDQKARFKG\n+NFEKWAREQRFSFFKKIYEKYNCETLYLAHHKDDFLESYFMQKESKRQPDFFGIKTENYIYGMKVVRPLV\n+DKVFKNEILEALHNKKIKYANDYTNDLPIYTRNRIRIWLKSLSNSQKSKIFDDIQKENNELAVLAQDTVL\n+EYEHWKKAQFSQDEFLNLSNKERLVYKFVHENYVDIKLSNRKIKSIISFILSNNRTSQYLIKNNVFIQKK\n+HGKLVF\n+>gi|290753085|emb|CBH41061.1| Peptidyl tRNA hydrolase [Mycoplasma agalactiae]\n+MKLIVGLGNPGNEYRFTRHNAGFLAIDKICEKLNISLNKEKFNGEFVVSDGFILAKPLTYMNKSGDFVYS\n+IASFYKINPSDIIVIYDDLSFSIGQAAIKIGGSSAGHKGIDSLMSKFSSNDFKRIRVGIGVNSGTTIKDY\n+VLSLFTKDEMIVVEEVLEKVADAAISLVYNDVNFVMNKFNTDNKKRVI\n+>gi|290753086|emb|CBH41062.1| Exodeoxyribonuclease V alpha chain [Mycoplasma agalactiae]\n+MFMSNESNSGAIRLKGKFLVVKWSGADNNIPRELWIFESSPERERFFIYTNKQELKSSCFYEIEVKLRAS\n+KRSKYQNSTYELLSFKIVSPDNDSDIEKMLVSNVAGLGVKGIQRIKSELGLSSIKELFDDVESAQNVLKT\n+AIYENLKAFINSFDQKDYDFFAENGLLKLYDKLRARFENNDFVSRYKNNGDPYELYVDHWIDFKLVDLFA\n+QCVNKNIEPYKIIRAFTYKILRTNFNNICTMYYDVLPFYKSLWNWYEDYRRDNSENSTLFEQSYVVSLLS\n+LLLQKRDISDDLIIESLNVMIQRGEVYFDSDSKRLSLNEVYEQELFVAKKLIKIRDSELKQQIIPLPSQK\n+LADEQKKAYASALNNPLSVITGYPGTGKSYLIAYIVETLLKDKHYKKKDIAVLTPTGRASTILAYKTGIE\n+ARTIHSFLKLSKSDEDDSFIESFEKENPIKVVVIDEFSMVSLPIMYELLKTCTSIERLILVGDRDQLPCI\n+GKGNLLEDIINSKKFPTFVLEEIHRTDKIDIFKHFIAINDNKVPKIDTENVKFIEQNGIQFLNNIVKIYE\n+EKVNKYSIDNVIILLPSYLELGQPGINEVNKRLQEWNIKRTGAKKNLSIHNNLTLFVGDRVIQTVNDYDK\n+NVFNGEIGIVEEINTDSKNTFIIVGFGQDKKVRYNRSEILENLTLAYAITVHKFQGSEASCVIFGILKNR\n+VEHMFTKKFMYTAVSRAKEELLLLGSKDLYIQKIQSRNADLKHYTNLKSLIEKEAK\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/proteomes/Mycoplasma_gallisepticum.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/proteomes/Mycoplasma_gallisepticum.faa Tue Oct 24 06:40:40 2017 -0400 |
| [ |
| b'@@ -0,0 +1,5394 @@\n+>gi|284811831|gb|AAP56351.2| ParA/Soj family protein [Mycoplasma gallisepticum str. R(low)]\n+MIISFINNKGGVLKTTLATNICGVFSKFFPKSRSVIVDLDGQGNVSATFGQHPERLKNTLIDIFRGEKDI\n+DDCVLNVFPSIDILPSNHELSFVDMDVARKEYKLSVIKNLIEKLEEMYDFVFLDTPPAMSTIVSVSMHIS\n+DMIVIPFEPDQYSILGLLRVIDTIETFRERNEDLKVLVVPTKVNARTRLHNDVLNIVKTKLSKKNIPLSK\n+NIVSFTTKSSASVGYEKLPIVLINQRSKYQEEYIEITKEIINLLKDNKNNEK\n+>gi|284811832|gb|AAP56352.2| unique hypothetical protein [Mycoplasma gallisepticum str. R(low)]\n+MKNKKAKKKERRFTDLSADLDEEVEKIDPEYEDFKEIKIEKNKDNQVIDKNDPFFYSESFEEARIQLIKD\n+KKVEVKKEEEKVQETTVKNKISEAKKEEAKDVYIDSSLEIASQEPLTKGMHFYTNSRIIRKVRECAKNKG\n+LSISRLITMILDKSIKEE\n+>gi|31541051|gb|AAP56353.1| chromosomal replication initiator protein DnaA [Mycoplasma gallisepticum str. R(low)]\n+MKTKLKRFLEEISVHFNEANSELLDAFVHSIDFVFEENDNIYIYFESPYFFNEFKNKLNHLINVENAVVF\n+NDYLSLEWKKIIKENKRVNLLNKKEADTLKEKLATLKKQEKYKINPLSKGIKEKYNFGNYLVFEFNKEAV\n+YLAKQIANKTTHSNWNPIIIEGKPGYGKSHLLQAIANERQKLFPEEKICVLSSDDFGSEFLKSVIAPDPT\n+HIESFKSKYKDYDLLMIDDVQIISNRPKTNETFFTIFNSLVDQKKTIVITLDCKIEEIQDKLTARMISRF\n+QKGINVRINQPNKNEIIQIFKQKFKENNLEKYMDDHVIEEISDFDEGDIRKIEGSVSTLVFMNQMYGSTK\n+TKDQILKSFIEKVTNRKNLILSKDPKYVFDKIKYHFNVSEDVLKSSKRKKEIVQARHICMYVLKNVYNKN\n+LSQIGKLLRKDHTTVRHGIDKVEEELENDPNLKSFLDLFKN\n+>gi|284811833|gb|AAP56354.2| ABC transporter component domain protein [Mycoplasma gallisepticum str. R(low)]\n+MRVNIFERYQSFSVKNTDKFEKASVLTRMTTDINFIHQSIQSGRTAIRGMSVFLFSLVLMFVTS\n+>gi|284811834|gb|AAP56355.2| ABC-type multidrug/protein/lipid (MdlB-like) transport system component domain protein [Mycoplasma gallisepticum str. R(low)]\n+MPVIIGGILLVYRFVIGNYKKLFKQYDQLNNLAKESIAGARVVKSYHQQDNEIQKFNRVAGFIYKNFTKI\n+ERITALISPIVLFCIYALAIAIAWIGTNNIVDGKLDIGSLASVFAYAFQMLINLLLLSVVYVTIITAKPS\n+KDRIIEVLTEKIDIKDKKYAIDTVSDYEVEYKDVSFKYVDTNPHHNLEKINIKIKKGQTIGIIGSTGSGK\n+TSIVNLLTRLYECNEGQVLLNNIQLNNYSIKALRDAIAIVPQKSILYSGTIKDNILMGGNYSDEEVEKAI\n+TQAQAAEFINKLPNKLDSIVEQKWN\n+>gi|284811835|gb|AAP56356.2| ABC-type multidrug/protein/lipid (MdlB-like) transport system component [Mycoplasma gallisepticum str. R(low)]\n+MSHKKERNAQKKKYFKELLRFIWKNKKWHLLIAFFLIIISSITLVLVNNFIKDLIDDYIAPLLREKSTGK\n+PLDFSGLIKYLSIIGLIFILGVLSNIISGQIMAKATHATLFKLRNNMYVHMQGLPIKYFDTTKHGDIMSY\n+YTNDVDTVRNLIVQIIPQSFQALVQIVVIFVFMLQISIVLTLITVLLLLPMLIFFGFFGKKTRVNFVANQ\n+VEIANLNGVIQEYIETQMISNLFNYSDQVIHKFKLANNKQAAIMKKANVLASIVFPVIFNYSNVMYIVVA\n+IASVFLFESYQNKPILGQQITLRVIVSFVALVRAFVGPLANISENVNFFARSKAGAERIYTMLDEKLEEN\n+KGKIILDYIEKYENGNWRIANKWTKQIGWVINGEIKPFQGKVEFKNVNFSYDGKKQVLKNINISGYPGEK\n+IALIGKTGSGKTTIANLISRFYNVSDGEIYFDDIPISSVDINSIRKTVGMVLQSTELFSGSIRDNIAYGN\n+KEAKLEDIIEAAKLANAHDFIMALPNEYDTYITNNGEGLSQGQKQLLTIARVSSMNPTIMVLDEATSNID\n+SRTEKVIKESMDKLMQNQTTFAIAHRLSTIKNFNQILVIQEGEIVERGNHEQLMAKKGLYESFYHSSFSD\n+EMS\n+>gi|31541055|gb|AAP56357.1| 50S ribosomal protein L34 [Mycoplasma gallisepticum str. R(low)]\n+MKRTYQPNKRKRAKTHGFRARMATASGRAVLAARKRKGRHILTVSDEAR\n+>gi|284811836|gb|AAP56358.2| ribonuclease P protein component [Mycoplasma gallisepticum str. R(low)]\n+MKRENSLKKITNFLELVKSKNKYYSNNYVIYAEKNRENKIKIGISVSKKLFAKAVIRNKIKREVRSFFDD\n+FTDWSKSLNILIKINNVNYLTNSYYLAKKEEFFDTYKKVVQKFKTI\n+>gi|31541057|gb|AAP56359.1| putative inner membrane protein translocase component YidC [Mycoplasma gallisepticum str. R(low)]\n+MNKVHSEIKTQSFNPFWNAATLKEKSRIDPNLKKALSYLWKFLKICVFLFLTVIGLWGCTQTYSEPWTVS\n+NPRIGVGLEIGYNYGVTGDYRYDLTSSNIGPYFSFANYQLSYGPFLAWFVWPASQIILPILYQTRVPLTQ\n+GIDYGLNTILAILILLFIIRLITIGITLNSTLNTERMGEVQGKIAEINAKYKNATDTQSKKMKQIEVMHI\n+YKKHKIKPAALFVQGFVTIPIFLIVYKMVSLTRPIKATILFGIWDLSVTPGTEIISDISRNWVYIFFVLL\n+VVPMQIVSQWLPQFWATRRNRNAKTTSQKGLEQLKKTRRIQWILIFVFALFPVITPSAVGLYWFLNSIFT\n+ILQSYITHVFIVKRRQRTKTISRLDQILNRELD\n+>gi|284811837|gb|AAP56360.2| dimethyladenosine transferase [Mycoplasma gallisepticum str. R(low)]\n+MINKINKFFKNNEFSPSKQRGQNFLIDQNIINNVVEAVSKINPSKVLEIGPGLGAISEQLIKRFADNYYA\n+IELDKKLFHHLNERLLKDHILHADALEIDWKSIFDNLGDNPTMVGNLPYNISSKLIKKFILSTYRCAIIM\n+VQKEMGLRLLAKINSKDYSAFSALCQYSLSVSKIIEINETAFIPQPKVRSTLLFLEKKDIAFNEGYEKFL\n+KLIFLSRRKTILNNLKNNYDPKLIIQSLVSLGFKKTSRAQELSPTQLFSLYESLSKLC\n+>gi|31541059|gb|AAP56361.1| diphosphocytidyl-2C-methyl-D-ery'..b"NYDKTNIYKYLINKKKQFVLVGNKVDEVDPTLNTG\n+EIQIKISAKNNDISDLIKYLEETSLAIFNDENKQDSIFQEEWQINLLQTALYNINLILNDPNQYHDLVIQ\n+HLNEANNSLLKVLSEYEDYNLIDEIFKNFCLGK\n+>gi|284812297|gb|AAP57070.2| DNA polymerase III subunit delta' [Mycoplasma gallisepticum str. R(low)]\n+MNLTNKYIPILLFENKGCYLKKYLEEYLINIVCTEANKPCKKCVWCSKIINNGYYDLIHVYPHNNVIRKQ\n+EIIDIQNKFNNTALESRGIKIYIIHQIEKANKESLNSLLKFLGEPKDNTIGILTTRKPYGVLDTIVSRCV\n+RYSTNSYEEKVEFKNKYKPKELELIKIMFYSYDDILQYESTKDIFKLLELIHLLELNNKKFDQIIKIRDL\n+FEKIDYYEISLVLNYLIFTGDFKRKSKLIPILNNLNLNLSKNAILISIID\n+>gi|284812298|gb|AAP57071.2| Thymidylate kinase [Mycoplasma gallisepticum str. R(low)]\n+MKKGVFIVIEGVDGSGKSSFLKRMMNEHTMINSQPIIYSREPGGCDTSEAVRELIMKLSNSDPLTEALLF\n+CASRNEHLKKKILPALNENKIAICDRFVVSSWIYQGLIKNAGYEKVKKINEYVTDGLEPDLTILFDVDPE\n+IAAKRISERSTMNHLDAYTKERINKIRNAYLERLKDNKKAKIINASLDLDTVYDQVVNIITLFVKNHELN\n+>gi|284812299|gb|AAP57072.2| Seryl-tRNA synthetase [Mycoplasma gallisepticum str. R(low)]\n+MLDKNLLKTNSKEIREQLKSRSFNLDWYDEFLRLEKQLSTLLRTIEKLNEQKNINAKKAATTESDAQRKK\n+LIQEGGLLRAELEKNEAKYNEIKEDFDYIYQRIPNLPTEDVPIGKDEKENVEMFKSRKPTFFDFKPLPHY\n+ELATKLEMIGLDVASKITGSRFSIYKKDGARLMRAIQQFCLYVNADKYEEYLPPVIVNKDSYYGSGQFPK\n+FVEDVFKLEGTNYYLASTAEVQLVNLHRNEILKEADLPKYYTASTACFRSEAGSAGKDTKGLIRQHQFYK\n+TELVKIVHPSTSKQEHEAMAKDAEKILELLELPYRRMVLCTGDMGFSATKTYDLEVWIPSENKYREISSI\n+SNCGDFQARRANIKFKDAISKKNLYVHTLNASALAHDRLFVAIVENYQQKDGSIKIPKALVKYFGKEYIK\n+>gi|31541774|gb|AAP57073.1| DNA gyrase subunit A [Mycoplasma gallisepticum str. R(low)]\n+MNPNDKNNIKELLNKTVVKEASITKELETSFMEYAMSVIVSRALPESRDGLKPVHRRVLYGAYTSGLTHD\n+KPYRKSAQIVGHVMGKYHPHSDSAIYETMVRMAQPFSLRYMLIDGHGNFGSIDGDSAAAMRYTEARLSKI\n+SAEMLRNIDKDTVDFVDNYDASEQEPIVLPSLFPNLLANGSSGIAVGMATNIPPHNLSELIGGIKHLLVN\n+ENATIEELKEFIKGPDFPTAAEILGETGINEYFNTGRGSVSVRAKSEIEELANNKSNIVITQIPYMVNKA\n+NLINKIAELVKTEQIQGIADLRDESNREGIRIVIETKRDVIPEVLLNQLYKSTQLQTNFSVAMLALVNNQ\n+PKVLNLKEALQIYIDHQFDILLRKTNFELKKAKASAHIVEGLVIATNNIDDVIETIKNAKDNEDAKNTLM\n+TKYELSDLQAKAILDMRLRSLSGLERENLQKELAKLKELIKDLEEILQNKERRIKIISDQLDEIDHKFGD\n+ERRTKICYGLNSTIDNEQLIPVETVVITRSSKGYLKRIPISAYKVQHRGGVGVKGMNTYEDDDVESLIVC\n+STHSDLLFFTNYGKVYRIRAHQVPLGSRISKGIPAINLISIEKDEKLMSLLSINDYDSGYFFFSTKKGLV\n+KRVKASEFSRIQNNGKIAIKLTENDSLFKVIKTAGDEEIYIGVSSGLLVRFKEDVVRSMGRTAQGVIGVK\n+FKNPNDEVIGLSSSHEGSLLLAVCEKGVGKMTDREEYRMTNRGSKGVITIKVTPKTGNIINTQLVNGNEE\n+LLMISSTGKIVRVPLAEVSEQGRNTSGVKLISLNEKETLQSVAIFDVEQDDSQQVGSDNPDTELSSDDSN\n+QDQDKE\n+>gi|31541775|gb|AAP57074.1| DNA gyrase subunit B [Mycoplasma gallisepticum str. R(low)]\n+MNNTKKDQYSSQSIKVLEGLSAVRKRPGMYIGSTDQKGLHHMIWEIIDNSVDEMMAGYGTTVKLTLKDNY\n+LVEVEDDGRGIPVDIHEKTNKSTVETVLTILHAGGKFDSDTYSMSGGLHGVGASVVNALSSSFKVWVNRD\n+YKIHYIEFKDGGVPLKPLEIIGTDSKKQGTRIQFVPDFSIMEQFEYDETIIADRIEQLAFLNKGIKFIFN\n+DERTDKKTKQEWLYEGGIKQYVENLNASKEPIIPQIIYGEKKTKVTLPKRNLEVTMLLEVAFQYTNGYYN\n+STYSFCNNIHTNQGGTHEEGFKNALYKIINRYALEKKFIKETDGKISKEDLSEGLTAIISIKHSEPQYQG\n+QTKDRLGNTEVREFTNSVVSELLERFFLENPEEAAKITAKAVSAMFSRKRSEAALESARKSPFESASLPG\n+KLADCTTKDMEISELYIVEGDSAGGSAKSGRDRFYQAILPLRGKVLNVEKANHEKIFKNEEIRTLITAIG\n+AGVNPEFSLDKIRYNKIIIMTDADVDGAHIRILLLTFFFRHMFPLIEKGHVYIAQPPLYRVSYNKQNKYI\n+YSDAQLEEWKNQNPNVRYELQRYKGLGEMDDVQLWETTMDPEKRTLLKVSINDAANADKTFSLLMGDEVS\n+PRRDFIEKNAKSVKNIDF\n+>gi|284812300|gb|AAP57075.2| DnaJ-like molecular chaperone [Mycoplasma gallisepticum str. R(low)]\n+MTLYELLEVDQNATLSEIKSSYKRLAKKYHPDVNKNGHDKFVQINNAYSILSDEVQREKYDFMLDHENSK\n+TFEFSADGLTYEYSGVEVWHENFTKNVSLTQQWDFNPSNYYYEEYNLYHKFDKISIDGLGAFLDFDISCA\n+FYELDTSFSLPNNLVKRLINRPDVIRYDISENELIEYLKHRYDFSSWLLLKKYFNIEAIIEVTQEEIDSQ\n+KIINIPIKIKVINLNRSFEIWHEELRNYAFIVPENTKTGDISEFFGKGNVALGWQGDLIVRFKVVPSVEK\n+RLKIFSSMLNNEKSSLWFLVPSENNKNPNTKIFNYKTYQFNN\n+>gi|284812301|gb|AAP57076.2| DNA polymerase III beta subunit DnaN [Mycoplasma gallisepticum str. R(low)]\n+MKFFTSKSSFLEAIKFSSNFSSDNNFEQLLKNLYIKIDNKECKIYSSNGQVSSIYKIEDDIDVEEEGEVI\n+VNAKKLITIIQSIVSDNFTLAKLDNQLIIRAGKMQTSLNLEEDVSYPEIEIDDSNFSVIDVDSFLFAKSI\n+KKVIHSTSFQTTKNSISSAINFQKEADDMNIWITGSDAIKLSSCYYKVNDTEDALKAKFNFSVNALSLSY\n+VAAFLKDKDQLLLKISKKSDKVVLTNNKFVLYLRVENEPFPEFKKILNANKVVSSFVVDKDLISNNLHAL\n+TGVLSLSDQGKNNADANFEILKNTLRISTNSFDIASYNSEFDISEFQGEVKDINLNPFYLQEHIKMFESK\n+DIEFKLLLQSAISGCILKVCEKNNDQFKLKFVQVLAPSSTN\n" |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/proteomes/Mycoplasma_genitalium.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/proteomes/Mycoplasma_genitalium.faa Tue Oct 24 06:40:40 2017 -0400 |
| [ |
| b'@@ -0,0 +1,3211 @@\n+>gi|84626162|gb|AAC71217.2| DNA polymerase III, beta subunit [Mycoplasma genitalium G37]\n+MKILINKSELNKILKKMNNVIISNNKIKPHHSYFLIEAKEKEINFYANNEYFSVKCNLNKNIDILEQGSL\n+IVKGKIFNDLINGIKEEIITIQEKDQTLLVKTKKTSINLNTINVNEFPRIRFNEKNDLSEFNQFKINYSL\n+LVKGIKKIFHSVSNNREISSKFNGVNFNGSNGKEIFLEASDTYKLSVFEIKQETEPFDFILESNLLSFIN\n+SFNPEEDKSIVFYYRKDNKDSFSTEMLISMDNFMISYTSVNEKFPEVNYFFEFEPETKIVVQKNELKDAL\n+QRIQTLAQNERTFLCDMQINSSELKIRAIVNNIGNSLEEISCLKFEGYKLNISFNPSSLLDHIESFESNE\n+INFDFQGNSKYFLITSKSEPELKQILVPSR\n+>gi|84626152|gb|AAC71218.2| DnaJ domain protein [Mycoplasma genitalium G37]\n+MNLYDLLELPTTASIKEIKIAYKRLAKRYHPDVNKLGSQTFVEINNAYSILSDPNQKEKYDSMLKVNDFQ\n+NRIKNLDISVRWHENFMEELELRKNWEFDFFSSDEDFFYSPFTKNKYASFLDKDVSLAFFQLYSKGKIDH\n+QLEKSLLKRRDVKEACQQNKNFIEVIKEQYNYFGWIEAKRYFNINVELELTQREIRDRDVVNLPLKIKVI\n+NNDFPNQLWYEIYKNYSFRLSWDIKNGEIAEFFNKGNRALGWKGDLIVRMKVVNKVNKRLRIFSSFFEND\n+KSKLWFLVPNDKQSNPNKGVFNYKTQHFID\n+>gi|1045671|gb|AAC71219.1| DNA gyrase, B subunit [Mycoplasma genitalium G37]\n+MEENNKANIYDSSSIKVLEGLEAVRKRPGMYIGSTGEEGLHHMIWEIVDNSIDEAMGGFASFVKLTLEDN\n+FVTRVEDDGRGIPVDIHPKTNRSTVETVFTVLHAGGKFDNDSYKVSGGLHGVGASVVNALSSSFKVWVFR\n+QNKKYFLSFSDGGKVIGDLVQEGNSEKEHGTIVEFVPDFSVMEKSDYKQTVIVSRLQQLAFLNKGIRIDF\n+VDNRKQNPQSFSWKYDGGLVEYIHHLNNEKEPLFNEVIADEKTETVKAVNRDENYTVKVEVAFQYNKTYN\n+QSIFSFCNNINTTEGGTHVEGFRNALVKIINRFAVENKFLKDSDEKINRDDVCEGLTAIISIKHPNPQYE\n+GQTKKKLGNTEVRPLVNSVVSEIFERFMLENPQEANAIIRKTLLAQEARRRSQEARELTRRKSPFDSGSL\n+PGKLADCTTRDPSISELYIVEGDSAGGTAKTGRDRYFQAILPLRGKILNVEKSNFEQIFNNAEISALVMA\n+IGCGIKPDFELEKLRYSKIVIMTDADVDGAHIRTLLLTFFFRFMYPLVEQGNIFIAQPPLYKVSYSHKDL\n+YMHTDVQLEQWKSQNPNVKFGLQRYKGLGEMDALQLWETTMDPKVRTLLKVTVEDASIADKAFSLLMGDE\n+VPPRREFIEKNARSVKNIDI\n+>gi|1045672|gb|AAC71220.1| DNA gyrase, A subunit [Mycoplasma genitalium G37]\n+MAKQQDQVDKIRENLDNSTVKSISLANELERSFMEYAMSVIVARALPDARDGLKPVHRRVLYGAYIGGMH\n+HDRPFKKSARIVGDVMSKFHPHGDMAIYDTMSRMAQDFSLRYLLIDGHGNFGSIDGDRPAAQRYTEARLS\n+KLAAELLKDIDKDTVDFIANYDGEEKEPTVLPAAFPNLLANGSSGIAVGMSTSIPSHNLSELIAGLIMLI\n+DNPQCTFQELLTVIKGPDFPTGANIIYTKGIESYFETGKGNVVIRSKVEIEQLQTRSALVVTEIPYMVNK\n+TTLIEKIVELVKAEEISGIADIRDESSREGIRLVIEVKRDTVPEVLLNQLFKSTRLQVRFPVNMLALVKG\n+APVLLNMKQALEVYLDHQIDVLVRKTKFVLNKQQERYHILSGLLIAALNIDEVVAIIKKSANNQEAINTL\n+NTKFKLDEIQAKAVLDMRLRSLSVLEVNKLQTEQKELKDSIEFCKKVLADQKLQLKIIKEELQKINDQFG\n+DERRSEILYDISEEIDDESLIKVENVVITMSTNGYLKRIGVDAYNLQHRGGVGVKGLTTYVDDSISQLLV\n+CSTHSDLLFFTDKGKVYRIRAHQIPYGFRTNKGIPAVNLIKIEKDERICSLLSVNNYDDGYFFFCTKNGI\n+VKRTSLNEFINILSNGKRAISFDDNDTLYSVIKTHGNDEIFIGSTNGFVVRFHENQLRVLSRTARGVFGI\n+SLNKGEFVNGLSTSSNGSLLLSVGQNGIGKLTSIDKYRLTKRNAKGVKTLRVTDRTGPVVTTTTVFGNED\n+LLMISSAGKIVRTSLQELSEQGKNTSGVKLIRLKDNERLERVTIFKEELEDKEMQLEDVGSKQITQ\n+>gi|1045673|gb|AAC71221.1| seryl-tRNA synthetase [Mycoplasma genitalium G37]\n+MLDPNKLRNNYDFFKKKLLERNVNEQLLNQFIQTDKLMRKNLQQLELANQKQSLLAKQVAKQKDNKKLLA\n+ESKELKQKIENLNNAYKDSQNISQDLLLNFPNIAHESVPVGKNESANLELLKEGRKPVFDFKPLPHRELC\n+EKLNLVAFDKATKISGTRFVAYTDKAAKLLRAITNLMIDLNKSKYQEWNLPVVINELSLRSTGQLPKFKD\n+DVFKLENTRYYLSPTLEVQLINLHANEIFNEEDLPKYYTATGINFRQEAGSAGKQTKGTIRLHQFQKTEL\n+VKFCKPENAINELEAMVRDAEQILKALKLPFRRLLLCTGDMGFSAEKTYDLEVWMAASNEYREVSSCSSC\n+GDFQARRAMIRYKDINNGKNSYVATLNGTALSIDRIFAAILENFQTKDGKILIPQALKKYLDFDTIK\n+>gi|1045674|gb|AAC71222.1| thymidylate kinase [Mycoplasma genitalium G37]\n+MNKGVFVVIEGVDGAGKTALIEGFKKLYPTKFLNYQLTYTREPGGTLLAEKIRQLLLNETMEPLTEAYLF\n+AAARTEHISKLIKPAIEKEQLVISDRFVFSSFAYQGLSKKIGIDTVKQINHHALRNMMPNFTFILDCNFK\n+EALQRMQKRGNDNLLDEFIKGKNDFDTVRSYYLSLVDKKNCFLINGDNKQEHLEKFIELLTRCLQQPTHY\n+>gi|1045675|gb|AAC71223.1| DNA polymerase III delta prime subunit, putative [Mycoplasma genitalium G37]\n+MLTTTHALLIIQRKGSFLKPFLDNYLTSIVCENKNGCKKCINCLEILNNKYNSLYWFDQINPFKRENALQ\n+LARIFNRERTSVNNKNIYLIEEIEKLSSNSINSLLRLVEDSPINSYGIFTTKNESLILSTFLSRVQKVVL\n+KKASKVPFKVSKNDQEIITSFFTVDEQIEAIENGSFNRFKIILDACLNKKTGTEQIYHAWQIFRDFSNSE\n+IAQLITLIINKTENIDKKSILFNCLKVLPYNPPKSTLFANLVSW\n+>gi|1045676|gb|AAC71224.1| tRNA modification GTPase TrmE [Mycoplasma genitalium G37]\n+MKSEINIFALATAPFNSALHIIRFSGPDVYEILNKITNKKITRKGMQIQRTWIVDENNKRIDDVLLFKFV\n+SPNSYTGEDLIEISCHGNMLIVNEICALLLKKGGVYAKPGEFTQRSFLNGKMSLQQASAVNKLILSPNLL\n+VKDIVLNNLAGEMDQQLEQ'..b'060|gb|AAC72485.1| ribonuclease P protein component [Mycoplasma genitalium G37]\n+MLNSRFPVSVKKSHSLRERKVFTTILQSKTRFFGTFINAYFIKNNHSTWRVAISIAKTKYKLAVQRNLIK\n+RQIRSIFQQISNNLEPWDILVIVNKGFIELTFKEKQKLFLQLLKRIKEVDAYQTSANK\n+>gi|3845061|gb|AAC72486.1| ribosomal protein L34 [Mycoplasma genitalium G37]\n+MKRTYQPSKLKRAKTHGFMARMATAQGRKVLRQRRFKNRAQLTVSSER\n+>gi|3845062|gb|AAC72487.1| ABC transporter, ATP-binding protein [Mycoplasma genitalium G37]\n+MKKGNKTVWNECIDILDNVKSPSFSANFDDYFKKSKSKPPKKNKKVLNNIKKAELKLKKKANKKQKANTL\n+YIPPFAQQAKGIVITINKMWKNVHNDDSKQEISILSDVSLQIAYGEIVIILGSSGSGKTTLLNLIGGYDS\n+ISLGSCIVANCPLEKCTSEQLLTYRKNNLGYVYQRYNLIELLSAYDNIAISQNLIPKYQRRLDIEELAEK\n+LDIKEILYKFPYEMSGGQKQRVAIARAIIKEPKLLLCDEPTGALDSNSAENIINLLQTINKTYKQTILMV\n+THDVSLTRIANRIIKISDGKIVSNQLVRPLV\n+>gi|3845063|gb|AAC72488.1| ABC transporter, permease protein [Mycoplasma genitalium G37]\n+MFSFFKQIFKSLKKFFFLLFGIIFVLFSIIFLETSIVQLSNNLVSTYTTLVSKTNSSDIVAPAILKEANP\n+VYIASLTNDSGYFSKIKIDDKKINYLFPYQENDFGSDSGQSNGSGDNQNKTIPRKGDVNEKDKLFLARKR\n+GILKAYGEANIAEKRIYKGLAVSFNNTDSFNGSDISDSITNRHIISDPQNLIYDASGNLLGYFADGLIKE\n+TISLRAGIARFPGDKGKSTGTQVKITQKQQTNNDPQKDSTVNSLYKTNNKDKVWFKSDETKADNTDISAN\n+YLFTGGNEAANWFPNLYANIPIDLEIDPGSQFWKDVNPFKEIVEEFQTQKESKDNQSFTLTFNLDISKLN\n+KLDNEQLKWLETNAKTIANNSSFGDWDLENKLKQLKKFELKINKDWLKKKVESEKDTILNSLPGFSDSDK\n+DTIFKTQNGMMVRNNNLSFQPSSNNLQLVQNQNSQASNGIADPNFSNVQTAYNKIHQSNNTPEKTLDAVY\n+AAVLDQWRSIFQEDLVKKTVDLLEKYRDHFLKATAFNNIDYSKQNIAIANNVSSAESASFLVSNKDEQRY\n+NDLSLIDGVDLKSWLFKPEQNESNPLDTIYGGQDANNGFLQKIDYEFKPSTSSGGMTASLKNTQALSPKS\n+TKFPIYPKLANIIAQAQLPEATNIPTTALDALKQWTNLDANGFNNLKEEDKRKAANNYLALLSYFTPAFQ\n+DPNELIETNRQMLEIPITVKNGVNPLILPTDQQNLVVQTPEAHGAVVSQQWLFRHNKEILPQEGEYAWKT\n+ALQTPNNFPNWLNDLPDRYKFSINGLTFAILGIGESVETGYPVLSLQSPLPNTQDEALIFVNDQAYRSIL\n+FAVPAANQENYYAFKSTDLKQHTDQDPVQFIANRLEGYLDVPRSDLAFNVKDISKFNYLTTARNYFPDLV\n+QSYLAIVSTVIAIFLIILALYLIILLIKSFIKKNQTEFSIIRAGGFSTTKFIVGMSVFAGIVAIVSSFLG\n+VLFAFLLEGQVKGIINRYWFIALPENSFNWLSFFGSFFITFFVFEFISWIAFKQLFSKPVNVLIDQGNET\n+KFSVLLHLLKHKSHTMSPLTKFRVSLIVSRFSRLFTYVGLSSVALLLIGIAGTIPQKFSAAQTSTSLNRN\n+FNYKLNLQTPTEQSGWYAIQPYSHFGVTDNNNGIKTLYNESVQANSQNEHPYKPSNLKLKNRQDQPIKAA\n+DGTELELGNLLLPSYGGAQQLNTDENFFRHASLSKWIIDFPIRVGGSNINPWEIVEKSIPKQITQLLSAS\n+SDQFLISVLTDDFFNNLNANGFLIRNPRTNQIQLDASRVLTTIDVFNPGGVKFNDSFLSFMLKVYGDFEL\n+AKQDSKLNFGIVPVDPAIEETYTYVEGPFGFQEDNLDENSPYTLTGINPESSFVNLIDGSGNSLRNLISS\n+DQEMNVIVNAGFQYANNINIGDYVYIKPKNTATRYSEKFLKAPLNNSTVAFKVVGVSTDAFGQELYINQH\n+IANNLLKLSGNQGRGIIRDVIKKTNGQSQSSDEYEIDYVKPNGYVPFNGVFSKELKPSLLNKALVLNSII\n+GVWGNFTDFGNNFQNLVRNKLDKVITSILPTDPEIINKLAQEKQIINTTSMNYESLRKELVNKYKTEWNS\n+VNLLSQNASSIFGNNIIAPVLNIDAAGTSAQIIRNNAEVLFNTVNQVDAFLLGTIIPFIFITCVVLGISM\n+LEEMKRIFISLKAIGYRDVQNLISLLTFFIPAFVLALLISIGVLAGVLIGIQAVVFNVAQVFLTNVFEFL\n+PYMVGIVLFGVTIFVIGSYFWIKLRSAELKEGF\n+>gi|3845064|gb|AAC72489.1| ABC transporter, ATP-binding protein [Mycoplasma genitalium G37]\n+MVLKTKENKKFDIYLKSSDFAVSKKASKLIKKLNKKHPKRKSLNSFEAKKYDIYFKEVCKAVTNGINNQL\n+ICNHINLKILPGEFVVILGKSGSGKTSLLSLISALDRPTSGDSFVCGTNTICCSDAKLTALRNKNVGYIF\n+QQYGLLRDLDVDDNIKLALPLKKRFNNNLEELLERLELKEHRHKKVHKLSGGQQQRVAIARALIKEPKIL\n+FGDEPTGAVNIDISKKILQFFVEYNRDKGTTIVIVTHNEKIVELAKRVIKIHDGKIIVDYLNQNPKTIEQ\n+INWV\n+>gi|3845066|gb|AAC72490.1| chromosomal replication initiator protein DnaA [Mycoplasma genitalium G37]\n+MEQFNAFKSLLKKHYEKTIGFHDKYIKDINRFVFKNNVLLILLENEFARNSLNDNSEIIHLAESLYEGIK\n+SVNFVNEQDFFFNLAKLEENSRDTLYQNSGLSKNYTFQNFVISEGNKRAYEAGVRLAETQDNEFSPLFIY\n+GETGLGKTHLLQAIGNEKFRNFPNARVKYVVSSDFAQEVVDAFYQRDKGIEKLKKNYENLDLVLIDDTQI\n+FGRKEKTLEILFNIFNNLVLNKKQIVLVSDKAPDELIDIDARMISRFKSGLLLKIEKHNLSSLCEILTVK\n+LKEKDPNIQITNEARHDAAQISGNDVRALNGIATKLLFFAKTSKQNLINTENLKEILFEEFEKFHKKSFD\n+PYLLIENVCRRFNVPMDSVLSENRKAELVRVRDVCNYLLRQKYNMQFQQIGKIFKRSHSSVLMAVKRVAK\n+MIENDSSLRDVITSLVI\n+>gi|3845067|gb|AAC72491.1| CobQ/CobB/MinD/ParA nucleotide binding domain [Mycoplasma genitalium G37]\n+MIISFVNNKGGVLKTTMATNVAGSLVKLCPERRKVILDLDGQGNVSASFGQNPERLNNTLIDILLKVPKF\n+SGSNNFIEIDDCLLSVYEGLDILPCNFELNFADIDISRKKYKASDIAEIVKQLAKRYEFVLLDTPPNMAT\n+LVSTAMSLSDVIVIPFEPDQYSMLGLMRIVETIDTFKEKNTNLKTILVPTKVNVRTRLHNEVIDLAKTKA\n+KKNNVAFSKNFVSLTSKSSAAVGYEKLPISLVSSPSKKYLNEYLEITKEILNLANYNVH\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/inputs/proteomes/Mycoplasma_hyopneumoniae.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/proteomes/Mycoplasma_hyopneumoniae.faa Tue Oct 24 06:40:40 2017 -0400 |
| [ |
| b'@@ -0,0 +1,4764 @@\n+>gi|144227417|gb|AAZ44095.2| chromosomal replication initiator protein [Mycoplasma hyopneumoniae J]\n+MQTNKNNLKVRTQQIRQQIENLLNDRMLYNNFFSTIYVLNETETEIIIDFTDLIAKQEVISRWVDTVEKA\n+IKNLEISKILTFNNTNNYTINSKESQNFSIKNKYCSFNINNVLNKFTFRNFIKSSYNFQIFSIYDAIVAN\n+SRLNYSPIFISGPSGIGKTHFINAIGNLLVEKQKKVFYINDYKFISCVSSWMQNGQNEKISEFLNWLSQV\n+DAFLFDDIQGLANKQQTSIVALEILNRFIEEDKTVIITSDKSPSLLGGFEERFITRFSSGLHIKLNKPKK\n+EDFLRIFKHKLVEEKLEKHIWTNDAFEFLSKHFRNSIRELEGALKSIVFYIQTNKNKFENEIYFDKKKMF\n+EIFVEKYEIEQTITPDLIIEVVSKYYGVSILDIKSEKRGKNIVHARDIAIWLIKNILDLTHNSVGTFFNN\n+RRHSTIISTLKKIDTLKQSNNNELEIALNHIYKQLNWSFKQRK\n+>gi|71851488|gb|AAZ44096.1| DNA polymerase III beta subunit [Mycoplasma hyopneumoniae J]\n+MKFTIEKKIIEWQIERMQSAILNNINSPLSSFFLKLTRSGLFIISTNSELSYKVFINKKDLIEIHDVGSC\n+LIDGVFLRDVIRKSDKQLSFHLIGSELKVFWEDALFSKTTRDSSFFPEINFEQKGIKLTVNAKNFKRAIK\n+NTAFATTNNPSQPILSAINLRSEAGFLHFSATDTSRFASEKIEISNKSRINISVSAKNLKDFIPPELDKD\n+IELNIESSKISYIYDNLTIQSRIFTIEYKDISNILPKDSEILYSLTINKRDILDLIDKTTIITPGKDNVI\n+NLSLSKNALKGYISQYDSGQSNVQTKNVLDFRFNPRFASDFRFDPELAQVNINYRYLKDAISVFDKVIDI\n+HINEKMNKMLIVSPEKPEICQLVGLVLV\n+>gi|144227418|gb|AAZ44097.2| glucose inhibited division protein A [Mycoplasma hyopneumoniae J]\n+MSKKSKNSSIEFDAIVVGGGHAGIEAVYALLKKKLKVVLITLDKKKLASMPCNPAIGGPAKGIITREIDA\n+LGGVQGKFSDLAMIQIKYLNESKGPAVLAIRAQIDKEKYSKLILKDLKKQENLLIIEDLVSELLVEKNRV\n+FGLKTAKKQVFFSKTVIITTGTYMDSKVLRGSLAIPSGPDGQQTSNLLSNNLKRLGFELQRLKTGTPPRI\n+FTSSIDFSKVEKEVLPVYNINFSFQSKHKIKKQISCYLTYTTAKTHDIINKNLGKSSMYSGLISGVGPRY\n+CPSIEDKIVRFSEKPRHQIFFEPETKKQDIMYINGLSTSMPEDVQLEMVKTIPGLENAKIAKFGYAIEYD\n+ALNPLELKKSLETKKVKGLFMAGQINGTSGYEEAAAQGLVAGINAGQFVLGKKPVEILRNDGYIGVLIDD\n+LVTKGTKEPYRMLTSRAEYRLILRNDNADIRMAKYALKSGLISKKEYLKIKAKYAKIDRKILELSKEFVS\n+PKDELAKKYNLEKRISKLKLISWPNVNFKDILPDFEFGYELTVMARLKGYIQKQNSEAQKMIRLEKLLIP\n+GDLNYEKVANLSSEALDKFQKVRPKTIGEASRISGVNPADIQMLLFHIKVLKMQKVSKI\n+>gi|144227419|gb|AAZ44098.2| conserved hypothetical protein [Mycoplasma hyopneumoniae J]\n+MKISIISFGSSPREWLGLYKKEINKIKQFKYQIEFINLSEHSQENIELKKMLETKDILQKIPKNSSCYLF\n+TERGKTVTSKEFSQLLNFSNICFIIGGSYGVDEKLIAKSRPDIGFLSFGKLTFAHKIFKLIVLEQIYRGF\n+SIKFNRKYHHAD\n+>gi|71851491|gb|AAZ44099.1| putative MgpA like-protein [Mycoplasma hyopneumoniae J]\n+MKRKNYEKIIQNIENHDNIFIFHHIRPDGDCLGAQQGFGYAIAKRFPKKKVFFIGDNENIFNFLNFHFDN\n+ENLIQDEFFQNSLAITVDTADIKRIKKLDFFLNSNFKTRIKIDHHPDIFEEIYNEKWVDPTFSAASEMIG\n+YLLMEENWEINSEISKFIYLGILTDSGRFLFPSTTSRTFQVAAFLMKFNFDFAKLNWFLSNRTEQEVAFC\n+AEVLANYKKKDKVLWYFVSKEIQNKFKLRNDQLSAVNILANIGDARIWLFLIEMENGIRVRIRSNGPKVN\n+EIASEYGGGGHEYAAGINLEKSEKTKEISQEIIEKLVIQVKEFEQNE\n+>gi|144227420|gb|AAZ44100.2| putative DHH family phosphoesterase [Mycoplasma hyopneumoniae J]\n+MSNIKIKEIIKLIENHDTIVIFHHIRPDGDCIGAQLGLKNLILDNFKNKKVFAVGNHKGSFSFLNAKTDS\n+IPDKLILKNSLAIIVDANFKNRIESVFLFDQFKFKTILRIDHHPNEDDFEQIYRWVDPSYVATCEQIADL\n+AYKAKWKISRKSATFIYLGIYTDSGRFLYKNTSARTHFLTGILFRTGFNFALIHEKLNQKKLSDIDFDSY\n+IFSVKKIYKNVIFYTLSMEEQKKLNKNPSNSVRPNLLANIENFRIWLCLVQEKENSWRVEFRSSGPNVQK\n+VAQNWGGGGHLNASGAIIESLDKLDLLIKDCQAEYESWFSQLK\n+>gi|144227421|gb|AAZ44101.2| hypothetical protein MHJ_0007 [Mycoplasma hyopneumoniae J]\n+MEGINITNFLKYLFAYYYIDTGEREVYRTWVQKILWFTHWKFYRMYQIPFFSENFQSYKYGPISWTVLQT\n+QFFGIESFKNSQYNIDEILDFHQNNLVDEFKNRLKEDFLNDFNEDFGETFDENQIKGDLDLRWSCFVFVF\n+EKLKKFRPKDLINLSHSQKSFKIAAKNPHSKVIFNETILDDEEISILES\n+>gi|71851494|gb|AAZ44102.1| cell division protein ftsY [Mycoplasma hyopneumoniae J]\n+MSFFRKIREKIFGTKQEKPANLDKYVAGLTKSRLSFFKQIVQLQKKHIKIDENFFEELEEILIMSDISPN\n+FVRTIIDSLKAEVRHHNLNNPDLIPEIIMDKMYTIYSNRSVVNTNLNIKDGRINVFLISGVNGSGKTTSI\n+AKVARKFIIEGKKVLIIAADTFRAAAVEQLEIWANRVGALILKPEANEKDPGSVVFRGLDFAIKEKTDLV\n+LIDTAGRLQNNVNLMQELKKINKIISQKVPNAPHESLLVIDATTGQNGVSQAANFAKITPVSGIILTKMD\n+GTSKGGIIFSIKDQLDISVKLVGLGEAMDDLQPFDLDLFIFAITKEVKNQYQV\n+>gi|144227422|gb|AAZ44103.2| conserved hypothetical protein [Mycoplasma hyopneumoniae J]\n+MAKISFFALGGQDENGKNCYILEIDDNIFIINSGAKIPLDSSVGVDTIIADFTYLEENQHKIRGVFITDA\n+KNESFSALPWLIMKLKKIKIYSSFFTKALIIERIHKYRLSESAFEVIPITSELKINEKISVSPFPVAGSM\n+PGTIGFCFHTEDGGIVFMANYVVGNLGVYGETNFELIKKISQNPKGILMFISDSGKSNLPGKAINKLFAK\n+NFLENFFLKADKNSRIVVSAYDEEMVSIQEIIDLSIKFNRQITAYGKKYDKLYDMIYKLDKLTTNKLKKL\n+'..b'FLTKKFFEKNKNKLVIEVLLSLWRIEPFKIKTNTTRRYIQYLSIKNVENFLKMFENELNYL\n+LENRAQAFKFIEKIAKIKEEYQILNKNFYNLYLKTELKPNIEQEKLNEKLKLSIPYPETKFENLKFSQTY\n+AQIALQTIKNDIKNVINHHNSLINSFDSDPYKIKIFITGYNCFLDLIKRSDNFRWLSSLQIYEIYFKFEQ\n+WLIKLLNQKALENILGTQNFFNNTFAEEFWGFWKQNSQQKILEERNKKAQKHFKVKKINSFHKENPYYQN\n+LKTNSKTLLRANILWQHEVIKMEKKLRNKNFQNSFFIKRIWVSSIENKLKKLKEKISKVEYENHFIFLKD\n+ALSDLKNFFYLKNLKKIDVFLKKNQFFIFCFDNKINFDILYKKYGVLTNDDLFFLETKKMQMGNYSRFLF\n+DEYSFLLETNYKQKLFQHFFNNGENSAQLFIYSRRTIKPIRDFSIIFIENGTLVEYIREIDLPLTPKTSF\n+GKFFYQNGTFERTNLPLLETQLYKQLQNEVFQNNSGGIKNNFESFINSWIPIKEFKLEFDSENKKYSLKK\n+DILVIDL\n+>gi|71852146|gb|AAZ44754.1| valyl-tRNA synthetase [Mycoplasma hyopneumoniae J]\n+MKNKYDFKLVEEKRNEKWQKKGFFIAPKQTKKPFSIISPPPNVTGQLHLGHSWNAFIQDSLVRYHKLQGF\n+DVLLLPSVDHAGIATQVKVEEDLAKKGIKKSDLKREEFIKKCYHWKEKQYLKIKEQWDKLGICYDFSKER\n+FTLDQDAQIAVSDFFIKLWEKNLIYRGQKAINWDIKLQTAISNIEVINKPVEQKMYYLKYFLENSNEFLT\n+VATTRIETISSDVALAINPKDKRYLHLVGKKVVHPLTKKLIIIIADSNVSSDFGSGIMKVSAHSILDFEI\n+MEKHNLESKDCIDNYGNLNHEVPEFQGQNRFFARDLIAKKLEKEGFLAKIETVISNVGFSQRSDEIVEIL\n+KKPQWFVKMDELAKSLISHLNSKDKIKFYPKNFEKNLRKWFEKIHDWTISRQLWWGHRIPVWCKNDEFKV\n+QIDSPGQGWIQDEDVLDTWFSSGISAFAFLGWPQNFDLIKSYFPTSLLVTGWDILFFWVARMYFSSLFIM\n+KQKPFEKVLLHGLIRDEIGRKMSKSLGNGLDPMEIIEKYGSDTLRQALIFNSSPGKDIKFNIEKLNTAWN\n+LNNKIWNIAKYIADLDTFFAKPDLIDLWMENKIYILKRQIVKNIKKYNFSVIGTEINNFIYGDFSSRYIE\n+LIKTRKNGFYARKLLRKVLIILHPFLPFLTDFLMEKIFKMEILEQKMPRIRQFKENQKVENILEIIDNLR\n+TYREKFQISKKIILEYCIINDKFSNAEIDIINKLTFGKWLENKELVIKTKNFEIAIKVPEELKKEQKGRE\n+LKEIQFLKSEILRAEKILTNKGFLEKAPREKIDLERTKLEKLKEKLVFYEKK\n+>gi|144227749|gb|AAZ44755.2| hypothetical protein MHJ_0672 [Mycoplasma hyopneumoniae J]\n+MKKLKIYKNLNYFLPSFVFLGGAFFVLVSCGSTHFGLNISRESQTGIENAKKLKKIVNSPNLIELSPENN\n+EKIYEDKDAKFFLFDLNSAVNGGKNLELMPEFTTKFSPKTEITYLNFINRYYNTRQLQQKKKSLNQDSNS\n+IYIPHVDEKFKDFWYVFMIPTSIGFSALELNGKKTVIDREKTKLPSTLIPYSSVEVKILKKGIISADKKN\n+YLQINVNQMINSFAFREKKSNEPNSSEINVFGFQDNKAYPNYKLIFDSLDSSKKIIKFKLHRKNDNLHEE\n+RSAKNKLNSYISVMNFIYKAKEYKQNLNPDDFFEKNTEQKDKNSEYPFVRFYTQTFIVPFEGKEEVFDSD\n+FSILIEKSE\n+>gi|144227750|gb|AAZ44756.2| hypothetical protein MHJ_0673 [Mycoplasma hyopneumoniae J]\n+MKNKITPCIWSLISNTHLRKAESLEILIRALLLNNEEINQNFKNKWLKIYKNKNWKPIGDLNEHLKLAAQ\n+LGVTKTDILTPGQQKINILAKLVNSGIIKIREYISIILFNLVSFINYEYRHIFKMTLELLKKQNNSPVSV\n+DEIFQNFNFGEPVCAEFNIKLLRYNLKQKDHIFYILISGVFFEVLSSRGKNQQYNINFFKIKLYDHWYSR\n+IDELIKRCNNQLESYNFEKASLIRLDSEKWSNYLTQNSQANYDYIVDVLMQKESNNLDEKNDNTINFKAS\n+INHLENQVQKNLENSLQETQINQDISTTISNNPEKVDIELEAILENSQENKVDLSELPANFNDKDQAESH\n+QISLENADLTSTNSVEKLEIEEKIQEKQSDIRIISNNLEQNCCPEQNVVEKEIEKTYEDNIEKNSFYSNF\n+YQDQFERDFNKISEPSGEKNLQDNAQSEICAAEKCCNHIQLEKENLEHIDSSKQEKVVKINSNYLNKGEK\n+NNSNTNKKVPSLPLLYQAKQEMQREISKYPISKSVNSKEHYYNYFIHKINKLFNFSLENMLNKTNFKQNF\n+FNILDFHKKNHEIILKPKKTIIKSGKNLLLISPSANLIYSKIKNELCKTEISEKNYEIVTFFDDYNPESF\n+IGYNDFVLGSKEKLNFIPGPFARILHKAYWNPEKKYCLILENIDNDAAKITLAPLKPLFIRGENGESLLG\n+ISQFDLSFYIFSHPEEKNFIPGNLTIIGTVNSNLDRDFVDLYPDFLENWEIKYLERDNLYSHITKYQICD\n+TGLSWKHFSEKLNSLLESENLNNKWFLPNQIETKILENPRIFVDKVLFSLWNFTSPEKRKIIFRSNSYSV\n+MVKEFLETKGSKRLNIFKFDYEKIKNI\n+>gi|71852149|gb|AAZ44757.1| conserved hypothetical protein [Mycoplasma hyopneumoniae J]\n+MKNRKIRPKAFDYFQSQNNQNKKTFKFKGFFKFLKIFFYTIIFGISLTGCIQSMVVKTSYNPGEALEFYN\n+SKEEITPNYTIFRESKNKDLPGIDIVTKNNNFLVSADNKKVNQEKILNALRKQIKNENAEFGEFSSLIMF\n+QKGENEFEYLKGDKNNEFIFFSSSENSIEQKTNWTEIKIPSPKYFSLKSDKQYFEKLRDVKSLPINTYSF\n+DKSSSENAAISEKIDSYFFNLDNKIPPVNRSYAIFARDVFQVIYNKLILLPQFSQGKLEKAIAEFEQKSG\n+KDVSPETEKILSGYANLVKKLVFPTNFSRIDIQNKTYSWNNNDESAAKNIAFQNKIPAFPIVSWAESWKL\n+GPFYAIFVYPLSKIILWVTASQSLYEWSGWITILSILAVVVFTKIISFIFRFKTIFGQNKQMELQLKKAK\n+IDAKYENYKKNKVMQQRHRQEIVDLYKKNNFSPFSPFSQILVTMPIFIAVWRALQGIPSFKVTYFLGLEL\n+AATSYQKLFEGYWIYLPIIIVTVLVQALQQIIPKILNKKKSNRIMNVQENETLKKQQKTQRIVSIIFIFF\n+GVIFQASLQIYWIIGGIWEILQTLGIFYLQKSNFYREKMRPWLERKKWV\n+>gi|71852150|gb|AAZ44758.1| ribonuclease P protein component [Mycoplasma hyopneumoniae J]\n+MQKIRSIKKNWEFQAIINKKNQIVTNYLIFYYVKSDFFEIGISVPKKFANAVKRNYYKRQIKNALYILWK\n+KGEIFLNFRVVLIARKNFLPLSFETKYQKLAKIFKELKRNEK\n+>gi|71852151|gb|AAZ44759.1| 50S ribosomal protein L34 [Mycoplasma hyopneumoniae J]\n+MKRTYQPNKRKHLKTHGFRARMSTADGRKILAARRAKGRKRLTVSDK\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/results/Orthogroups.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results/Orthogroups.csv Tue Oct 24 06:40:40 2017 -0400 |
| b |
| b'@@ -0,0 +1,537 @@\n+\tMycoplasma_agalactiae\tMycoplasma_gallisepticum\tMycoplasma_genitalium\tMycoplasma_hyopneumoniae\r\n+OG0000000\t\tgi|284811953|gb|ADB96857.1|, gi|284811954|gb|ADB96858.1|, gi|284811955|gb|AAP56548.2|, gi|284811956|gb|ADB96859.1|, gi|284811957|gb|ADB96860.1|, gi|284811958|gb|ADB96861.1|, gi|284811959|gb|ADB96862.1|, gi|284811960|gb|ADB96863.1|, gi|284811961|gb|ADB96864.1|, gi|284811962|gb|ADB96865.1|, gi|284812039|gb|AAP56686.2|, gi|284812040|gb|ADB96873.1|, gi|284812041|gb|ADB96874.1|, gi|284812042|gb|ADB96875.1|, gi|284812103|gb|ADB96879.1|, gi|284812104|gb|ADB96880.1|, gi|284812105|gb|AAP56776.2|, gi|284812107|gb|ADB96881.1|, gi|284812108|gb|ADB96882.1|, gi|284812128|gb|AAP56805.2|, gi|284812129|gb|AAP56806.2|, gi|284812217|gb|ADB96891.1|, gi|284812218|gb|ADB96892.1|, gi|284812219|gb|AAP56940.2|, gi|31541243|gb|AAP56545.1|, gi|31541245|gb|AAP56547.1|, gi|31541247|gb|AAP56549.1|, gi|31541248|gb|AAP56550.1|, gi|31541249|gb|AAP56551.1|, gi|31541250|gb|AAP56552.1|, gi|31541251|gb|AAP56553.1|, gi|31541252|gb|AAP56554.1|, gi|31541253|gb|AAP56555.1|, gi|31541386|gb|AAP56687.1|, gi|31541387|gb|AAP56688.1|, gi|31541388|gb|AAP56689.1|, gi|31541389|gb|AAP56690.1|, gi|31541390|gb|AAP56691.1|, gi|31541391|gb|AAP56692.1|, gi|31541392|gb|AAP56693.1|, gi|31541393|gb|AAP56694.1|, gi|31541394|gb|AAP56695.1|, gi|31541395|gb|AAP56696.1|, gi|31541396|gb|AAP56697.1|, gi|31541398|gb|AAP56699.1|, gi|31541472|gb|AAP56773.1|, gi|31541473|gb|AAP56774.1|, gi|31541474|gb|AAP56775.1|, gi|31541478|gb|AAP56779.1|, gi|31541641|gb|AAP56941.1|, gi|31541642|gb|AAP56942.1|, gi|31541643|gb|AAP56943.1|, gi|31541644|gb|AAP56944.1|, gi|31541645|gb|AAP56945.1|, gi|31541646|gb|AAP56946.1|, gi|31541647|gb|AAP56947.1|\t\t\r\n+OG0000001\tgi|290752501|emb|CBH40473.1|, gi|290752503|emb|CBH40475.1|, gi|290752692|emb|CBH40666.1|, gi|290752693|emb|CBH40667.1|, gi|290752812|emb|CBH40787.1|, gi|290752813|emb|CBH40788.1|, gi|290752814|emb|CBH40789.1|, gi|290752815|emb|CBH40790.1|, gi|290752816|emb|CBH40791.1|, gi|290752817|emb|CBH40792.1|, gi|290752818|emb|CBH40793.1|, gi|290753029|emb|CBH41005.1|, gi|290753030|emb|CBH41006.1|, gi|290753031|emb|CBH41007.1|, gi|290753032|emb|CBH41008.1|, gi|290753033|emb|CBH41009.1|, gi|290753034|emb|CBH41010.1|, gi|290753035|emb|CBH41011.1|, gi|290753036|emb|CBH41012.1|, gi|290753037|emb|CBH41013.1|, gi|290753040|emb|CBH41016.1|, gi|290753041|emb|CBH41017.1|, gi|290753042|emb|CBH41018.1|, gi|290753043|emb|CBH41019.1|, gi|290753044|emb|CBH41020.1|, gi|290753045|emb|CBH41021.1|, gi|290753046|emb|CBH41022.1|\t\t\t\r\n+OG0000002\tgi|290752269|emb|CBH40240.1|, gi|290752270|emb|CBH40241.1|, gi|290752414|emb|CBH40385.1|, gi|290752490|emb|CBH40462.1|, gi|290752766|emb|CBH40741.1|\tgi|31541260|gb|AAP56562.1|, gi|31541382|gb|AAP56683.1|\tgi|1046010|gb|AAC71532.1|, gi|3844907|gb|AAC71551.1|, gi|3844927|gb|AAC71569.1|\tgi|144227478|gb|AAZ44221.2|\r\n+OG0000003\tgi|290753066|emb|CBH41042.1|\tgi|284811924|gb|AAP56500.2|, gi|284811927|gb|ADB96855.1|, gi|284811928|gb|ADB96856.1|, gi|284812192|gb|AAP56901.2|, gi|31541553|gb|AAP56853.1|\tgi|1046012|gb|AAC71534.1|, gi|3844628|gb|AAC71235.1|, gi|3844797|gb|AAC71418.1|, gi|3844975|gb|AAC71613.1|\tgi|71851550|gb|AAZ44158.1|\r\n+OG0000004\tgi|290752526|emb|CBH40498.1|, gi|290753081|emb|CBH41057.1|\tgi|31541070|gb|AAP56372.1|, gi|31541268|gb|AAP56569.1|\tgi|1045740|gb|AAC71283.1|, gi|1045987|gb|AAC71511.1|, gi|3845062|gb|AAC72487.1|, gi|3845064|gb|AAC72489.1|\tgi|144227640|gb|AAZ44535.2|, gi|71851837|gb|AAZ44445.1|\r\n+OG0000005\tgi|290752591|emb|CBH40563.1|, gi|290752592|emb|CBH40564.1|, gi|290752893|emb|CBH40868.1|, gi|290752894|emb|CBH40869.1|\tgi|284811835|gb|AAP56356.2|, gi|284812058|gb|AAP56715.2|, gi|31541415|gb|AAP56716.1|\tgi|1045683|gb|AAC71230.1|, gi|1045684|gb|AAC71231.1|\t\r\n+OG0000006\t\tgi|31541304|gb|AAP56605.1|\t\tgi|71851504|gb|AAZ44112.1|, gi|71851505|gb|AAZ44113.1|, gi|71851506|gb|AAZ44114.1|, gi|71851779|gb|AAZ44387.1|, gi|71851788|gb|AAZ44396.1|, gi|71851789|gb|AAZ44397.1|, gi|71851814|gb|AAZ44422.1|, gi|71851859|gb|AA'..b'\tgi|284811949|gb|AAP56536.2|\tgi|1045973|gb|AAC71500.1|\t\r\n+OG0000478\t\tgi|284811950|gb|AAP56538.2|\tgi|1045972|gb|AAC71499.1|\t\r\n+OG0000479\t\tgi|31541239|gb|AAP56541.1|\tgi|3844896|gb|AAC71541.1|\t\r\n+OG0000480\t\tgi|284811951|gb|AAP56544.2|\t\tgi|144227642|gb|AAZ44540.2|\r\n+OG0000481\t\tgi|284811972|gb|AAP56572.2|\tgi|1045980|gb|AAC71506.1|\t\r\n+OG0000482\t\tgi|31541272|gb|AAP56573.1|\tgi|1045981|gb|AAC71507.1|\t\r\n+OG0000483\t\tgi|284811973|gb|AAP56574.2|\tgi|1045982|gb|AAC71508.1|\t\r\n+OG0000484\t\tgi|284811978|gb|AAP56579.2|\tgi|3845040|gb|AAC72467.1|\t\r\n+OG0000485\t\tgi|31541293|gb|AAP56594.1|\tgi|1045977|gb|AAC71503.1|\t\r\n+OG0000486\t\tgi|284811990|gb|AAP56599.2|\t\tgi|144227563|gb|AAZ44390.2|\r\n+OG0000487\t\tgi|284811995|gb|AAP56607.2|\t\tgi|144227427|gb|AAZ44116.2|\r\n+OG0000488\t\tgi|284812002|gb|AAP56617.2|\tgi|3844925|gb|AAC71567.1|\t\r\n+OG0000489\t\tgi|284812013|gb|AAP56637.2|\tgi|3845048|gb|AAC72474.1|\t\r\n+OG0000490\t\tgi|31541356|gb|AAP56657.1|\tgi|3844990|gb|AAC71626.1|\t\r\n+OG0000491\t\tgi|31541362|gb|AAP56663.1|\t\tgi|71851833|gb|AAZ44441.1|\r\n+OG0000492\t\tgi|284812025|gb|AAP56664.2|\tgi|3844809|gb|AAC71429.1|\t\r\n+OG0000493\t\tgi|31541364|gb|AAP56665.1|\tgi|84626132|gb|ABC59631.1|\t\r\n+OG0000494\t\tgi|31541370|gb|AAP56671.1|\tgi|3844818|gb|AAC71437.1|\t\r\n+OG0000495\t\tgi|31541380|gb|AAP56681.1|\tgi|1045963|gb|AAC71491.1|\t\r\n+OG0000496\t\tgi|284812060|gb|AAP56718.2|\tgi|3844837|gb|AAC71454.1|\t\r\n+OG0000497\t\tgi|284812061|gb|AAP56721.2|\tgi|3844840|gb|AAC71457.1|\t\r\n+OG0000498\t\tgi|284812062|gb|AAP56722.2|\tgi|3844841|gb|AAC71458.1|\t\r\n+OG0000499\t\tgi|284812074|gb|AAP56734.2|\tgi|3844846|gb|AAC71463.1|\t\r\n+OG0000500\t\tgi|284812077|gb|AAP56738.2|\tgi|1045939|gb|AAC71468.1|\t\r\n+OG0000501\t\tgi|31541448|gb|AAP56749.1|\tgi|3844826|gb|AAC71444.1|\t\r\n+OG0000502\t\tgi|284812091|gb|AAP56756.2|\tgi|3844811|gb|AAC71430.1|\t\r\n+OG0000503\t\tgi|31541465|gb|AAP56766.1|\t\tgi|144227651|gb|AAZ44558.2|\r\n+OG0000504\t\tgi|31541498|gb|AAP56798.1|\tgi|3844971|gb|AAC71609.1|\t\r\n+OG0000505\t\tgi|284812125|gb|AAP56801.2|\tgi|3844978|gb|AAC71616.1|\t\r\n+OG0000506\t\tgi|31541512|gb|AAP56812.1|\tgi|3844689|gb|AAC71319.1|\t\r\n+OG0000507\t\tgi|284812140|gb|AAP56821.2|\tgi|3844721|gb|AAC71348.1|\t\r\n+OG0000508\t\tgi|284812145|gb|AAP56827.2|\tgi|84626131|gb|AAC71620.2|\t\r\n+OG0000509\t\tgi|31541528|gb|AAP56828.1|\tgi|3844984|gb|AAC71621.1|\t\r\n+OG0000510\t\tgi|31541549|gb|AAP56849.1|\tgi|3844959|gb|AAC71598.1|\t\r\n+OG0000511\t\tgi|31541558|gb|AAP56858.1|\tgi|3844638|gb|AAC71244.1|\t\r\n+OG0000512\t\tgi|284812164|gb|AAP56866.2|\tgi|3844898|gb|AAC71543.1|\t\r\n+OG0000513\t\tgi|284812171|gb|AAP56875.2|\tgi|84626128|gb|AAC71502.2|\t\r\n+OG0000514\t\tgi|284812173|gb|AAP56879.2|\tgi|3845020|gb|AAC72448.1|\t\r\n+OG0000515\t\tgi|31541590|gb|AAP56890.1|\tgi|3844885|gb|AAC71528.1|\t\r\n+OG0000516\t\tgi|31541595|gb|AAP56895.1|\tgi|3844719|gb|AAC71346.1|\t\r\n+OG0000517\t\tgi|284812188|gb|AAP56896.2|\tgi|3844718|gb|AAC71345.1|\t\r\n+OG0000518\t\tgi|284812202|gb|AAP56917.2|\tgi|3844893|gb|AAC71538.1|\t\r\n+OG0000519\t\tgi|284812208|gb|AAP56924.2|\tgi|1045731|gb|AAC71274.1|\t\r\n+OG0000520\t\tgi|284812210|gb|AAP56926.2|\tgi|3844778|gb|AAC71401.1|\t\r\n+OG0000521\t\tgi|31541648|gb|AAP56948.1|\tgi|1045712|gb|AAC71256.1|\t\r\n+OG0000522\t\tgi|31541655|gb|AAP56955.1|\tgi|3844989|gb|AAC71625.1|\t\r\n+OG0000523\t\tgi|284812225|gb|AAP56960.2|\tgi|3844682|gb|AAC71313.1|\t\r\n+OG0000524\t\tgi|284812227|gb|AAP56967.2|\tgi|3844647|gb|AAC71253.1|\t\r\n+OG0000525\t\tgi|284812245|gb|AAP56998.2|\tgi|1045728|gb|AAC71271.1|\t\r\n+OG0000526\t\tgi|284812254|gb|AAP57010.2|\tgi|3844631|gb|AAC71238.1|\t\r\n+OG0000527\t\tgi|31541720|gb|AAP57020.1|\t\tgi|144227662|gb|AAZ44577.2|\r\n+OG0000528\t\tgi|284812276|gb|AAP57047.2|, gi|284812287|gb|AAP57056.2|\t\t\r\n+OG0000529\t\tgi|284812281|gb|AAP57051.2|\tgi|3845001|gb|AAC71636.1|\t\r\n+OG0000530\t\tgi|284812282|gb|AAP57052.2|\tgi|84626126|gb|AAC71234.2|\t\r\n+OG0000531\t\tgi|31541763|gb|AAP57062.1|\tgi|84626158|gb|AAC72481.2|\t\r\n+OG0000532\t\tgi|284812300|gb|AAP57075.2|\tgi|84626152|gb|AAC71218.2|\t\r\n+OG0000533\t\t\tgi|84626147|gb|AAC71280.2|\tgi|71851703|gb|AAZ44311.1|\r\n+OG0000534\t\t\tgi|3844705|gb|AAC71333.1|\tgi|71851627|gb|AAZ44235.1|\r\n+OG0000535\t\t\tgi|3844873|gb|AAC71515.1|\tgi|71851777|gb|AAZ44385.1|\r\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/results/Orthogroups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results/Orthogroups.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
| b'@@ -0,0 +1,1331 @@\n+OG0000000: gi|284811953|gb|ADB96857.1| gi|284811954|gb|ADB96858.1| gi|284811955|gb|AAP56548.2| gi|284811956|gb|ADB96859.1| gi|284811957|gb|ADB96860.1| gi|284811958|gb|ADB96861.1| gi|284811959|gb|ADB96862.1| gi|284811960|gb|ADB96863.1| gi|284811961|gb|ADB96864.1| gi|284811962|gb|ADB96865.1| gi|284812039|gb|AAP56686.2| gi|284812040|gb|ADB96873.1| gi|284812041|gb|ADB96874.1| gi|284812042|gb|ADB96875.1| gi|284812103|gb|ADB96879.1| gi|284812104|gb|ADB96880.1| gi|284812105|gb|AAP56776.2| gi|284812107|gb|ADB96881.1| gi|284812108|gb|ADB96882.1| gi|284812128|gb|AAP56805.2| gi|284812129|gb|AAP56806.2| gi|284812217|gb|ADB96891.1| gi|284812218|gb|ADB96892.1| gi|284812219|gb|AAP56940.2| gi|31541243|gb|AAP56545.1| gi|31541245|gb|AAP56547.1| gi|31541247|gb|AAP56549.1| gi|31541248|gb|AAP56550.1| gi|31541249|gb|AAP56551.1| gi|31541250|gb|AAP56552.1| gi|31541251|gb|AAP56553.1| gi|31541252|gb|AAP56554.1| gi|31541253|gb|AAP56555.1| gi|31541386|gb|AAP56687.1| gi|31541387|gb|AAP56688.1| gi|31541388|gb|AAP56689.1| gi|31541389|gb|AAP56690.1| gi|31541390|gb|AAP56691.1| gi|31541391|gb|AAP56692.1| gi|31541392|gb|AAP56693.1| gi|31541393|gb|AAP56694.1| gi|31541394|gb|AAP56695.1| gi|31541395|gb|AAP56696.1| gi|31541396|gb|AAP56697.1| gi|31541398|gb|AAP56699.1| gi|31541472|gb|AAP56773.1| gi|31541473|gb|AAP56774.1| gi|31541474|gb|AAP56775.1| gi|31541478|gb|AAP56779.1| gi|31541641|gb|AAP56941.1| gi|31541642|gb|AAP56942.1| gi|31541643|gb|AAP56943.1| gi|31541644|gb|AAP56944.1| gi|31541645|gb|AAP56945.1| gi|31541646|gb|AAP56946.1| gi|31541647|gb|AAP56947.1|\n+OG0000001: gi|290752501|emb|CBH40473.1| gi|290752503|emb|CBH40475.1| gi|290752692|emb|CBH40666.1| gi|290752693|emb|CBH40667.1| gi|290752812|emb|CBH40787.1| gi|290752813|emb|CBH40788.1| gi|290752814|emb|CBH40789.1| gi|290752815|emb|CBH40790.1| gi|290752816|emb|CBH40791.1| gi|290752817|emb|CBH40792.1| gi|290752818|emb|CBH40793.1| gi|290753029|emb|CBH41005.1| gi|290753030|emb|CBH41006.1| gi|290753031|emb|CBH41007.1| gi|290753032|emb|CBH41008.1| gi|290753033|emb|CBH41009.1| gi|290753034|emb|CBH41010.1| gi|290753035|emb|CBH41011.1| gi|290753036|emb|CBH41012.1| gi|290753037|emb|CBH41013.1| gi|290753040|emb|CBH41016.1| gi|290753041|emb|CBH41017.1| gi|290753042|emb|CBH41018.1| gi|290753043|emb|CBH41019.1| gi|290753044|emb|CBH41020.1| gi|290753045|emb|CBH41021.1| gi|290753046|emb|CBH41022.1|\n+OG0000002: gi|1046010|gb|AAC71532.1| gi|144227478|gb|AAZ44221.2| gi|290752269|emb|CBH40240.1| gi|290752270|emb|CBH40241.1| gi|290752414|emb|CBH40385.1| gi|290752490|emb|CBH40462.1| gi|290752766|emb|CBH40741.1| gi|31541260|gb|AAP56562.1| gi|31541382|gb|AAP56683.1| gi|3844907|gb|AAC71551.1| gi|3844927|gb|AAC71569.1|\n+OG0000003: gi|1046012|gb|AAC71534.1| gi|284811924|gb|AAP56500.2| gi|284811927|gb|ADB96855.1| gi|284811928|gb|ADB96856.1| gi|284812192|gb|AAP56901.2| gi|290753066|emb|CBH41042.1| gi|31541553|gb|AAP56853.1| gi|3844628|gb|AAC71235.1| gi|3844797|gb|AAC71418.1| gi|3844975|gb|AAC71613.1| gi|71851550|gb|AAZ44158.1|\n+OG0000004: gi|1045740|gb|AAC71283.1| gi|1045987|gb|AAC71511.1| gi|144227640|gb|AAZ44535.2| gi|290752526|emb|CBH40498.1| gi|290753081|emb|CBH41057.1| gi|31541070|gb|AAP56372.1| gi|31541268|gb|AAP56569.1| gi|3845062|gb|AAC72487.1| gi|3845064|gb|AAC72489.1| gi|71851837|gb|AAZ44445.1|\n+OG0000005: gi|1045683|gb|AAC71230.1| gi|1045684|gb|AAC71231.1| gi|284811835|gb|AAP56356.2| gi|284812058|gb|AAP56715.2| gi|290752591|emb|CBH40563.1| gi|290752592|emb|CBH40564.1| gi|290752893|emb|CBH40868.1| gi|290752894|emb|CBH40869.1| gi|31541415|gb|AAP56716.1|\n+OG0000006: gi|31541304|gb|AAP56605.1| gi|71851504|gb|AAZ44112.1| gi|71851505|gb|AAZ44113.1| gi|71851506|gb|AAZ44114.1| gi|71851779|gb|AAZ44387.1| gi|71851788|gb|AAZ44396.1| gi|71851789|gb|AAZ44397.1| gi|71851814|gb|AAZ44422.1| gi|71851859|gb|AAZ44467.1|\n+OG0000007: gi|31541315|gb|AAP56616.1| gi|71851791|gb|AAZ44399.1| gi|71851810|gb|AAZ44418.1| gi|71851917|gb|AAZ44525.1| gi|71851970|gb|AAZ44578.1| gi|71851995|gb|AAZ44603.1| gi|71852017|gb|AAZ44625.1| gi|7185'..b'01230: gi|144227613|gb|AAZ44488.2|\n+OG0001231: gi|71851881|gb|AAZ44489.1|\n+OG0001232: gi|144227616|gb|AAZ44498.2|\n+OG0001233: gi|144227617|gb|AAZ44499.2|\n+OG0001234: gi|144227618|gb|AAZ44501.2|\n+OG0001235: gi|71851895|gb|AAZ44503.1|\n+OG0001236: gi|71851899|gb|AAZ44507.1|\n+OG0001237: gi|71851900|gb|AAZ44508.1|\n+OG0001238: gi|71851902|gb|AAZ44510.1|\n+OG0001239: gi|144227625|gb|AAZ44516.2|\n+OG0001240: gi|71851909|gb|AAZ44517.1|\n+OG0001241: gi|144227629|gb|AAZ44523.2|\n+OG0001242: gi|144227630|gb|AAZ44524.2|\n+OG0001243: gi|144227631|gb|AAZ44526.2|\n+OG0001244: gi|144227632|gb|AAZ44527.2|\n+OG0001245: gi|144227633|gb|ABO93479.1|\n+OG0001246: gi|144227634|gb|AAZ44528.2|\n+OG0001247: gi|71851921|gb|AAZ44529.1|\n+OG0001248: gi|144227635|gb|AAZ44530.2|\n+OG0001249: gi|144227636|gb|AAZ44531.2|\n+OG0001250: gi|71851929|gb|AAZ44537.1|\n+OG0001251: gi|71851936|gb|AAZ44544.1|\n+OG0001252: gi|144227644|gb|AAZ44545.2|\n+OG0001253: gi|144227645|gb|AAZ44546.2|\n+OG0001254: gi|144227647|gb|AAZ44549.2|\n+OG0001255: gi|144227650|gb|AAZ44554.2|\n+OG0001256: gi|71851956|gb|AAZ44564.1|\n+OG0001257: gi|144227656|gb|AAZ44567.2|\n+OG0001258: gi|144227660|gb|AAZ44572.2|\n+OG0001259: gi|71851966|gb|AAZ44574.1|\n+OG0001260: gi|144227661|gb|AAZ44576.2|\n+OG0001261: gi|71851971|gb|AAZ44579.1|\n+OG0001262: gi|71851972|gb|AAZ44580.1|\n+OG0001263: gi|71851985|gb|AAZ44593.1|\n+OG0001264: gi|71851986|gb|AAZ44594.1|\n+OG0001265: gi|144227667|gb|AAZ44595.2|\n+OG0001266: gi|71851988|gb|AAZ44596.1|\n+OG0001267: gi|71851989|gb|AAZ44597.1|\n+OG0001268: gi|144227668|gb|AAZ44598.2|\n+OG0001269: gi|71851991|gb|AAZ44599.1|\n+OG0001270: gi|144227669|gb|AAZ44600.2|\n+OG0001271: gi|144227670|gb|AAZ44601.2|\n+OG0001272: gi|144227671|gb|AAZ44602.2|\n+OG0001273: gi|144227672|gb|AAZ44604.2|\n+OG0001274: gi|144227673|gb|AAZ44605.2|\n+OG0001275: gi|144227674|gb|AAZ44606.2|\n+OG0001276: gi|144227675|gb|AAZ44607.2|\n+OG0001277: gi|144227676|gb|ABO93480.1|\n+OG0001278: gi|144227681|gb|AAZ44617.2|\n+OG0001279: gi|144227683|gb|AAZ44623.2|\n+OG0001280: gi|144227688|gb|ABO93481.1|\n+OG0001281: gi|144227689|gb|AAZ44632.2|\n+OG0001282: gi|71852025|gb|AAZ44633.1|\n+OG0001283: gi|144227690|gb|AAZ44637.2|\n+OG0001284: gi|71852030|gb|AAZ44638.1|\n+OG0001285: gi|144227691|gb|AAZ44639.2|\n+OG0001286: gi|71852032|gb|AAZ44640.1|\n+OG0001287: gi|71852034|gb|AAZ44642.1|\n+OG0001288: gi|71852035|gb|AAZ44643.1|\n+OG0001289: gi|144227693|gb|AAZ44644.2|\n+OG0001290: gi|144227694|gb|ABO93482.1|\n+OG0001291: gi|144227695|gb|AAZ44645.2|\n+OG0001292: gi|71852038|gb|AAZ44646.1|\n+OG0001293: gi|144227696|gb|AAZ44647.2|\n+OG0001294: gi|71852040|gb|AAZ44648.1|\n+OG0001295: gi|144227697|gb|AAZ44650.2|\n+OG0001296: gi|71852043|gb|AAZ44651.1|\n+OG0001297: gi|144227698|gb|ABO93483.1|\n+OG0001298: gi|144227699|gb|AAZ44652.2|\n+OG0001299: gi|144227700|gb|AAZ44653.2|\n+OG0001300: gi|144227701|gb|AAZ44654.2|\n+OG0001301: gi|71852048|gb|AAZ44656.1|\n+OG0001302: gi|144227703|gb|AAZ44657.2|\n+OG0001303: gi|144227704|gb|AAZ44658.2|\n+OG0001304: gi|71852052|gb|AAZ44660.1|\n+OG0001305: gi|144227707|gb|AAZ44671.2|\n+OG0001306: gi|144227709|gb|ABO93484.1|\n+OG0001307: gi|144227715|gb|AAZ44680.2|\n+OG0001308: gi|144227716|gb|AAZ44681.2|\n+OG0001309: gi|144227717|gb|AAZ44682.2|\n+OG0001310: gi|71852075|gb|AAZ44683.1|\n+OG0001311: gi|144227718|gb|AAZ44684.2|\n+OG0001312: gi|71852077|gb|AAZ44685.1|\n+OG0001313: gi|144227719|gb|AAZ44686.2|\n+OG0001314: gi|144227725|gb|AAZ44696.2|\n+OG0001315: gi|144227730|gb|AAZ44708.2|\n+OG0001316: gi|71852101|gb|AAZ44709.1|\n+OG0001317: gi|144227731|gb|AAZ44711.2|\n+OG0001318: gi|144227732|gb|AAZ44712.2|\n+OG0001319: gi|144227736|gb|AAZ44718.2|\n+OG0001320: gi|71852114|gb|AAZ44722.1|\n+OG0001321: gi|144227745|gb|AAZ44743.2|\n+OG0001322: gi|144227746|gb|AAZ44744.2|\n+OG0001323: gi|144227747|gb|AAZ44745.2|\n+OG0001324: gi|71852138|gb|AAZ44746.1|\n+OG0001325: gi|71852139|gb|AAZ44747.1|\n+OG0001326: gi|71852141|gb|AAZ44749.1|\n+OG0001327: gi|144227748|gb|AAZ44751.2|\n+OG0001328: gi|71852145|gb|AAZ44753.1|\n+OG0001329: gi|144227749|gb|AAZ44755.2|\n+OG0001330: gi|144227750|gb|AAZ44756.2|\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/results/Orthogroups_SpeciesOverlaps.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results/Orthogroups_SpeciesOverlaps.csv Tue Oct 24 06:40:40 2017 -0400 |
| b |
| @@ -0,0 +1,5 @@ + Mycoplasma_agalactiae Mycoplasma_gallisepticum Mycoplasma_genitalium Mycoplasma_hyopneumoniae +Mycoplasma_agalactiae 432 363 305 391 +Mycoplasma_gallisepticum 363 462 385 346 +Mycoplasma_genitalium 305 385 394 296 +Mycoplasma_hyopneumoniae 391 346 296 416 |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/results/Orthogroups_UnassignedGenes.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results/Orthogroups_UnassignedGenes.csv Tue Oct 24 06:40:40 2017 -0400 |
| b |
| b'@@ -0,0 +1,796 @@\n+\tMycoplasma_agalactiae\tMycoplasma_gallisepticum\tMycoplasma_genitalium\tMycoplasma_hyopneumoniae\r\n+OG0000536\tgi|290752272|emb|CBH40243.1|\t\t\t\r\n+OG0000537\tgi|290752276|emb|CBH40247.1|\t\t\t\r\n+OG0000538\tgi|290752279|emb|CBH40250.1|\t\t\t\r\n+OG0000539\tgi|290752285|emb|CBH40256.1|\t\t\t\r\n+OG0000540\tgi|290752286|emb|CBH40257.1|\t\t\t\r\n+OG0000541\tgi|290752287|emb|CBH40258.1|\t\t\t\r\n+OG0000542\tgi|290752288|emb|CBH40259.1|\t\t\t\r\n+OG0000543\tgi|290752289|emb|CBH40260.1|\t\t\t\r\n+OG0000544\tgi|290752290|emb|CBH40261.1|\t\t\t\r\n+OG0000545\tgi|290752291|emb|CBH40262.1|\t\t\t\r\n+OG0000546\tgi|290752293|emb|CBH40264.1|\t\t\t\r\n+OG0000547\tgi|290752294|emb|CBH40265.1|\t\t\t\r\n+OG0000548\tgi|290752295|emb|CBH40266.1|\t\t\t\r\n+OG0000549\tgi|290752296|emb|CBH40267.1|\t\t\t\r\n+OG0000550\tgi|290752297|emb|CBH40268.1|\t\t\t\r\n+OG0000551\tgi|290752306|emb|CBH40277.1|\t\t\t\r\n+OG0000552\tgi|290752310|emb|CBH40281.1|\t\t\t\r\n+OG0000553\tgi|290752313|emb|CBH40284.1|\t\t\t\r\n+OG0000554\tgi|290752314|emb|CBH40285.1|\t\t\t\r\n+OG0000555\tgi|290752319|emb|CBH40290.1|\t\t\t\r\n+OG0000556\tgi|290752342|emb|CBH40313.1|\t\t\t\r\n+OG0000557\tgi|290752345|emb|CBH40316.1|\t\t\t\r\n+OG0000558\tgi|290752348|emb|CBH40319.1|\t\t\t\r\n+OG0000559\tgi|290752349|emb|CBH40320.1|\t\t\t\r\n+OG0000560\tgi|290752350|emb|CBH40321.1|\t\t\t\r\n+OG0000561\tgi|290752353|emb|CBH40324.1|\t\t\t\r\n+OG0000562\tgi|290752355|emb|CBH40326.1|\t\t\t\r\n+OG0000563\tgi|290752359|emb|CBH40330.1|\t\t\t\r\n+OG0000564\tgi|290752362|emb|CBH40333.1|\t\t\t\r\n+OG0000565\tgi|290752367|emb|CBH40338.1|\t\t\t\r\n+OG0000566\tgi|290752368|emb|CBH40339.1|\t\t\t\r\n+OG0000567\tgi|290752374|emb|CBH40345.1|\t\t\t\r\n+OG0000568\tgi|290752375|emb|CBH40346.1|\t\t\t\r\n+OG0000569\tgi|290752377|emb|CBH40348.1|\t\t\t\r\n+OG0000570\tgi|290752380|emb|CBH40351.1|\t\t\t\r\n+OG0000571\tgi|290752387|emb|CBH40358.1|\t\t\t\r\n+OG0000572\tgi|290752389|emb|CBH40360.1|\t\t\t\r\n+OG0000573\tgi|290752396|emb|CBH40367.1|\t\t\t\r\n+OG0000574\tgi|290752398|emb|CBH40369.1|\t\t\t\r\n+OG0000575\tgi|290752399|emb|CBH40370.1|\t\t\t\r\n+OG0000576\tgi|290752400|emb|CBH40371.1|\t\t\t\r\n+OG0000577\tgi|290752405|emb|CBH40376.1|\t\t\t\r\n+OG0000578\tgi|290752407|emb|CBH40378.1|\t\t\t\r\n+OG0000579\tgi|290752409|emb|CBH40380.1|\t\t\t\r\n+OG0000580\tgi|290752411|emb|CBH40382.1|\t\t\t\r\n+OG0000581\tgi|290752412|emb|CBH40383.1|\t\t\t\r\n+OG0000582\tgi|290752413|emb|CBH40384.1|\t\t\t\r\n+OG0000583\tgi|290752415|emb|CBH40386.1|\t\t\t\r\n+OG0000584\tgi|290752417|emb|CBH40388.1|\t\t\t\r\n+OG0000585\tgi|290752419|emb|CBH40390.1|\t\t\t\r\n+OG0000586\tgi|290752421|emb|CBH40392.1|\t\t\t\r\n+OG0000587\tgi|290752423|emb|CBH40394.1|\t\t\t\r\n+OG0000588\tgi|290752424|emb|CBH40395.1|\t\t\t\r\n+OG0000589\tgi|290752425|emb|CBH40396.1|\t\t\t\r\n+OG0000590\tgi|290752428|emb|CBH40399.1|\t\t\t\r\n+OG0000591\tgi|290752429|emb|CBH40400.1|\t\t\t\r\n+OG0000592\tgi|290752430|emb|CBH40401.1|\t\t\t\r\n+OG0000593\tgi|290752432|emb|CBH40403.1|\t\t\t\r\n+OG0000594\tgi|290752436|emb|CBH40407.1|\t\t\t\r\n+OG0000595\tgi|290752439|emb|CBH40410.1|\t\t\t\r\n+OG0000596\tgi|290752444|emb|CBH40415.1|\t\t\t\r\n+OG0000597\tgi|290752447|emb|CBH40418.1|\t\t\t\r\n+OG0000598\tgi|290752448|emb|CBH40420.1|\t\t\t\r\n+OG0000599\tgi|290752449|emb|CBH40421.1|\t\t\t\r\n+OG0000600\tgi|290752453|emb|CBH40425.1|\t\t\t\r\n+OG0000601\tgi|290752457|emb|CBH40429.1|\t\t\t\r\n+OG0000602\tgi|290752462|emb|CBH40434.1|\t\t\t\r\n+OG0000603\tgi|290752466|emb|CBH40438.1|\t\t\t\r\n+OG0000604\tgi|290752472|emb|CBH40444.1|\t\t\t\r\n+OG0000605\tgi|290752473|emb|CBH40445.1|\t\t\t\r\n+OG0000606\tgi|290752474|emb|CBH40446.1|\t\t\t\r\n+OG0000607\tgi|290752475|emb|CBH40447.1|\t\t\t\r\n+OG0000608\tgi|290752476|emb|CBH40448.1|\t\t\t\r\n+OG0000609\tgi|290752495|emb|CBH40467.1|\t\t\t\r\n+OG0000610\tgi|290752500|emb|CBH40472.1|\t\t\t\r\n+OG0000611\tgi|290752502|emb|CBH40474.1|\t\t\t\r\n+OG0000612\tgi|290752505|emb|CBH40477.1|\t\t\t\r\n+OG0000613\tgi|290752506|emb|CBH40478.1|\t\t\t\r\n+OG0000614\tgi|290752507|emb|CBH40479.1|\t\t\t\r\n+OG0000615\tgi|290752509|emb|CBH40481.1|\t\t\t\r\n+OG0000616\tgi|290752510|emb|CBH40482.1|\t\t\t\r\n+OG0000617\tgi|290752511|emb|CBH40483.1|\t\t\t\r\n+OG0000618\tgi|290752512|emb|CBH40484.1|\t\t\t\r\n+OG0000619\tgi|290752514|emb|CBH40486.1|\t\t\t\r\n+OG0000620\tgi|290752517|emb|CBH40489.1|\t\t\t\r\n+OG0000621\tgi|290752524|emb|CBH40496.1|\t\t\t\r\n+OG0000622\tgi|290752528|emb|CBH40500.1|\t\t\t\r\n+OG0000623\tgi|290752537|emb|CBH40509.1|\t\t\t\r\n+OG0000624\tg'..b'\t\t\t\tgi|71851900|gb|AAZ44508.1|\r\n+OG0001238\t\t\t\tgi|71851902|gb|AAZ44510.1|\r\n+OG0001239\t\t\t\tgi|144227625|gb|AAZ44516.2|\r\n+OG0001240\t\t\t\tgi|71851909|gb|AAZ44517.1|\r\n+OG0001241\t\t\t\tgi|144227629|gb|AAZ44523.2|\r\n+OG0001242\t\t\t\tgi|144227630|gb|AAZ44524.2|\r\n+OG0001243\t\t\t\tgi|144227631|gb|AAZ44526.2|\r\n+OG0001244\t\t\t\tgi|144227632|gb|AAZ44527.2|\r\n+OG0001245\t\t\t\tgi|144227633|gb|ABO93479.1|\r\n+OG0001246\t\t\t\tgi|144227634|gb|AAZ44528.2|\r\n+OG0001247\t\t\t\tgi|71851921|gb|AAZ44529.1|\r\n+OG0001248\t\t\t\tgi|144227635|gb|AAZ44530.2|\r\n+OG0001249\t\t\t\tgi|144227636|gb|AAZ44531.2|\r\n+OG0001250\t\t\t\tgi|71851929|gb|AAZ44537.1|\r\n+OG0001251\t\t\t\tgi|71851936|gb|AAZ44544.1|\r\n+OG0001252\t\t\t\tgi|144227644|gb|AAZ44545.2|\r\n+OG0001253\t\t\t\tgi|144227645|gb|AAZ44546.2|\r\n+OG0001254\t\t\t\tgi|144227647|gb|AAZ44549.2|\r\n+OG0001255\t\t\t\tgi|144227650|gb|AAZ44554.2|\r\n+OG0001256\t\t\t\tgi|71851956|gb|AAZ44564.1|\r\n+OG0001257\t\t\t\tgi|144227656|gb|AAZ44567.2|\r\n+OG0001258\t\t\t\tgi|144227660|gb|AAZ44572.2|\r\n+OG0001259\t\t\t\tgi|71851966|gb|AAZ44574.1|\r\n+OG0001260\t\t\t\tgi|144227661|gb|AAZ44576.2|\r\n+OG0001261\t\t\t\tgi|71851971|gb|AAZ44579.1|\r\n+OG0001262\t\t\t\tgi|71851972|gb|AAZ44580.1|\r\n+OG0001263\t\t\t\tgi|71851985|gb|AAZ44593.1|\r\n+OG0001264\t\t\t\tgi|71851986|gb|AAZ44594.1|\r\n+OG0001265\t\t\t\tgi|144227667|gb|AAZ44595.2|\r\n+OG0001266\t\t\t\tgi|71851988|gb|AAZ44596.1|\r\n+OG0001267\t\t\t\tgi|71851989|gb|AAZ44597.1|\r\n+OG0001268\t\t\t\tgi|144227668|gb|AAZ44598.2|\r\n+OG0001269\t\t\t\tgi|71851991|gb|AAZ44599.1|\r\n+OG0001270\t\t\t\tgi|144227669|gb|AAZ44600.2|\r\n+OG0001271\t\t\t\tgi|144227670|gb|AAZ44601.2|\r\n+OG0001272\t\t\t\tgi|144227671|gb|AAZ44602.2|\r\n+OG0001273\t\t\t\tgi|144227672|gb|AAZ44604.2|\r\n+OG0001274\t\t\t\tgi|144227673|gb|AAZ44605.2|\r\n+OG0001275\t\t\t\tgi|144227674|gb|AAZ44606.2|\r\n+OG0001276\t\t\t\tgi|144227675|gb|AAZ44607.2|\r\n+OG0001277\t\t\t\tgi|144227676|gb|ABO93480.1|\r\n+OG0001278\t\t\t\tgi|144227681|gb|AAZ44617.2|\r\n+OG0001279\t\t\t\tgi|144227683|gb|AAZ44623.2|\r\n+OG0001280\t\t\t\tgi|144227688|gb|ABO93481.1|\r\n+OG0001281\t\t\t\tgi|144227689|gb|AAZ44632.2|\r\n+OG0001282\t\t\t\tgi|71852025|gb|AAZ44633.1|\r\n+OG0001283\t\t\t\tgi|144227690|gb|AAZ44637.2|\r\n+OG0001284\t\t\t\tgi|71852030|gb|AAZ44638.1|\r\n+OG0001285\t\t\t\tgi|144227691|gb|AAZ44639.2|\r\n+OG0001286\t\t\t\tgi|71852032|gb|AAZ44640.1|\r\n+OG0001287\t\t\t\tgi|71852034|gb|AAZ44642.1|\r\n+OG0001288\t\t\t\tgi|71852035|gb|AAZ44643.1|\r\n+OG0001289\t\t\t\tgi|144227693|gb|AAZ44644.2|\r\n+OG0001290\t\t\t\tgi|144227694|gb|ABO93482.1|\r\n+OG0001291\t\t\t\tgi|144227695|gb|AAZ44645.2|\r\n+OG0001292\t\t\t\tgi|71852038|gb|AAZ44646.1|\r\n+OG0001293\t\t\t\tgi|144227696|gb|AAZ44647.2|\r\n+OG0001294\t\t\t\tgi|71852040|gb|AAZ44648.1|\r\n+OG0001295\t\t\t\tgi|144227697|gb|AAZ44650.2|\r\n+OG0001296\t\t\t\tgi|71852043|gb|AAZ44651.1|\r\n+OG0001297\t\t\t\tgi|144227698|gb|ABO93483.1|\r\n+OG0001298\t\t\t\tgi|144227699|gb|AAZ44652.2|\r\n+OG0001299\t\t\t\tgi|144227700|gb|AAZ44653.2|\r\n+OG0001300\t\t\t\tgi|144227701|gb|AAZ44654.2|\r\n+OG0001301\t\t\t\tgi|71852048|gb|AAZ44656.1|\r\n+OG0001302\t\t\t\tgi|144227703|gb|AAZ44657.2|\r\n+OG0001303\t\t\t\tgi|144227704|gb|AAZ44658.2|\r\n+OG0001304\t\t\t\tgi|71852052|gb|AAZ44660.1|\r\n+OG0001305\t\t\t\tgi|144227707|gb|AAZ44671.2|\r\n+OG0001306\t\t\t\tgi|144227709|gb|ABO93484.1|\r\n+OG0001307\t\t\t\tgi|144227715|gb|AAZ44680.2|\r\n+OG0001308\t\t\t\tgi|144227716|gb|AAZ44681.2|\r\n+OG0001309\t\t\t\tgi|144227717|gb|AAZ44682.2|\r\n+OG0001310\t\t\t\tgi|71852075|gb|AAZ44683.1|\r\n+OG0001311\t\t\t\tgi|144227718|gb|AAZ44684.2|\r\n+OG0001312\t\t\t\tgi|71852077|gb|AAZ44685.1|\r\n+OG0001313\t\t\t\tgi|144227719|gb|AAZ44686.2|\r\n+OG0001314\t\t\t\tgi|144227725|gb|AAZ44696.2|\r\n+OG0001315\t\t\t\tgi|144227730|gb|AAZ44708.2|\r\n+OG0001316\t\t\t\tgi|71852101|gb|AAZ44709.1|\r\n+OG0001317\t\t\t\tgi|144227731|gb|AAZ44711.2|\r\n+OG0001318\t\t\t\tgi|144227732|gb|AAZ44712.2|\r\n+OG0001319\t\t\t\tgi|144227736|gb|AAZ44718.2|\r\n+OG0001320\t\t\t\tgi|71852114|gb|AAZ44722.1|\r\n+OG0001321\t\t\t\tgi|144227745|gb|AAZ44743.2|\r\n+OG0001322\t\t\t\tgi|144227746|gb|AAZ44744.2|\r\n+OG0001323\t\t\t\tgi|144227747|gb|AAZ44745.2|\r\n+OG0001324\t\t\t\tgi|71852138|gb|AAZ44746.1|\r\n+OG0001325\t\t\t\tgi|71852139|gb|AAZ44747.1|\r\n+OG0001326\t\t\t\tgi|71852141|gb|AAZ44749.1|\r\n+OG0001327\t\t\t\tgi|144227748|gb|AAZ44751.2|\r\n+OG0001328\t\t\t\tgi|71852145|gb|AAZ44753.1|\r\n+OG0001329\t\t\t\tgi|144227749|gb|AAZ44755.2|\r\n+OG0001330\t\t\t\tgi|144227750|gb|AAZ44756.2|\r\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/results/Statistics_Overall.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results/Statistics_Overall.csv Tue Oct 24 06:40:40 2017 -0400 |
| b |
| @@ -0,0 +1,51 @@ +Number of genes 2733 +Number of genes in orthogroups 1938 +Number of unassigned genes 795 +Percentage of genes in orthogroups 70.9 +Percentage of unassigned genes 29.1 +Number of orthogroups 536 +Number of species-specific orthogroups 6 +Number of genes in species-specific orthogroups 97 +Percentage of genes in species-specific orthogroups 3.5 +Mean orthogroup size 3.6 +Median orthogroup size 4.0 +G50 (assigned genes) 4 +G50 (all genes) 4 +O50 (assigned genes) 200 +O50 (all genes) 299 +Number of orthogroups with all species present 280 +Number of single-copy orthogroups 254 +Date 2017-06-06 +Orthogroups file Orthogroups.csv +Unassigned genes file Orthogroups_UnassignedGenes.csv +Per-species statistics Statistics_PerSpecies.csv +Overall statistics Statistics_Overall.csv +Orthogroups shared between species Orthogroups_SpeciesOverlaps.csv + +Average number of genes per-species in orthogroup Number of orthogroups Percentage of orthogroups Number of genes Percentage of genes +<1 222 41.4 510 26.3 +'1 304 56.7 1270 65.5 +'2 8 1.5 75 3.9 +'3 0 0.0 0 0.0 +'4 0 0.0 0 0.0 +'5 0 0.0 0 0.0 +'6 1 0.2 27 1.4 +'7 0 0.0 0 0.0 +'8 0 0.0 0 0.0 +'9 0 0.0 0 0.0 +'10 0 0.0 0 0.0 +11-15 1 0.2 56 2.9 +16-20 0 0.0 0 0.0 +21-50 0 0.0 0 0.0 +51-100 0 0.0 0 0.0 +101-150 0 0.0 0 0.0 +151-200 0 0.0 0 0.0 +201-500 0 0.0 0 0.0 +501-1000 0 0.0 0 0.0 +'1001+ 0 0.0 0 0.0 + +Number of species in orthogroup Number of orthogroups +1 6 +2 172 +3 78 +4 280 |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/results/Statistics_PerSpecies.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results/Statistics_PerSpecies.csv Tue Oct 24 06:40:40 2017 -0400 |
| b |
| @@ -0,0 +1,100 @@ + Mycoplasma_agalactiae Mycoplasma_gallisepticum Mycoplasma_genitalium Mycoplasma_hyopneumoniae +Number of genes 820 763 476 674 +Number of genes in orthogroups 503 561 429 445 +Number of unassigned genes 317 202 47 229 +Percentage of genes in orthogroups 61.3 73.5 90.1 66.0 +Percentage of unassigned genes 38.7 26.5 9.9 34.0 +Number of orthogroups containing species 432 462 394 416 +Percentage of orthogroups containing species 80.6 86.2 73.5 77.6 +Number of species-specific orthogroups 2 3 0 1 +Number of genes in species-specific orthogroups 29 63 0 5 +Percentage of genes in species-specific orthogroups 3.5 8.3 0.0 0.7 + + +Number of genes per-species in orthogroup Number of orthogroups Number of orthogroups Number of orthogroups Number of orthogroups +'0 104 74 142 120 +'1 400 429 368 403 +'2 22 24 19 9 +'3 6 6 5 1 +'4 1 0 2 0 +'5 2 2 0 1 +'6 0 0 0 0 +'7 0 0 0 0 +'8 0 0 0 2 +'9 0 0 0 0 +'10 0 0 0 0 +11-15 0 0 0 0 +16-20 0 0 0 0 +21-50 1 0 0 0 +51-100 0 1 0 0 +101-150 0 0 0 0 +151-200 0 0 0 0 +201-500 0 0 0 0 +501-1000 0 0 0 0 +'1001+ 0 0 0 0 + +Number of genes per-species in orthogroup Percentage of orthogroups Percentage of orthogroups Percentage of orthogroups Percentage of orthogroups +'0 19.4 13.8 26.5 22.4 +'1 74.6 80.0 68.7 75.2 +'2 4.1 4.5 3.5 1.7 +'3 1.1 1.1 0.9 0.2 +'4 0.2 0.0 0.4 0.0 +'5 0.4 0.4 0.0 0.2 +'6 0.0 0.0 0.0 0.0 +'7 0.0 0.0 0.0 0.0 +'8 0.0 0.0 0.0 0.4 +'9 0.0 0.0 0.0 0.0 +'10 0.0 0.0 0.0 0.0 +11-15 0.0 0.0 0.0 0.0 +16-20 0.0 0.0 0.0 0.0 +21-50 0.2 0.0 0.0 0.0 +51-100 0.0 0.2 0.0 0.0 +101-150 0.0 0.0 0.0 0.0 +151-200 0.0 0.0 0.0 0.0 +201-500 0.0 0.0 0.0 0.0 +501-1000 0.0 0.0 0.0 0.0 +'1001+ 0.0 0.0 0.0 0.0 + +Number of genes per-species in orthogroup Number of genes Number of genes Number of genes Number of genes +'0 0 0 0 0 +'1 400 429 368 403 +'2 44 48 38 18 +'3 18 18 15 3 +'4 4 0 8 0 +'5 10 10 0 5 +'6 0 0 0 0 +'7 0 0 0 0 +'8 0 0 0 16 +'9 0 0 0 0 +'10 0 0 0 0 +11-15 0 0 0 0 +16-20 0 0 0 0 +21-50 27 0 0 0 +51-100 0 56 0 0 +101-150 0 0 0 0 +151-200 0 0 0 0 +201-500 0 0 0 0 +501-1000 0 0 0 0 +'1001+ 0 0 0 0 + +Number of genes per-species in orthogroup Percentage of genes Percentage of genes Percentage of genes Percentage of genes +'0 0.0 0.0 0.0 0.0 +'1 48.8 56.2 77.3 59.8 +'2 5.4 6.3 8.0 2.7 +'3 2.2 2.4 3.2 0.4 +'4 0.5 0.0 1.7 0.0 +'5 1.2 1.3 0.0 0.7 +'6 0.0 0.0 0.0 0.0 +'7 0.0 0.0 0.0 0.0 +'8 0.0 0.0 0.0 2.4 +'9 0.0 0.0 0.0 0.0 +'10 0.0 0.0 0.0 0.0 +11-15 0.0 0.0 0.0 0.0 +16-20 0.0 0.0 0.0 0.0 +21-50 3.3 0.0 0.0 0.0 +51-100 0.0 7.3 0.0 0.0 +101-150 0.0 0.0 0.0 0.0 +151-200 0.0 0.0 0.0 0.0 +201-500 0.0 0.0 0.0 0.0 +501-1000 0.0 0.0 0.0 0.0 +'1001+ 0.0 0.0 0.0 0.0 |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/results_fromblast/Orthogroups.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results_fromblast/Orthogroups.csv Tue Oct 24 06:40:40 2017 -0400 |
| b |
| b'@@ -0,0 +1,537 @@\n+\tMycoplasma_agalactiae\tMycoplasma_gallisepticum\tMycoplasma_genitalium\tMycoplasma_hyopneumoniae\r\n+OG0000000\t\tgi|284811953|gb|ADB96857.1|, gi|284811954|gb|ADB96858.1|, gi|284811955|gb|AAP56548.2|, gi|284811956|gb|ADB96859.1|, gi|284811957|gb|ADB96860.1|, gi|284811958|gb|ADB96861.1|, gi|284811959|gb|ADB96862.1|, gi|284811960|gb|ADB96863.1|, gi|284811961|gb|ADB96864.1|, gi|284811962|gb|ADB96865.1|, gi|284812039|gb|AAP56686.2|, gi|284812040|gb|ADB96873.1|, gi|284812041|gb|ADB96874.1|, gi|284812042|gb|ADB96875.1|, gi|284812103|gb|ADB96879.1|, gi|284812104|gb|ADB96880.1|, gi|284812105|gb|AAP56776.2|, gi|284812107|gb|ADB96881.1|, gi|284812108|gb|ADB96882.1|, gi|284812128|gb|AAP56805.2|, gi|284812129|gb|AAP56806.2|, gi|284812217|gb|ADB96891.1|, gi|284812218|gb|ADB96892.1|, gi|284812219|gb|AAP56940.2|, gi|31541243|gb|AAP56545.1|, gi|31541245|gb|AAP56547.1|, gi|31541247|gb|AAP56549.1|, gi|31541248|gb|AAP56550.1|, gi|31541249|gb|AAP56551.1|, gi|31541250|gb|AAP56552.1|, gi|31541251|gb|AAP56553.1|, gi|31541252|gb|AAP56554.1|, gi|31541253|gb|AAP56555.1|, gi|31541386|gb|AAP56687.1|, gi|31541387|gb|AAP56688.1|, gi|31541388|gb|AAP56689.1|, gi|31541389|gb|AAP56690.1|, gi|31541390|gb|AAP56691.1|, gi|31541391|gb|AAP56692.1|, gi|31541392|gb|AAP56693.1|, gi|31541393|gb|AAP56694.1|, gi|31541394|gb|AAP56695.1|, gi|31541395|gb|AAP56696.1|, gi|31541396|gb|AAP56697.1|, gi|31541398|gb|AAP56699.1|, gi|31541472|gb|AAP56773.1|, gi|31541473|gb|AAP56774.1|, gi|31541474|gb|AAP56775.1|, gi|31541478|gb|AAP56779.1|, gi|31541641|gb|AAP56941.1|, gi|31541642|gb|AAP56942.1|, gi|31541643|gb|AAP56943.1|, gi|31541644|gb|AAP56944.1|, gi|31541645|gb|AAP56945.1|, gi|31541646|gb|AAP56946.1|, gi|31541647|gb|AAP56947.1|\t\t\r\n+OG0000001\tgi|290752501|emb|CBH40473.1|, gi|290752503|emb|CBH40475.1|, gi|290752692|emb|CBH40666.1|, gi|290752693|emb|CBH40667.1|, gi|290752812|emb|CBH40787.1|, gi|290752813|emb|CBH40788.1|, gi|290752814|emb|CBH40789.1|, gi|290752815|emb|CBH40790.1|, gi|290752816|emb|CBH40791.1|, gi|290752817|emb|CBH40792.1|, gi|290752818|emb|CBH40793.1|, gi|290753029|emb|CBH41005.1|, gi|290753030|emb|CBH41006.1|, gi|290753031|emb|CBH41007.1|, gi|290753032|emb|CBH41008.1|, gi|290753033|emb|CBH41009.1|, gi|290753034|emb|CBH41010.1|, gi|290753035|emb|CBH41011.1|, gi|290753036|emb|CBH41012.1|, gi|290753037|emb|CBH41013.1|, gi|290753040|emb|CBH41016.1|, gi|290753041|emb|CBH41017.1|, gi|290753042|emb|CBH41018.1|, gi|290753043|emb|CBH41019.1|, gi|290753044|emb|CBH41020.1|, gi|290753045|emb|CBH41021.1|, gi|290753046|emb|CBH41022.1|\t\t\t\r\n+OG0000002\tgi|290752526|emb|CBH40498.1|, gi|290752801|emb|CBH40776.1|, gi|290752802|emb|CBH40777.1|, gi|290753081|emb|CBH41057.1|\tgi|31541070|gb|AAP56372.1|, gi|31541268|gb|AAP56569.1|, gi|31541628|gb|AAP56928.1|, gi|31541629|gb|AAP56929.1|\tgi|1045740|gb|AAC71283.1|, gi|1045987|gb|AAC71511.1|, gi|3844775|gb|AAC71398.1|, gi|3844776|gb|AAC71399.1|, gi|3844882|gb|AAC71525.1|, gi|3845062|gb|AAC72487.1|, gi|3845064|gb|AAC72489.1|, gi|84626133|gb|AAC71526.2|\tgi|144227640|gb|AAZ44535.2|, gi|71851738|gb|AAZ44346.1|, gi|71851739|gb|AAZ44347.1|, gi|71851837|gb|AAZ44445.1|\r\n+OG0000003\tgi|290752269|emb|CBH40240.1|, gi|290752270|emb|CBH40241.1|, gi|290752414|emb|CBH40385.1|, gi|290752490|emb|CBH40462.1|, gi|290752766|emb|CBH40741.1|\tgi|31541260|gb|AAP56562.1|, gi|31541382|gb|AAP56683.1|\tgi|1046010|gb|AAC71532.1|, gi|3844907|gb|AAC71551.1|, gi|3844927|gb|AAC71569.1|\tgi|144227478|gb|AAZ44221.2|\r\n+OG0000004\tgi|290753066|emb|CBH41042.1|\tgi|284811924|gb|AAP56500.2|, gi|284811927|gb|ADB96855.1|, gi|284811928|gb|ADB96856.1|, gi|284812192|gb|AAP56901.2|, gi|31541553|gb|AAP56853.1|\tgi|1046012|gb|AAC71534.1|, gi|3844628|gb|AAC71235.1|, gi|3844797|gb|AAC71418.1|, gi|3844975|gb|AAC71613.1|\tgi|71851550|gb|AAZ44158.1|\r\n+OG0000005\tgi|290752591|emb|CBH40563.1|, gi|290752592|emb|CBH40564.1|, gi|290752893|emb|CBH40868.1|, gi|290752894|emb|CBH40869.1|\tgi|284811835|gb|AAP56356.2|, gi|284812058|gb|AAP56715.2|, gi|31541415|gb|AAP56716.1|\tgi|1045683|gb|AAC71230.1|, '..b'477\t\tgi|284811945|gb|AAP56529.2|\tgi|3844895|gb|AAC71540.1|\t\r\n+OG0000478\t\tgi|284811949|gb|AAP56536.2|\tgi|1045973|gb|AAC71500.1|\t\r\n+OG0000479\t\tgi|284811950|gb|AAP56538.2|\tgi|1045972|gb|AAC71499.1|\t\r\n+OG0000480\t\tgi|31541239|gb|AAP56541.1|\tgi|3844896|gb|AAC71541.1|\t\r\n+OG0000481\t\tgi|284811951|gb|AAP56544.2|\t\tgi|144227642|gb|AAZ44540.2|\r\n+OG0000482\t\tgi|284811972|gb|AAP56572.2|\tgi|1045980|gb|AAC71506.1|\t\r\n+OG0000483\t\tgi|31541272|gb|AAP56573.1|\tgi|1045981|gb|AAC71507.1|\t\r\n+OG0000484\t\tgi|284811973|gb|AAP56574.2|\tgi|1045982|gb|AAC71508.1|\t\r\n+OG0000485\t\tgi|284811978|gb|AAP56579.2|\tgi|3845040|gb|AAC72467.1|\t\r\n+OG0000486\t\tgi|31541293|gb|AAP56594.1|\tgi|1045977|gb|AAC71503.1|\t\r\n+OG0000487\t\tgi|284811990|gb|AAP56599.2|\t\tgi|144227563|gb|AAZ44390.2|\r\n+OG0000488\t\tgi|284811995|gb|AAP56607.2|\t\tgi|144227427|gb|AAZ44116.2|\r\n+OG0000489\t\tgi|284812002|gb|AAP56617.2|\tgi|3844925|gb|AAC71567.1|\t\r\n+OG0000490\t\tgi|284812013|gb|AAP56637.2|\tgi|3845048|gb|AAC72474.1|\t\r\n+OG0000491\t\tgi|31541356|gb|AAP56657.1|\tgi|3844990|gb|AAC71626.1|\t\r\n+OG0000492\t\tgi|31541362|gb|AAP56663.1|\t\tgi|71851833|gb|AAZ44441.1|\r\n+OG0000493\t\tgi|284812025|gb|AAP56664.2|\tgi|3844809|gb|AAC71429.1|\t\r\n+OG0000494\t\tgi|31541364|gb|AAP56665.1|\tgi|84626132|gb|ABC59631.1|\t\r\n+OG0000495\t\tgi|31541370|gb|AAP56671.1|\tgi|3844818|gb|AAC71437.1|\t\r\n+OG0000496\t\tgi|31541380|gb|AAP56681.1|\tgi|1045963|gb|AAC71491.1|\t\r\n+OG0000497\t\tgi|284812060|gb|AAP56718.2|\tgi|3844837|gb|AAC71454.1|\t\r\n+OG0000498\t\tgi|284812061|gb|AAP56721.2|\tgi|3844840|gb|AAC71457.1|\t\r\n+OG0000499\t\tgi|284812062|gb|AAP56722.2|\tgi|3844841|gb|AAC71458.1|\t\r\n+OG0000500\t\tgi|284812074|gb|AAP56734.2|\tgi|3844846|gb|AAC71463.1|\t\r\n+OG0000501\t\tgi|284812077|gb|AAP56738.2|\tgi|1045939|gb|AAC71468.1|\t\r\n+OG0000502\t\tgi|31541448|gb|AAP56749.1|\tgi|3844826|gb|AAC71444.1|\t\r\n+OG0000503\t\tgi|284812091|gb|AAP56756.2|\tgi|3844811|gb|AAC71430.1|\t\r\n+OG0000504\t\tgi|31541465|gb|AAP56766.1|\t\tgi|144227651|gb|AAZ44558.2|\r\n+OG0000505\t\tgi|31541498|gb|AAP56798.1|\tgi|3844971|gb|AAC71609.1|\t\r\n+OG0000506\t\tgi|284812125|gb|AAP56801.2|\tgi|3844978|gb|AAC71616.1|\t\r\n+OG0000507\t\tgi|31541512|gb|AAP56812.1|\tgi|3844689|gb|AAC71319.1|\t\r\n+OG0000508\t\tgi|284812140|gb|AAP56821.2|\tgi|3844721|gb|AAC71348.1|\t\r\n+OG0000509\t\tgi|284812145|gb|AAP56827.2|\tgi|84626131|gb|AAC71620.2|\t\r\n+OG0000510\t\tgi|31541528|gb|AAP56828.1|\tgi|3844984|gb|AAC71621.1|\t\r\n+OG0000511\t\tgi|31541549|gb|AAP56849.1|\tgi|3844959|gb|AAC71598.1|\t\r\n+OG0000512\t\tgi|31541558|gb|AAP56858.1|\tgi|3844638|gb|AAC71244.1|\t\r\n+OG0000513\t\tgi|284812164|gb|AAP56866.2|\tgi|3844898|gb|AAC71543.1|\t\r\n+OG0000514\t\tgi|284812171|gb|AAP56875.2|\tgi|84626128|gb|AAC71502.2|\t\r\n+OG0000515\t\tgi|284812173|gb|AAP56879.2|\tgi|3845020|gb|AAC72448.1|\t\r\n+OG0000516\t\tgi|31541590|gb|AAP56890.1|\tgi|3844885|gb|AAC71528.1|\t\r\n+OG0000517\t\tgi|31541595|gb|AAP56895.1|\tgi|3844719|gb|AAC71346.1|\t\r\n+OG0000518\t\tgi|284812188|gb|AAP56896.2|\tgi|3844718|gb|AAC71345.1|\t\r\n+OG0000519\t\tgi|284812202|gb|AAP56917.2|\tgi|3844893|gb|AAC71538.1|\t\r\n+OG0000520\t\tgi|284812208|gb|AAP56924.2|\tgi|1045731|gb|AAC71274.1|\t\r\n+OG0000521\t\tgi|284812210|gb|AAP56926.2|\tgi|3844778|gb|AAC71401.1|\t\r\n+OG0000522\t\tgi|31541648|gb|AAP56948.1|\tgi|1045712|gb|AAC71256.1|\t\r\n+OG0000523\t\tgi|31541655|gb|AAP56955.1|\tgi|3844989|gb|AAC71625.1|\t\r\n+OG0000524\t\tgi|284812225|gb|AAP56960.2|\tgi|3844682|gb|AAC71313.1|\t\r\n+OG0000525\t\tgi|284812227|gb|AAP56967.2|\tgi|3844647|gb|AAC71253.1|\t\r\n+OG0000526\t\tgi|284812245|gb|AAP56998.2|\tgi|1045728|gb|AAC71271.1|\t\r\n+OG0000527\t\tgi|284812254|gb|AAP57010.2|\tgi|3844631|gb|AAC71238.1|\t\r\n+OG0000528\t\tgi|31541720|gb|AAP57020.1|\t\tgi|144227662|gb|AAZ44577.2|\r\n+OG0000529\t\tgi|284812281|gb|AAP57051.2|\tgi|3845001|gb|AAC71636.1|\t\r\n+OG0000530\t\tgi|284812282|gb|AAP57052.2|\tgi|84626126|gb|AAC71234.2|\t\r\n+OG0000531\t\tgi|31541763|gb|AAP57062.1|\tgi|84626158|gb|AAC72481.2|\t\r\n+OG0000532\t\tgi|284812300|gb|AAP57075.2|\tgi|84626152|gb|AAC71218.2|\t\r\n+OG0000533\t\t\tgi|84626147|gb|AAC71280.2|\tgi|71851703|gb|AAZ44311.1|\r\n+OG0000534\t\t\tgi|3844705|gb|AAC71333.1|\tgi|71851627|gb|AAZ44235.1|\r\n+OG0000535\t\t\tgi|3844873|gb|AAC71515.1|\tgi|71851777|gb|AAZ44385.1|\r\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/results_fromblast/Orthogroups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results_fromblast/Orthogroups.txt Tue Oct 24 06:40:40 2017 -0400 |
| b |
| b'@@ -0,0 +1,1331 @@\n+OG0000000: gi|284811953|gb|ADB96857.1| gi|284811954|gb|ADB96858.1| gi|284811955|gb|AAP56548.2| gi|284811956|gb|ADB96859.1| gi|284811957|gb|ADB96860.1| gi|284811958|gb|ADB96861.1| gi|284811959|gb|ADB96862.1| gi|284811960|gb|ADB96863.1| gi|284811961|gb|ADB96864.1| gi|284811962|gb|ADB96865.1| gi|284812039|gb|AAP56686.2| gi|284812040|gb|ADB96873.1| gi|284812041|gb|ADB96874.1| gi|284812042|gb|ADB96875.1| gi|284812103|gb|ADB96879.1| gi|284812104|gb|ADB96880.1| gi|284812105|gb|AAP56776.2| gi|284812107|gb|ADB96881.1| gi|284812108|gb|ADB96882.1| gi|284812128|gb|AAP56805.2| gi|284812129|gb|AAP56806.2| gi|284812217|gb|ADB96891.1| gi|284812218|gb|ADB96892.1| gi|284812219|gb|AAP56940.2| gi|31541243|gb|AAP56545.1| gi|31541245|gb|AAP56547.1| gi|31541247|gb|AAP56549.1| gi|31541248|gb|AAP56550.1| gi|31541249|gb|AAP56551.1| gi|31541250|gb|AAP56552.1| gi|31541251|gb|AAP56553.1| gi|31541252|gb|AAP56554.1| gi|31541253|gb|AAP56555.1| gi|31541386|gb|AAP56687.1| gi|31541387|gb|AAP56688.1| gi|31541388|gb|AAP56689.1| gi|31541389|gb|AAP56690.1| gi|31541390|gb|AAP56691.1| gi|31541391|gb|AAP56692.1| gi|31541392|gb|AAP56693.1| gi|31541393|gb|AAP56694.1| gi|31541394|gb|AAP56695.1| gi|31541395|gb|AAP56696.1| gi|31541396|gb|AAP56697.1| gi|31541398|gb|AAP56699.1| gi|31541472|gb|AAP56773.1| gi|31541473|gb|AAP56774.1| gi|31541474|gb|AAP56775.1| gi|31541478|gb|AAP56779.1| gi|31541641|gb|AAP56941.1| gi|31541642|gb|AAP56942.1| gi|31541643|gb|AAP56943.1| gi|31541644|gb|AAP56944.1| gi|31541645|gb|AAP56945.1| gi|31541646|gb|AAP56946.1| gi|31541647|gb|AAP56947.1|\n+OG0000001: gi|290752501|emb|CBH40473.1| gi|290752503|emb|CBH40475.1| gi|290752692|emb|CBH40666.1| gi|290752693|emb|CBH40667.1| gi|290752812|emb|CBH40787.1| gi|290752813|emb|CBH40788.1| gi|290752814|emb|CBH40789.1| gi|290752815|emb|CBH40790.1| gi|290752816|emb|CBH40791.1| gi|290752817|emb|CBH40792.1| gi|290752818|emb|CBH40793.1| gi|290753029|emb|CBH41005.1| gi|290753030|emb|CBH41006.1| gi|290753031|emb|CBH41007.1| gi|290753032|emb|CBH41008.1| gi|290753033|emb|CBH41009.1| gi|290753034|emb|CBH41010.1| gi|290753035|emb|CBH41011.1| gi|290753036|emb|CBH41012.1| gi|290753037|emb|CBH41013.1| gi|290753040|emb|CBH41016.1| gi|290753041|emb|CBH41017.1| gi|290753042|emb|CBH41018.1| gi|290753043|emb|CBH41019.1| gi|290753044|emb|CBH41020.1| gi|290753045|emb|CBH41021.1| gi|290753046|emb|CBH41022.1|\n+OG0000002: gi|1045740|gb|AAC71283.1| gi|1045987|gb|AAC71511.1| gi|144227640|gb|AAZ44535.2| gi|290752526|emb|CBH40498.1| gi|290752801|emb|CBH40776.1| gi|290752802|emb|CBH40777.1| gi|290753081|emb|CBH41057.1| gi|31541070|gb|AAP56372.1| gi|31541268|gb|AAP56569.1| gi|31541628|gb|AAP56928.1| gi|31541629|gb|AAP56929.1| gi|3844775|gb|AAC71398.1| gi|3844776|gb|AAC71399.1| gi|3844882|gb|AAC71525.1| gi|3845062|gb|AAC72487.1| gi|3845064|gb|AAC72489.1| gi|71851738|gb|AAZ44346.1| gi|71851739|gb|AAZ44347.1| gi|71851837|gb|AAZ44445.1| gi|84626133|gb|AAC71526.2|\n+OG0000003: gi|1046010|gb|AAC71532.1| gi|144227478|gb|AAZ44221.2| gi|290752269|emb|CBH40240.1| gi|290752270|emb|CBH40241.1| gi|290752414|emb|CBH40385.1| gi|290752490|emb|CBH40462.1| gi|290752766|emb|CBH40741.1| gi|31541260|gb|AAP56562.1| gi|31541382|gb|AAP56683.1| gi|3844907|gb|AAC71551.1| gi|3844927|gb|AAC71569.1|\n+OG0000004: gi|1046012|gb|AAC71534.1| gi|284811924|gb|AAP56500.2| gi|284811927|gb|ADB96855.1| gi|284811928|gb|ADB96856.1| gi|284812192|gb|AAP56901.2| gi|290753066|emb|CBH41042.1| gi|31541553|gb|AAP56853.1| gi|3844628|gb|AAC71235.1| gi|3844797|gb|AAC71418.1| gi|3844975|gb|AAC71613.1| gi|71851550|gb|AAZ44158.1|\n+OG0000005: gi|1045683|gb|AAC71230.1| gi|1045684|gb|AAC71231.1| gi|284811835|gb|AAP56356.2| gi|284812058|gb|AAP56715.2| gi|290752591|emb|CBH40563.1| gi|290752592|emb|CBH40564.1| gi|290752893|emb|CBH40868.1| gi|290752894|emb|CBH40869.1| gi|31541415|gb|AAP56716.1|\n+OG0000006: gi|31541304|gb|AAP56605.1| gi|71851504|gb|AAZ44112.1| gi|71851505|gb|AAZ44113.1| gi|71851506|gb|AAZ44114.1| gi|71851779|gb|AAZ44387.1| gi|71851788|gb|AAZ44396.1| gi|71851789|gb|AAZ'..b'01230: gi|144227613|gb|AAZ44488.2|\n+OG0001231: gi|71851881|gb|AAZ44489.1|\n+OG0001232: gi|144227616|gb|AAZ44498.2|\n+OG0001233: gi|144227617|gb|AAZ44499.2|\n+OG0001234: gi|144227618|gb|AAZ44501.2|\n+OG0001235: gi|71851895|gb|AAZ44503.1|\n+OG0001236: gi|71851899|gb|AAZ44507.1|\n+OG0001237: gi|71851900|gb|AAZ44508.1|\n+OG0001238: gi|71851902|gb|AAZ44510.1|\n+OG0001239: gi|144227625|gb|AAZ44516.2|\n+OG0001240: gi|71851909|gb|AAZ44517.1|\n+OG0001241: gi|144227629|gb|AAZ44523.2|\n+OG0001242: gi|144227630|gb|AAZ44524.2|\n+OG0001243: gi|144227631|gb|AAZ44526.2|\n+OG0001244: gi|144227632|gb|AAZ44527.2|\n+OG0001245: gi|144227633|gb|ABO93479.1|\n+OG0001246: gi|144227634|gb|AAZ44528.2|\n+OG0001247: gi|71851921|gb|AAZ44529.1|\n+OG0001248: gi|144227635|gb|AAZ44530.2|\n+OG0001249: gi|144227636|gb|AAZ44531.2|\n+OG0001250: gi|71851929|gb|AAZ44537.1|\n+OG0001251: gi|71851936|gb|AAZ44544.1|\n+OG0001252: gi|144227644|gb|AAZ44545.2|\n+OG0001253: gi|144227645|gb|AAZ44546.2|\n+OG0001254: gi|144227647|gb|AAZ44549.2|\n+OG0001255: gi|144227650|gb|AAZ44554.2|\n+OG0001256: gi|71851956|gb|AAZ44564.1|\n+OG0001257: gi|144227656|gb|AAZ44567.2|\n+OG0001258: gi|144227660|gb|AAZ44572.2|\n+OG0001259: gi|71851966|gb|AAZ44574.1|\n+OG0001260: gi|144227661|gb|AAZ44576.2|\n+OG0001261: gi|71851971|gb|AAZ44579.1|\n+OG0001262: gi|71851972|gb|AAZ44580.1|\n+OG0001263: gi|71851985|gb|AAZ44593.1|\n+OG0001264: gi|71851986|gb|AAZ44594.1|\n+OG0001265: gi|144227667|gb|AAZ44595.2|\n+OG0001266: gi|71851988|gb|AAZ44596.1|\n+OG0001267: gi|71851989|gb|AAZ44597.1|\n+OG0001268: gi|144227668|gb|AAZ44598.2|\n+OG0001269: gi|71851991|gb|AAZ44599.1|\n+OG0001270: gi|144227669|gb|AAZ44600.2|\n+OG0001271: gi|144227670|gb|AAZ44601.2|\n+OG0001272: gi|144227671|gb|AAZ44602.2|\n+OG0001273: gi|144227672|gb|AAZ44604.2|\n+OG0001274: gi|144227673|gb|AAZ44605.2|\n+OG0001275: gi|144227674|gb|AAZ44606.2|\n+OG0001276: gi|144227675|gb|AAZ44607.2|\n+OG0001277: gi|144227676|gb|ABO93480.1|\n+OG0001278: gi|144227681|gb|AAZ44617.2|\n+OG0001279: gi|144227683|gb|AAZ44623.2|\n+OG0001280: gi|144227688|gb|ABO93481.1|\n+OG0001281: gi|144227689|gb|AAZ44632.2|\n+OG0001282: gi|71852025|gb|AAZ44633.1|\n+OG0001283: gi|144227690|gb|AAZ44637.2|\n+OG0001284: gi|71852030|gb|AAZ44638.1|\n+OG0001285: gi|144227691|gb|AAZ44639.2|\n+OG0001286: gi|71852032|gb|AAZ44640.1|\n+OG0001287: gi|71852034|gb|AAZ44642.1|\n+OG0001288: gi|71852035|gb|AAZ44643.1|\n+OG0001289: gi|144227693|gb|AAZ44644.2|\n+OG0001290: gi|144227694|gb|ABO93482.1|\n+OG0001291: gi|144227695|gb|AAZ44645.2|\n+OG0001292: gi|71852038|gb|AAZ44646.1|\n+OG0001293: gi|144227696|gb|AAZ44647.2|\n+OG0001294: gi|71852040|gb|AAZ44648.1|\n+OG0001295: gi|144227697|gb|AAZ44650.2|\n+OG0001296: gi|71852043|gb|AAZ44651.1|\n+OG0001297: gi|144227698|gb|ABO93483.1|\n+OG0001298: gi|144227699|gb|AAZ44652.2|\n+OG0001299: gi|144227700|gb|AAZ44653.2|\n+OG0001300: gi|144227701|gb|AAZ44654.2|\n+OG0001301: gi|71852048|gb|AAZ44656.1|\n+OG0001302: gi|144227703|gb|AAZ44657.2|\n+OG0001303: gi|144227704|gb|AAZ44658.2|\n+OG0001304: gi|71852052|gb|AAZ44660.1|\n+OG0001305: gi|144227707|gb|AAZ44671.2|\n+OG0001306: gi|144227709|gb|ABO93484.1|\n+OG0001307: gi|144227715|gb|AAZ44680.2|\n+OG0001308: gi|144227716|gb|AAZ44681.2|\n+OG0001309: gi|144227717|gb|AAZ44682.2|\n+OG0001310: gi|71852075|gb|AAZ44683.1|\n+OG0001311: gi|144227718|gb|AAZ44684.2|\n+OG0001312: gi|71852077|gb|AAZ44685.1|\n+OG0001313: gi|144227719|gb|AAZ44686.2|\n+OG0001314: gi|144227725|gb|AAZ44696.2|\n+OG0001315: gi|144227730|gb|AAZ44708.2|\n+OG0001316: gi|71852101|gb|AAZ44709.1|\n+OG0001317: gi|144227731|gb|AAZ44711.2|\n+OG0001318: gi|144227732|gb|AAZ44712.2|\n+OG0001319: gi|144227736|gb|AAZ44718.2|\n+OG0001320: gi|71852114|gb|AAZ44722.1|\n+OG0001321: gi|144227745|gb|AAZ44743.2|\n+OG0001322: gi|144227746|gb|AAZ44744.2|\n+OG0001323: gi|144227747|gb|AAZ44745.2|\n+OG0001324: gi|71852138|gb|AAZ44746.1|\n+OG0001325: gi|71852139|gb|AAZ44747.1|\n+OG0001326: gi|71852141|gb|AAZ44749.1|\n+OG0001327: gi|144227748|gb|AAZ44751.2|\n+OG0001328: gi|71852145|gb|AAZ44753.1|\n+OG0001329: gi|144227749|gb|AAZ44755.2|\n+OG0001330: gi|144227750|gb|AAZ44756.2|\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/results_fromblast/Orthogroups_SpeciesOverlaps.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results_fromblast/Orthogroups_SpeciesOverlaps.csv Tue Oct 24 06:40:40 2017 -0400 |
| b |
| @@ -0,0 +1,5 @@ + Mycoplasma_agalactiae Mycoplasma_gallisepticum Mycoplasma_genitalium Mycoplasma_hyopneumoniae +Mycoplasma_agalactiae 430 358 302 389 +Mycoplasma_gallisepticum 358 459 383 344 +Mycoplasma_genitalium 302 383 392 294 +Mycoplasma_hyopneumoniae 389 344 294 416 |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/results_fromblast/Orthogroups_UnassignedGenes.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results_fromblast/Orthogroups_UnassignedGenes.csv Tue Oct 24 06:40:40 2017 -0400 |
| b |
| b'@@ -0,0 +1,796 @@\n+\tMycoplasma_agalactiae\tMycoplasma_gallisepticum\tMycoplasma_genitalium\tMycoplasma_hyopneumoniae\r\n+OG0000536\tgi|290752272|emb|CBH40243.1|\t\t\t\r\n+OG0000537\tgi|290752276|emb|CBH40247.1|\t\t\t\r\n+OG0000538\tgi|290752279|emb|CBH40250.1|\t\t\t\r\n+OG0000539\tgi|290752285|emb|CBH40256.1|\t\t\t\r\n+OG0000540\tgi|290752286|emb|CBH40257.1|\t\t\t\r\n+OG0000541\tgi|290752287|emb|CBH40258.1|\t\t\t\r\n+OG0000542\tgi|290752288|emb|CBH40259.1|\t\t\t\r\n+OG0000543\tgi|290752289|emb|CBH40260.1|\t\t\t\r\n+OG0000544\tgi|290752290|emb|CBH40261.1|\t\t\t\r\n+OG0000545\tgi|290752291|emb|CBH40262.1|\t\t\t\r\n+OG0000546\tgi|290752293|emb|CBH40264.1|\t\t\t\r\n+OG0000547\tgi|290752294|emb|CBH40265.1|\t\t\t\r\n+OG0000548\tgi|290752295|emb|CBH40266.1|\t\t\t\r\n+OG0000549\tgi|290752296|emb|CBH40267.1|\t\t\t\r\n+OG0000550\tgi|290752297|emb|CBH40268.1|\t\t\t\r\n+OG0000551\tgi|290752306|emb|CBH40277.1|\t\t\t\r\n+OG0000552\tgi|290752310|emb|CBH40281.1|\t\t\t\r\n+OG0000553\tgi|290752313|emb|CBH40284.1|\t\t\t\r\n+OG0000554\tgi|290752314|emb|CBH40285.1|\t\t\t\r\n+OG0000555\tgi|290752319|emb|CBH40290.1|\t\t\t\r\n+OG0000556\tgi|290752342|emb|CBH40313.1|\t\t\t\r\n+OG0000557\tgi|290752345|emb|CBH40316.1|\t\t\t\r\n+OG0000558\tgi|290752348|emb|CBH40319.1|\t\t\t\r\n+OG0000559\tgi|290752349|emb|CBH40320.1|\t\t\t\r\n+OG0000560\tgi|290752350|emb|CBH40321.1|\t\t\t\r\n+OG0000561\tgi|290752353|emb|CBH40324.1|\t\t\t\r\n+OG0000562\tgi|290752355|emb|CBH40326.1|\t\t\t\r\n+OG0000563\tgi|290752359|emb|CBH40330.1|\t\t\t\r\n+OG0000564\tgi|290752362|emb|CBH40333.1|\t\t\t\r\n+OG0000565\tgi|290752367|emb|CBH40338.1|\t\t\t\r\n+OG0000566\tgi|290752368|emb|CBH40339.1|\t\t\t\r\n+OG0000567\tgi|290752374|emb|CBH40345.1|\t\t\t\r\n+OG0000568\tgi|290752375|emb|CBH40346.1|\t\t\t\r\n+OG0000569\tgi|290752377|emb|CBH40348.1|\t\t\t\r\n+OG0000570\tgi|290752380|emb|CBH40351.1|\t\t\t\r\n+OG0000571\tgi|290752387|emb|CBH40358.1|\t\t\t\r\n+OG0000572\tgi|290752389|emb|CBH40360.1|\t\t\t\r\n+OG0000573\tgi|290752396|emb|CBH40367.1|\t\t\t\r\n+OG0000574\tgi|290752398|emb|CBH40369.1|\t\t\t\r\n+OG0000575\tgi|290752399|emb|CBH40370.1|\t\t\t\r\n+OG0000576\tgi|290752400|emb|CBH40371.1|\t\t\t\r\n+OG0000577\tgi|290752405|emb|CBH40376.1|\t\t\t\r\n+OG0000578\tgi|290752407|emb|CBH40378.1|\t\t\t\r\n+OG0000579\tgi|290752409|emb|CBH40380.1|\t\t\t\r\n+OG0000580\tgi|290752411|emb|CBH40382.1|\t\t\t\r\n+OG0000581\tgi|290752412|emb|CBH40383.1|\t\t\t\r\n+OG0000582\tgi|290752413|emb|CBH40384.1|\t\t\t\r\n+OG0000583\tgi|290752415|emb|CBH40386.1|\t\t\t\r\n+OG0000584\tgi|290752417|emb|CBH40388.1|\t\t\t\r\n+OG0000585\tgi|290752419|emb|CBH40390.1|\t\t\t\r\n+OG0000586\tgi|290752421|emb|CBH40392.1|\t\t\t\r\n+OG0000587\tgi|290752423|emb|CBH40394.1|\t\t\t\r\n+OG0000588\tgi|290752424|emb|CBH40395.1|\t\t\t\r\n+OG0000589\tgi|290752425|emb|CBH40396.1|\t\t\t\r\n+OG0000590\tgi|290752428|emb|CBH40399.1|\t\t\t\r\n+OG0000591\tgi|290752429|emb|CBH40400.1|\t\t\t\r\n+OG0000592\tgi|290752430|emb|CBH40401.1|\t\t\t\r\n+OG0000593\tgi|290752432|emb|CBH40403.1|\t\t\t\r\n+OG0000594\tgi|290752436|emb|CBH40407.1|\t\t\t\r\n+OG0000595\tgi|290752439|emb|CBH40410.1|\t\t\t\r\n+OG0000596\tgi|290752444|emb|CBH40415.1|\t\t\t\r\n+OG0000597\tgi|290752447|emb|CBH40418.1|\t\t\t\r\n+OG0000598\tgi|290752448|emb|CBH40420.1|\t\t\t\r\n+OG0000599\tgi|290752449|emb|CBH40421.1|\t\t\t\r\n+OG0000600\tgi|290752453|emb|CBH40425.1|\t\t\t\r\n+OG0000601\tgi|290752457|emb|CBH40429.1|\t\t\t\r\n+OG0000602\tgi|290752462|emb|CBH40434.1|\t\t\t\r\n+OG0000603\tgi|290752466|emb|CBH40438.1|\t\t\t\r\n+OG0000604\tgi|290752472|emb|CBH40444.1|\t\t\t\r\n+OG0000605\tgi|290752473|emb|CBH40445.1|\t\t\t\r\n+OG0000606\tgi|290752474|emb|CBH40446.1|\t\t\t\r\n+OG0000607\tgi|290752475|emb|CBH40447.1|\t\t\t\r\n+OG0000608\tgi|290752476|emb|CBH40448.1|\t\t\t\r\n+OG0000609\tgi|290752495|emb|CBH40467.1|\t\t\t\r\n+OG0000610\tgi|290752500|emb|CBH40472.1|\t\t\t\r\n+OG0000611\tgi|290752502|emb|CBH40474.1|\t\t\t\r\n+OG0000612\tgi|290752505|emb|CBH40477.1|\t\t\t\r\n+OG0000613\tgi|290752506|emb|CBH40478.1|\t\t\t\r\n+OG0000614\tgi|290752507|emb|CBH40479.1|\t\t\t\r\n+OG0000615\tgi|290752509|emb|CBH40481.1|\t\t\t\r\n+OG0000616\tgi|290752510|emb|CBH40482.1|\t\t\t\r\n+OG0000617\tgi|290752511|emb|CBH40483.1|\t\t\t\r\n+OG0000618\tgi|290752512|emb|CBH40484.1|\t\t\t\r\n+OG0000619\tgi|290752514|emb|CBH40486.1|\t\t\t\r\n+OG0000620\tgi|290752517|emb|CBH40489.1|\t\t\t\r\n+OG0000621\tgi|290752524|emb|CBH40496.1|\t\t\t\r\n+OG0000622\tgi|290752528|emb|CBH40500.1|\t\t\t\r\n+OG0000623\tgi|290752537|emb|CBH40509.1|\t\t\t\r\n+OG0000624\tg'..b'\t\t\t\tgi|71851900|gb|AAZ44508.1|\r\n+OG0001238\t\t\t\tgi|71851902|gb|AAZ44510.1|\r\n+OG0001239\t\t\t\tgi|144227625|gb|AAZ44516.2|\r\n+OG0001240\t\t\t\tgi|71851909|gb|AAZ44517.1|\r\n+OG0001241\t\t\t\tgi|144227629|gb|AAZ44523.2|\r\n+OG0001242\t\t\t\tgi|144227630|gb|AAZ44524.2|\r\n+OG0001243\t\t\t\tgi|144227631|gb|AAZ44526.2|\r\n+OG0001244\t\t\t\tgi|144227632|gb|AAZ44527.2|\r\n+OG0001245\t\t\t\tgi|144227633|gb|ABO93479.1|\r\n+OG0001246\t\t\t\tgi|144227634|gb|AAZ44528.2|\r\n+OG0001247\t\t\t\tgi|71851921|gb|AAZ44529.1|\r\n+OG0001248\t\t\t\tgi|144227635|gb|AAZ44530.2|\r\n+OG0001249\t\t\t\tgi|144227636|gb|AAZ44531.2|\r\n+OG0001250\t\t\t\tgi|71851929|gb|AAZ44537.1|\r\n+OG0001251\t\t\t\tgi|71851936|gb|AAZ44544.1|\r\n+OG0001252\t\t\t\tgi|144227644|gb|AAZ44545.2|\r\n+OG0001253\t\t\t\tgi|144227645|gb|AAZ44546.2|\r\n+OG0001254\t\t\t\tgi|144227647|gb|AAZ44549.2|\r\n+OG0001255\t\t\t\tgi|144227650|gb|AAZ44554.2|\r\n+OG0001256\t\t\t\tgi|71851956|gb|AAZ44564.1|\r\n+OG0001257\t\t\t\tgi|144227656|gb|AAZ44567.2|\r\n+OG0001258\t\t\t\tgi|144227660|gb|AAZ44572.2|\r\n+OG0001259\t\t\t\tgi|71851966|gb|AAZ44574.1|\r\n+OG0001260\t\t\t\tgi|144227661|gb|AAZ44576.2|\r\n+OG0001261\t\t\t\tgi|71851971|gb|AAZ44579.1|\r\n+OG0001262\t\t\t\tgi|71851972|gb|AAZ44580.1|\r\n+OG0001263\t\t\t\tgi|71851985|gb|AAZ44593.1|\r\n+OG0001264\t\t\t\tgi|71851986|gb|AAZ44594.1|\r\n+OG0001265\t\t\t\tgi|144227667|gb|AAZ44595.2|\r\n+OG0001266\t\t\t\tgi|71851988|gb|AAZ44596.1|\r\n+OG0001267\t\t\t\tgi|71851989|gb|AAZ44597.1|\r\n+OG0001268\t\t\t\tgi|144227668|gb|AAZ44598.2|\r\n+OG0001269\t\t\t\tgi|71851991|gb|AAZ44599.1|\r\n+OG0001270\t\t\t\tgi|144227669|gb|AAZ44600.2|\r\n+OG0001271\t\t\t\tgi|144227670|gb|AAZ44601.2|\r\n+OG0001272\t\t\t\tgi|144227671|gb|AAZ44602.2|\r\n+OG0001273\t\t\t\tgi|144227672|gb|AAZ44604.2|\r\n+OG0001274\t\t\t\tgi|144227673|gb|AAZ44605.2|\r\n+OG0001275\t\t\t\tgi|144227674|gb|AAZ44606.2|\r\n+OG0001276\t\t\t\tgi|144227675|gb|AAZ44607.2|\r\n+OG0001277\t\t\t\tgi|144227676|gb|ABO93480.1|\r\n+OG0001278\t\t\t\tgi|144227681|gb|AAZ44617.2|\r\n+OG0001279\t\t\t\tgi|144227683|gb|AAZ44623.2|\r\n+OG0001280\t\t\t\tgi|144227688|gb|ABO93481.1|\r\n+OG0001281\t\t\t\tgi|144227689|gb|AAZ44632.2|\r\n+OG0001282\t\t\t\tgi|71852025|gb|AAZ44633.1|\r\n+OG0001283\t\t\t\tgi|144227690|gb|AAZ44637.2|\r\n+OG0001284\t\t\t\tgi|71852030|gb|AAZ44638.1|\r\n+OG0001285\t\t\t\tgi|144227691|gb|AAZ44639.2|\r\n+OG0001286\t\t\t\tgi|71852032|gb|AAZ44640.1|\r\n+OG0001287\t\t\t\tgi|71852034|gb|AAZ44642.1|\r\n+OG0001288\t\t\t\tgi|71852035|gb|AAZ44643.1|\r\n+OG0001289\t\t\t\tgi|144227693|gb|AAZ44644.2|\r\n+OG0001290\t\t\t\tgi|144227694|gb|ABO93482.1|\r\n+OG0001291\t\t\t\tgi|144227695|gb|AAZ44645.2|\r\n+OG0001292\t\t\t\tgi|71852038|gb|AAZ44646.1|\r\n+OG0001293\t\t\t\tgi|144227696|gb|AAZ44647.2|\r\n+OG0001294\t\t\t\tgi|71852040|gb|AAZ44648.1|\r\n+OG0001295\t\t\t\tgi|144227697|gb|AAZ44650.2|\r\n+OG0001296\t\t\t\tgi|71852043|gb|AAZ44651.1|\r\n+OG0001297\t\t\t\tgi|144227698|gb|ABO93483.1|\r\n+OG0001298\t\t\t\tgi|144227699|gb|AAZ44652.2|\r\n+OG0001299\t\t\t\tgi|144227700|gb|AAZ44653.2|\r\n+OG0001300\t\t\t\tgi|144227701|gb|AAZ44654.2|\r\n+OG0001301\t\t\t\tgi|71852048|gb|AAZ44656.1|\r\n+OG0001302\t\t\t\tgi|144227703|gb|AAZ44657.2|\r\n+OG0001303\t\t\t\tgi|144227704|gb|AAZ44658.2|\r\n+OG0001304\t\t\t\tgi|71852052|gb|AAZ44660.1|\r\n+OG0001305\t\t\t\tgi|144227707|gb|AAZ44671.2|\r\n+OG0001306\t\t\t\tgi|144227709|gb|ABO93484.1|\r\n+OG0001307\t\t\t\tgi|144227715|gb|AAZ44680.2|\r\n+OG0001308\t\t\t\tgi|144227716|gb|AAZ44681.2|\r\n+OG0001309\t\t\t\tgi|144227717|gb|AAZ44682.2|\r\n+OG0001310\t\t\t\tgi|71852075|gb|AAZ44683.1|\r\n+OG0001311\t\t\t\tgi|144227718|gb|AAZ44684.2|\r\n+OG0001312\t\t\t\tgi|71852077|gb|AAZ44685.1|\r\n+OG0001313\t\t\t\tgi|144227719|gb|AAZ44686.2|\r\n+OG0001314\t\t\t\tgi|144227725|gb|AAZ44696.2|\r\n+OG0001315\t\t\t\tgi|144227730|gb|AAZ44708.2|\r\n+OG0001316\t\t\t\tgi|71852101|gb|AAZ44709.1|\r\n+OG0001317\t\t\t\tgi|144227731|gb|AAZ44711.2|\r\n+OG0001318\t\t\t\tgi|144227732|gb|AAZ44712.2|\r\n+OG0001319\t\t\t\tgi|144227736|gb|AAZ44718.2|\r\n+OG0001320\t\t\t\tgi|71852114|gb|AAZ44722.1|\r\n+OG0001321\t\t\t\tgi|144227745|gb|AAZ44743.2|\r\n+OG0001322\t\t\t\tgi|144227746|gb|AAZ44744.2|\r\n+OG0001323\t\t\t\tgi|144227747|gb|AAZ44745.2|\r\n+OG0001324\t\t\t\tgi|71852138|gb|AAZ44746.1|\r\n+OG0001325\t\t\t\tgi|71852139|gb|AAZ44747.1|\r\n+OG0001326\t\t\t\tgi|71852141|gb|AAZ44749.1|\r\n+OG0001327\t\t\t\tgi|144227748|gb|AAZ44751.2|\r\n+OG0001328\t\t\t\tgi|71852145|gb|AAZ44753.1|\r\n+OG0001329\t\t\t\tgi|144227749|gb|AAZ44755.2|\r\n+OG0001330\t\t\t\tgi|144227750|gb|AAZ44756.2|\r\n' |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/results_fromblast/Statistics_Overall.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results_fromblast/Statistics_Overall.csv Tue Oct 24 06:40:40 2017 -0400 |
| b |
| @@ -0,0 +1,51 @@ +Number of genes 2733 +Number of genes in orthogroups 1938 +Number of unassigned genes 795 +Percentage of genes in orthogroups 70.9 +Percentage of unassigned genes 29.1 +Number of orthogroups 536 +Number of species-specific orthogroups 6 +Number of genes in species-specific orthogroups 100 +Percentage of genes in species-specific orthogroups 3.7 +Mean orthogroup size 3.6 +Median orthogroup size 4.0 +G50 (assigned genes) 4 +G50 (all genes) 4 +O50 (assigned genes) 199 +O50 (all genes) 299 +Number of orthogroups with all species present 278 +Number of single-copy orthogroups 254 +Date 2017-06-08 +Orthogroups file Orthogroups.csv +Unassigned genes file Orthogroups_UnassignedGenes.csv +Per-species statistics Statistics_PerSpecies.csv +Overall statistics Statistics_Overall.csv +Orthogroups shared between species Orthogroups_SpeciesOverlaps.csv + +Average number of genes per-species in orthogroup Number of orthogroups Percentage of orthogroups Number of genes Percentage of genes +<1 224 41.8 516 26.6 +'1 302 56.3 1254 64.7 +'2 7 1.3 65 3.4 +'3 0 0.0 0 0.0 +'4 0 0.0 0 0.0 +'5 1 0.2 20 1.0 +'6 1 0.2 27 1.4 +'7 0 0.0 0 0.0 +'8 0 0.0 0 0.0 +'9 0 0.0 0 0.0 +'10 0 0.0 0 0.0 +11-15 1 0.2 56 2.9 +16-20 0 0.0 0 0.0 +21-50 0 0.0 0 0.0 +51-100 0 0.0 0 0.0 +101-150 0 0.0 0 0.0 +151-200 0 0.0 0 0.0 +201-500 0 0.0 0 0.0 +501-1000 0 0.0 0 0.0 +'1001+ 0 0.0 0 0.0 + +Number of species in orthogroup Number of orthogroups +1 6 +2 177 +3 75 +4 278 |
| b |
| diff -r 000000000000 -r bfb20dbe1309 test-data/results_fromblast/Statistics_PerSpecies.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results_fromblast/Statistics_PerSpecies.csv Tue Oct 24 06:40:40 2017 -0400 |
| b |
| @@ -0,0 +1,100 @@ + Mycoplasma_agalactiae Mycoplasma_gallisepticum Mycoplasma_genitalium Mycoplasma_hyopneumoniae +Number of genes 820 763 476 674 +Number of genes in orthogroups 503 561 429 445 +Number of unassigned genes 317 202 47 229 +Percentage of genes in orthogroups 61.3 73.5 90.1 66.0 +Percentage of unassigned genes 38.7 26.5 9.9 34.0 +Number of orthogroups containing species 430 459 392 416 +Percentage of orthogroups containing species 80.2 85.6 73.1 77.6 +Number of species-specific orthogroups 3 2 0 1 +Number of genes in species-specific orthogroups 34 61 0 5 +Percentage of genes in species-specific orthogroups 4.1 8.0 0.0 0.7 + + +Number of genes per-species in orthogroup Number of orthogroups Number of orthogroups Number of orthogroups Number of orthogroups +'0 106 77 144 120 +'1 398 427 368 405 +'2 21 21 17 6 +'3 6 6 5 1 +'4 2 2 1 1 +'5 2 2 0 1 +'6 0 0 0 0 +'7 0 0 0 0 +'8 0 0 1 2 +'9 0 0 0 0 +'10 0 0 0 0 +11-15 0 0 0 0 +16-20 0 0 0 0 +21-50 1 0 0 0 +51-100 0 1 0 0 +101-150 0 0 0 0 +151-200 0 0 0 0 +201-500 0 0 0 0 +501-1000 0 0 0 0 +'1001+ 0 0 0 0 + +Number of genes per-species in orthogroup Percentage of orthogroups Percentage of orthogroups Percentage of orthogroups Percentage of orthogroups +'0 19.8 14.4 26.9 22.4 +'1 74.3 79.7 68.7 75.6 +'2 3.9 3.9 3.2 1.1 +'3 1.1 1.1 0.9 0.2 +'4 0.4 0.4 0.2 0.2 +'5 0.4 0.4 0.0 0.2 +'6 0.0 0.0 0.0 0.0 +'7 0.0 0.0 0.0 0.0 +'8 0.0 0.0 0.2 0.4 +'9 0.0 0.0 0.0 0.0 +'10 0.0 0.0 0.0 0.0 +11-15 0.0 0.0 0.0 0.0 +16-20 0.0 0.0 0.0 0.0 +21-50 0.2 0.0 0.0 0.0 +51-100 0.0 0.2 0.0 0.0 +101-150 0.0 0.0 0.0 0.0 +151-200 0.0 0.0 0.0 0.0 +201-500 0.0 0.0 0.0 0.0 +501-1000 0.0 0.0 0.0 0.0 +'1001+ 0.0 0.0 0.0 0.0 + +Number of genes per-species in orthogroup Number of genes Number of genes Number of genes Number of genes +'0 0 0 0 0 +'1 398 427 368 405 +'2 42 42 34 12 +'3 18 18 15 3 +'4 8 8 4 4 +'5 10 10 0 5 +'6 0 0 0 0 +'7 0 0 0 0 +'8 0 0 8 16 +'9 0 0 0 0 +'10 0 0 0 0 +11-15 0 0 0 0 +16-20 0 0 0 0 +21-50 27 0 0 0 +51-100 0 56 0 0 +101-150 0 0 0 0 +151-200 0 0 0 0 +201-500 0 0 0 0 +501-1000 0 0 0 0 +'1001+ 0 0 0 0 + +Number of genes per-species in orthogroup Percentage of genes Percentage of genes Percentage of genes Percentage of genes +'0 0.0 0.0 0.0 0.0 +'1 48.5 56.0 77.3 60.1 +'2 5.1 5.5 7.1 1.8 +'3 2.2 2.4 3.2 0.4 +'4 1.0 1.0 0.8 0.6 +'5 1.2 1.3 0.0 0.7 +'6 0.0 0.0 0.0 0.0 +'7 0.0 0.0 0.0 0.0 +'8 0.0 0.0 1.7 2.4 +'9 0.0 0.0 0.0 0.0 +'10 0.0 0.0 0.0 0.0 +11-15 0.0 0.0 0.0 0.0 +16-20 0.0 0.0 0.0 0.0 +21-50 3.3 0.0 0.0 0.0 +51-100 0.0 7.3 0.0 0.0 +101-150 0.0 0.0 0.0 0.0 +151-200 0.0 0.0 0.0 0.0 +201-500 0.0 0.0 0.0 0.0 +501-1000 0.0 0.0 0.0 0.0 +'1001+ 0.0 0.0 0.0 0.0 |