| Next changeset 1:2eebe7f521f3 (2024-03-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a |
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added:
macros.xml omark.xml test-data/db/test.h5 test-data/input.fasta test-data/omamer.loc test-data/output.omamer test-data/output.omq test-data/output.pdf test-data/output.png test-data/output.sum test-data/output.tax test-data/output.ump test-data/output_Ho.omamer test-data/output_detailed_summary.txt test-data/test.fasta tool-data/omamer.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r ce13b4c42256 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Feb 21 19:27:16 2024 +0000 |
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| @@ -0,0 +1,15 @@ +<macros> + <token name="@TOOL_VERSION@">0.3.0</token> + + <xml name="requirements"> + <requirement type="package" version="@TOOL_VERSION@">omark</requirement> + <requirement type="package" version="2.0.2">omamer</requirement> + </xml> + + <xml name="citation"> + <citations> + <citation type="doi">10.1101/2022.11.25.517970</citation> + </citations> + </xml> + +</macros> |
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| diff -r 000000000000 -r ce13b4c42256 omark.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omark.xml Wed Feb 21 19:27:16 2024 +0000 |
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| @@ -0,0 +1,108 @@ +<?xml version="1.0"?> +<tool id="omark" name="OMArk" version="@TOOL_VERSION@+galaxy0" profile="21.05"> + <description>proteome quality assessment</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <expand macro="requirements" /> + </requirements> + + <command detect_errors="exit_code"><![CDATA[ + omamer search --db '$database' --query '$input' --out 'output_omamer' + && + + omark + -f 'output_omamer' + -d '$database' + $omark_mode + -i '$input_iso' + -t 't' + -r 'r' + -o omark_galaxy + + ]]></command> + + <inputs> + <param name="input" type="data" format="fasta" label="Protein sequences"/> + <param name="input_iso" type="data" format="txt" optional="true" label="Input isoform file" help="A semi-colon separated file, listing all isoforms of each genes, with one gene per line."/> + <param argument="-c" name="omark_mode" type="boolean" checked="false" label="Only compute a list of conserved HOGs" help="Can be used to obtain a set of genes on which to train"/> + <param name="database" label="OMAmer database" type="select"> + <options from_data_table="omamer"/> + </param> + + <param argument="-t" type="text" optional="true" label="Taxonomic identifier" help="NCBI taxid corresponding to the input proteome"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + </sanitizer> + <validator type="regex">[0-9a-zA-Z_]+</validator> + </param> + <param argument="-r" type="text" optional="true" label="Taxonomic rank"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + </sanitizer> + <validator type="regex">[0-9a-zA-Z_]+</validator> + </param> + + <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated"> + <option value="detail_sum" selected="true">Detailed summary</option> + <option value="hog">HOG identifiers</option> + <option value="pdf">PDF Graphic representation </option> + <option value="png">PNG Graphic representation </option> + <option value="sum">Comparative proteome analysis</option> + <option value="tax">Taxomony</option> + <option value="ump">Protein identifiers</option> + </param> + </inputs> + + <outputs> + <data name="omark_detail_sum" format="txt" label="${tool.name} on ${on_string}: Detailed summary" from_work_dir="omark_galaxy/*detailed_summary.txt"> + <filter>outputs and 'detail_sum' in outputs</filter> + </data> + <data name="omark_hog" format="omq" label="${tool.name} on ${on_string}: HOG identifiers" from_work_dir="omark_galaxy/*.omq"> + <filter>outputs and 'hog' in outputs</filter> + </data> + <data name="omark_pdf" format="pdf" label="${tool.name} on ${on_string}: Graphic representation (pdf)" from_work_dir="omark_galaxy/*.pdf"> + <filter>outputs and 'pdf' in outputs</filter> + </data> + <data name="omark_png" format="png" label="${tool.name} on ${on_string}: Graphic representation (png)" from_work_dir="omark_galaxy/*.png"> + <filter>outputs and 'png' in outputs</filter> + </data> + <data name="omark_sum" format="sum" label="${tool.name} on ${on_string}: Comparative proteome analysis" from_work_dir="omark_galaxy/*.sum"> + <filter>outputs and 'sum' in outputs</filter> + </data> + <data name="omark_tax" format="txt" label="${tool.name} on ${on_string}: Taxomony" from_work_dir="omark_galaxy/*.tax"> + <filter>outputs and 'tax' in outputs</filter> + </data> + <data name="omark_ump" format="ump" label="${tool.name} on ${on_string}: Protein identifiers" from_work_dir="omark_galaxy/*.ump"> + <filter>outputs and 'ump' in outputs</filter> + </data> + </outputs> + + <tests> + <test expect_failure="true"> + <param name="input" value="input.fasta"/> + <param name="outputs" value="sum,detail_sum,png,hog,pdf,ump,tax"/> + <param name="database" value="test"/> + </test> + </tests> + + + <help><![CDATA[ + OMark_: is a software for proteome quality assessment. + It provides measures of proteome completeness, characterizes the consistency + of all protein coding genes with regard to their homologs, and identifies the + presence of contamination from other species. + + OMArk relies on the OMA orthology database. + For more information, please refer to the OMamer_ documentaion. + + .. _OMark: https://github.com/DessimozLab/OMArk + .. _OMamer: https://github.com/DessimozLab/omamer + ]]></help> + <expand macro="citation"/> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r ce13b4c42256 test-data/input.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fasta Wed Feb 21 19:27:16 2024 +0000 |
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| b'@@ -0,0 +1,403 @@\n+>tr|A0A2R8YED5|A0A2R8YED5_HUMAN Olfactory receptor OS=Homo sapiens OX=9606 GN=OR5BS1P PE=3 SV=1\n+MEVSNMTTVTVFILLGLSNNPQVQALLFVLFLVIYLLTLLGNLLMVLVISTDSHLCTPMY\n+FFLRQLSFLDAFYSSIIVPKLLENLLSKGETISFLECFTQISLVIFSGATEACLLSVMAY\n+DRFQAMCHPLLYVVIINRRVCAGLVGASWAIGMGTGLINTLLLAQQHFCGPNVIHSFACE\n+LPPVLLLTCSDPCASIVSILTTMSVLGLGTLVLLLGSYSCIIMTALRINSATGRSKIFST\n+CSSHFLVVTIFYTSGVLRYMIPASGSALEQVLSVQYSVITPLLNPLIYSLKSQEVKVALR\n+RMLARKSRLPL\n+>sp|A0JD32|TV382_HUMAN T cell receptor alpha variable 38-2/delta variable 8 OS=Homo sapiens OX=9606 GN=TRAV38-2DV8 PE=3 SV=1\n+MACPGFLWALVISTCLEFSMAQTVTQSQPEMSVQEAETVTLSCTYDTSESDYYLFWYKQP\n+PSRQMILVIRQEAYKQQNATENRFSVNFQKAAKSFSLKISDSQLGDAAMYFCAYRS\n+>sp|A5D6W6|FITM1_HUMAN Fat storage-inducing transmembrane protein 1 OS=Homo sapiens OX=9606 GN=FITM1 PE=2 SV=1\n+MERGPVVGAGLGAGARIQALLGCLLKVLLWVASALLYFGSEQAARLLGSPCLRRLYHAWL\n+AAVVIFGPLLQFHVNPRTIFASHGNFFNIKFVNSAWGWTCTFLGGFVLLVVFLATRRVAV\n+TARHLSRLVVGAAVWRGAGRAFLLIEDLTGSCFEPLPQGLLLHELPDRRSCLAAGHQWRG\n+YTVSSHTFLLTFCCLLMAEEAAVFAKYLAHGLPAGAPLRLVFLLNVLLLGLWNFLLLCTV\n+IYFHQYTHKVVGAAVGTFAWYLTYGSWYHQPWSPGSPGHGLFPRPHSSRKHN\n+>sp|A6NH00|OR2T8_HUMAN Olfactory receptor 2T8 OS=Homo sapiens OX=9606 GN=OR2T8 PE=3 SV=1\n+MENGSYTSYFILLGLFNHTRAHQVLFMMVLSIVLTSLFGNSLMILLIHWDHRLHTPMYFL\n+LSQLSLMDVMLVSTTVPKMAADYLTGSKAISRAGCGAQIFFLPTLGGGECFLLAAMAYDR\n+YAAVCHPLRYPTLMSWQLCLRMNLSCWLLGAADGLLQAVATLSFPYCGAHEIDHFFCETP\n+VLVRLACADTSVFENAMYICCVLMLLVPFSLILSSYGLILAAVLHMRSTEARKKAFATCS\n+SHVAVVGLFYGAAIFTYMRPKSHRSTNHDKVVSAFYTMFTPLLNPLIYSVKNSEVKGALT\n+RCMGRCVALSRE\n+>sp|B3EWG5|FM25C_HUMAN Protein FAM25C OS=Homo sapiens OX=9606 GN=FAM25C PE=1 SV=1\n+MLGGLGKLAAEGLAHRTEKATEGAIHAVEEVVKEVVGHAKETGEKAIAEAIKKAQESGDK\n+KMKEITETVTNTVTNAITHAAESLDKLGQ\n+>sp|D6RGX4|F90AP_HUMAN Putative protein FAM90A26 OS=Homo sapiens OX=9606 GN=FAM90A26 PE=5 SV=1\n+MMACRDPKPGAKRLVRAQTLQKQRRAPVGPRAPPPDEEDPRLKCKNCGAFGHMARSTRCP\n+MKCWKAALVPPTLGKKEGKENLKPWKPQVEANPGPLNKDKGEKEERPRQQDPQRKALLHI\n+FSGKPPEKPLPNRKGSTESSVYLRVASGPMPVHTTSKRPRVDPVLADRSATEMSDRGSAL\n+ASLSPLRKASLSSSSSLGPKERQTGAAADIPQPAVRHQGPEPLLVVKPTHSSPEGGCREV\n+PQAASKTHGLLQAISPQAQDKRPAVTSQPCPPAATHSLGLGSNLSFGPGAKRPAQAPIQA\n+CLNFPKKPRLGPFQIPESAIQGGELGAPEYLQPPPATTELGPSTSPQMGRRTPAQVSSVD\n+RQPPHSRPCLPTAQACTMSHHPATSHDGAQPLRVLFRRLENGRWSSSLLAAPSFHSPEKP\n+GAFLAQSPHVSEKSEVPRVRVPPNVLYEDLQVSSSSEDSDSDLE\n+>sp|O00451|GFRA2_HUMAN GDNF family receptor alpha-2 OS=Homo sapiens OX=9606 GN=GFRA2 PE=1 SV=2\n+MILANVFCLFFFLDETLRSLASPSSLQGPELHGWRPPVDCVRANELCAAESNCSSRYRTL\n+RQCLAGRDRNTMLANKECQAALEVLQESPLYDCRCKRGMKKELQCLQIYWSIHLGLTEGE\n+EFYEASPYEPVTSRLSDIFRLASIFSGTGADPVVSAKSNHCLDAAKACNLNDNCKKLRSS\n+YISICNREISPTERCNRRKCHKALRQFFDRVPSEYTYRMLFCSCQDQACAERRRQTILPS\n+CSYEDKEKPNCLDLRGVCRTDHLCRSRLADFHANCRASYQTVTSCPADNYQACLGSYAGM\n+IGFDMTPNYVDSSPTGIVVSPWCSCRGSGNMEEECEKFLRDFTENPCLRNAIQAFGNGTD\n+VNVSPKGPSFQATQAPRVEKTPSLPDDLSDSTSLGTSVITTCTSVQEQGLKANNSKELSM\n+CFTELTTNIIPGSNKVIKPNSGPSRARPSAALTVLSVLMLKLAL\n+>sp|O14817|TSN4_HUMAN Tetraspanin-4 OS=Homo sapiens OX=9606 GN=TSPAN4 PE=1 SV=1\n+MARACLQAVKYLMFAFNLLFWLGGCGVLGVGIWLAATQGSFATLSSSFPSLSAANLLIIT\n+GAFVMAIGFVGCLGAIKENKCLLLTFFLLLLLVFLLEATIAILFFAYTDKIDRYAQQDLK\n+KGLHLYGTQGNVGLTNAWSIIQTDFRCCGVSNYTDWFEVYNATRVPDSCCLEFSESCGLH\n+APGTWWKAPCYETVKVWLQENLLAVGIFGLCTALVQILGLTFAMTMYCQVVKADTYCA\n+>sp|O14901|KLF11_HUMAN Krueppel-like factor 11 OS=Homo sapiens OX=9606 GN=KLF11 PE=1 SV=2\n+MHTPDFAGPDDARAVDIMDICESILERKRHDSERSTCSILEQTDMEAVEALVCMSSWGQR\n+SQKGDLLRIRPLTPVSDSGDVTTTVHMDAATPELPKDFHSLSTLCITPPQSPDLVEPSTR\n+TPVSPQVTDSKACTATDVLQSSAVVARALSGGAERGLLGLEPVPSSPCRAKGTSVIRHTG\n+ESPAACFPTIQTPDCRLSDSREGEEQLLGHFETLQDTHLTDSLLSTNLVSCQPCLHKSGG\n+LLLTDKGQQAGWPGAVQTCSPKNYENDLPRKTTPLISVSVPAPPVLCQMIPVTGQSSMLP\n+AFLKPPPQLSVGTVRPILAQAAPAPQPVFVGPAVPQGAVMLVLPQGALPPPAPCAANVMA\n+AGNTKLLPLAPAPVFITSSQNCVPQVDFSRRRNYVCSFPGCRKTYFKSSHLKAHLRTHTG\n+EKPFNCSWDGCDKKFARSDELSRHRRTHTGEKKFVCPVCDRRFMRSDHLTKHARRHMTTK\n+KIPGWQAEVGKLNRIASAESPGSPLVSMPASA\n+>sp|O15079|SNPH_HUMAN Syntaphilin OS=Homo sapiens OX=9606 GN=SNPH PE=1 SV=2\n+MAMSLPGSRRTSAGSRRRTSPPVSVRDAYGTSSLSSSSNSGSYKGSDSSPTPRRSMKYTL\n+CSDNHGIKPPTPEQYLTPLQQKEVCIRHLKARLKDTQDRLQDRDTEIDDLKTQLSRMQED\n+WIEEECHRV'..b'\n+QTLAQKDQALGKLEQSLRLMEEASFDGTFLWKITNVTRRCHESACGRTVSLFSPAFYTAK\n+YGYKLCLRLYLNGDGTGKRTHLSLFIVIMRGEYDALLPWPFRNKVTFMLLDQNNREHAID\n+AFRPDLSSASFQRPQSETNVASGCPLFFPLSKLQSPKHAYVKDDTMFLKCIVETST\n+>sp|Q14765|STAT4_HUMAN Signal transducer and activator of transcription 4 OS=Homo sapiens OX=9606 GN=STAT4 PE=1 SV=1\n+MSQWNQVQQLEIKFLEQVDQFYDDNFPMEIRHLLAQWIENQDWEAASNNETMATILLQNL\n+LIQLDEQLGRVSKEKNLLLIHNLKRIRKVLQGKFHGNPMHVAVVISNCLREERRILAAAN\n+MPVQGPLEKSLQSSSVSERQRNVEHKVAAIKNSVQMTEQDTKYLEDLQDEFDYRYKTIQT\n+MDQSDKNSAMVNQEVLTLQEMLNSLDFKRKEALSKMTQIIHETDLLMNTMLIEELQDWKR\n+RQQIACIGGPLHNGLDQLQNCFTLLAESLFQLRRQLEKLEEQSTKMTYEGDPIPMQRTHM\n+LERVTFLIYNLFKNSFVVERQPCMPTHPQRPLVLKTLIQFTVKLRLLIKLPELNYQVKVK\n+ASIDKNVSTLSNRRFVLCGTNVKAMSIEESSNGSLSVEFRHLQPKEMKSSAGGKGNEGCH\n+MVTEELHSITFETQICLYGLTIDLETSSLPVVMISNVSQLPNAWASIIWYNVSTNDSQNL\n+VFFNNPPPATLSQLLEVMSWQFSSYVGRGLNSDQLHMLAEKLTVQSSYSDGHLTWAKFCK\n+EHLPGKSFTFWTWLEAILDLIKKHILPLWIDGYVMGFVSKEKERLLLKDKMPGTFLLRFS\n+ESHLGGITFTWVDHSESGEVRFHSVEPYNKGRLSALPFADILRDYKVIMAENIPENPLKY\n+LYPDIPKDKAFGKHYSSQPCEVSRPTERGDKGYVPSVFIPISTIRSDSTEPHSPSDLLPM\n+SPSVYAVLRENLSPTTIETAMKSPYSAE\n+>sp|Q15019|SEPT2_HUMAN Septin-2 OS=Homo sapiens OX=9606 GN=SEPTIN2 PE=1 SV=1\n+MSKQQPTQFINPETPGYVGFANLPNQVHRKSVKKGFEFTLMVVGESGLGKSTLINSLFLT\n+DLYPERVIPGAAEKIERTVQIEASTVEIEERGVKLRLTVVDTPGYGDAINCRDCFKTIIS\n+YIDEQFERYLHDESGLNRRHIIDNRVHCCFYFISPFGHGLKPLDVAFMKAIHNKVNIVPV\n+IAKADTLTLKERERLKKRILDEIEEHNIKIYHLPDAESDEDEDFKEQTRLLKASIPFSVV\n+GSNQLIEAKGKKVRGRLYPWGVVEVENPEHNDFLKLRTMLITHMQDLQEVTQDLHYENFR\n+SERLKRGGRKVENEDMNKDQILLEKEAELRRMQEMIARMQAQMQMQMQGGDGDGGALGHH\n+V\n+>sp|Q15468|STIL_HUMAN SCL-interrupting locus protein OS=Homo sapiens OX=9606 GN=STIL PE=1 SV=2\n+MEPIYPFARPQMNTRFPSSRMVPFHFPPSKCALWNPTPTGDFIYLHLSYYRNPKLVVTEK\n+TIRLAYRHAKQNKKNSSCFLLGSLTADEDEEGVTLTVDRFDPGREVPECLEITPTASLPG\n+DFLIPCKVHTQELCSREMIVHSVDDFSSALKALQCHICSKDSLDCGKLLSLRVHITSRES\n+LDSVEFDLHWAAVTLANNFKCTPVKPIPIIPTALARNLSSNLNISQVQGTYKYGYLTMDE\n+TRKLLLLLESDPKVYSLPLVGIWLSGITHIYSPQVWACCLRYIFNSSVQERVFSESGNFI\n+IVLYSMTHKEPEFYECFPCDGKIPDFRFQLLTSKETLHLFKNVEPPDKNPIRCELSAESQ\n+NAETEFFSKASKNFSIKRSSQKLSSGKMPIHDHDSGVEDEDFSPRPIPSPHPVSQKISKI\n+QPSVPELSLVLDGNFIESNPLPTPLEMVNNENPPLINHLEHLKPLQPQLYDEKHSPEVEA\n+GEPSLRGIPNQLNQDKPALLRHCKVRQPPAYKKGNPHTRNSIKPSSHNGPSHDIFEKLQT\n+VSAGNVQNEEYPIRPSTLNSRQSSLAPQSQPHDFVFSPHNSGRPMELQIPTPPLPSYCST\n+NVCRCCQHHSHIQYSPLNSWQGANTVGSIQDVQSEALQKHSLFHPSGCPALYCNAFCSSS\n+SPIALRPQGDMGSCSPHSNIEPSPVARPPSHMDLCNPQPCTVCMHTPKTESDNGMMGLSP\n+DAYRFLTEQDRQLRLLQAQIQRLLEAQSLMPCSPKTTAVEDTVQAGRQMELVSVEAQSSP\n+GLHMRKGVSIAVSTGASLFWNAAGEDQEPDSQMKQDDTKISSEDMNFSVDINNEVTSLPG\n+SASSLKAVDIPSFEESNIAVEEEFNQPLSVSNSSLVVRKEPDVPVFFPSGQLAESVSMCL\n+QTGPTGGASNNSETSEEPKIEHVMQPLLHQPSDNQKIYQDLLGQVNHLLNSSSKETEQPS\n+TKAVIISHECTRTQNVYHTKKKTHHSRLVDKDCVLNATLKQLRSLGVKIDSPTKVKKNAH\n+NVDHASVLACISPEAVISGLNCMSFANVGMSGLSPNGVDLSMEANAIALKYLNENQLSQL\n+SVTRSNQNNCDPFSLLHINTDRSTVGLSLISPNNMSFATKKYMKRYGLLQSSDNSEDEEE\n+PPDNADSKSEYLLNQNLRSIPEQLGGQKEPSKNDHEIINCSNCESVGTNADTPVLRNITN\n+EVLQTKAKQQLTEKPAFLVKNLKPSPAVNLRTGKAEFTQHPEKENEGDITIFPESLQPSE\n+TLKQMNSMNSVGTFLDVKRLRQLPKLF\n+>sp|Q3BBV2|NBPF8_HUMAN Putative neuroblastoma breakpoint family member 8 OS=Homo sapiens OX=9606 GN=NBPF8 PE=5 SV=1\n+MVVSAGPWSSEKAEMNILEINEKLRPQLAENKQQFVNLKEMFSNSTGRLPGQPTEEIQQY\n+KVLVHSQERELTQLKEKLREGRDASRSLNEHLQALLTLDEPDKSQGQDLQEQLAEGCRLA\n+QHLVQKLSPENDEDEDEDVQVEEDEKVLESSAPREVQKAEESKVPEDSLEECAITCSNSH\n+GPCDSIQPHKNIKITFEEDKVNSSLVVDRESSHDGCQDALNILPVPGPTSSATNVSMVVS\n+AGPLSSEKAEMNILEINEKLCPQLAEKKQQFRSLKEKCFVTQVACFLAKQQNKYKYEECK\n+DLIKSMLRNERQFKEEKLAEQLKQAEELRQYKVLVHSQERELTQLREKLREGRDASRSLN\n+EHLQALLTPDEPDKSQGQDLQEQLAEGCRLAQHLVQKLSPENDNDDDEDVQVEVAEKVQK\n+SSSPREMQKAEEKEVPEDSLEECAITCSNSHGPYDSNQPHRKTKITFEEDKVDSTLIGSS\n+SHVEWEDAVHIIPENESDDEEEEEKGPVSPRNLQESEEEEVPQESWDEGYSTLSIPPERL\n+ASYQSYSSTFHSLEEQQVCMAVDIGRHRWDQVKKEDQEATGPRLSRELLDEKGPEVLQDS\n+LDRCYSTPSGCLELTDSCQPYRSAFYILEQQRVGLAVDMDEIEKYQEVEEDQDPSCPRLS\n+RELLDEKEPEVLQDSLDRCYSTPSGYLELPDLGQPYSSAVYSLEEQYLGLALDVDRIKKD\n+QEEEEDQGPPCPRLSRELLEVVEPEVLQDSLDRCYSTPSSCLEQPDSCQPYGSSFYALEE\n+KHVGFSLDVGEIEKKGKGKIGRGRRSKKKRRRGRKEGEEDQNPPCPRLNSVLMEVEEPEV\n+LQDSLDRCYSTPSMYCELRDSFQHYRSVF\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r ce13b4c42256 test-data/omamer.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/omamer.loc Wed Feb 21 19:27:16 2024 +0000 |
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| @@ -0,0 +1,6 @@ +# Tab separated with 4 columns: +# - value +# - name +# - version +# - /path/to/data +test test 2.0.2 ${__HERE__}/db/ \ No newline at end of file |
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| diff -r 000000000000 -r ce13b4c42256 test-data/output.omamer --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.omamer Wed Feb 21 19:27:16 2024 +0000 |
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| @@ -0,0 +1,52 @@ +!omamer-version: 2.0.2 +!query-md5: 773e472d79d92b3d6d165033accb6f52 +!date-run: 2023-11-23T14:29:15.310914 +!db-path: Primates-v2.0.0.h5 +!db-info-source: OMA / All.Jul2023 +!db-info-root_level: Primates +!db-info-database_hash: 27645bb5ca4c995ad24f8459dae3c107 +qseqid hogid hoglevel family_p family_count family_normcount subfamily_score subfamily_count qseqlen subfamily_medianseqlen qseq_overlap +tr|A0A2R8YED5|A0A2R8YED5_HUMAN HOG:D0610483 Primates 2638.1419438166727 306 1.0 0.9999760969041518 306 312 312 1.0 +sp|A0JD32|TV382_HUMAN HOG:D0617450.2b.4a.11a Homo sapiens 1087.8571886143745 111 1.0 0.999999812279352 6 117 117 1.0 +sp|A5D6W6|FITM1_HUMAN HOG:D0630383 Primates 2734.0000255164123 286 1.0 0.9999850762084821 286 293 293 1.0 +sp|A6NH00|OR2T8_HUMAN HOG:D0615771.2e.5a.12a Homo sapiens 2404.939866884583 307 1.0 0.9999997809925772 7 313 313 1.0 +sp|B3EWG5|FM25C_HUMAN HOG:D0615645.1b Hominoidea 836.2635328481995 84 1.0 0.999999812279352 6 90 90 1.0 +sp|D6RGX4|F90AP_HUMAN HOG:D0607131.3b.4b.2h Homo sapiens 3466.867512384198 459 1.0 0.9999980289331958 63 465 465 1.0 +sp|O00451|GFRA2_HUMAN HOG:D0637239.1g.14a Primates 4275.204165438652 459 1.0 0.9999703088508377 459 465 461 1.0 +sp|O14817|TSN4_HUMAN HOG:D0639114.1b.8b Primates 2206.494860536379 233 1.0 0.9999844504729888 233 239 239 1.0 +sp|O14901|KLF11_HUMAN HOG:D0630531 Primates 4040.9704983680986 505 1.0 0.9999356743912775 505 513 511 1.0 +sp|O15079|SNPH_HUMAN HOG:D0631579 Primates 4235.616199577423 489 1.0 0.9999724989250646 489 495 533 1.0 +sp|O15400|STX7_HUMAN HOG:D0671137.5c.35d.18b.8b.4a Primates 2525.8039622379742 256 1.0 0.999983949884594 256 262 262 1.0 +sp|O15547|P2RX6_HUMAN HOG:D0692878.1e.7a.24a Primates 3735.3683950810037 436 1.0 0.9999472504979056 436 442 441 1.0 +sp|O43598|DNPH1_HUMAN HOG:D0900595.1b.1a.4b.2b.2a Catarrhini 1400.0640249439814 169 1.0 0.9999953382705741 17 175 206 1.0 +sp|O75078|ADA11_HUMAN HOG:D0639405.1a.1a Primates 6459.427248727791 764 1.0 0.9999506607563446 764 770 770 1.0 +sp|O75347|TBCA_HUMAN HOG:D0685997.6b.12a.16b.7a.3a.4e.4a Simiiformes 1000.5425844202465 103 1.0 0.9999947438218554 9 109 109 1.0 +sp|O94913|PCF11_HUMAN HOG:D0645798.6a Primates 11929.968463962005 1502 1.0 0.9999100505228223 1502 1556 1658 1.0 +sp|O95210|STBD1_HUMAN HOG:D0613610 Primates 2963.2232053752086 353 1.0 0.9999462180343415 353 359 359 1.0 +sp|O95274|LYPD3_HUMAN HOG:D0616795 Primates 2866.7497463302734 340 1.0 0.9999594210532524 340 347 353 1.0 +sp|O95415|BRI3_HUMAN HOG:D0674725.2a.1a.3a Primates 1064.9029691067599 120 1.0 0.9999939929392633 120 126 126 1.0 +sp|P00491|PNPH_HUMAN HOG:D0680682.1a.1b.3b.3a.9b.14a.10a Primates 2692.3703255880287 284 1.0 0.9999724676382901 284 290 290 1.0 +sp|P03999|OPSB_HUMAN HOG:D0622973 Primates 3175.263453504967 343 1.0 0.9999679310559627 343 349 350 1.0 +sp|P09466|PAEP_HUMAN HOG:D0615657.2b.1b.1a Catarrhini 1559.31373622314 175 1.0 0.9999865779736663 148 181 181 1.0 +sp|P09544|WNT2_HUMAN HOG:D0658980.4g.16b.11b Primates 3150.596993999258 355 1.0 0.9999818849574658 355 361 361 1.0 +sp|P0C629|O10J4_HUMAN HOG:D0613697.2a Primates 517.9354158365237 83 0.2710903805261581 0.27120240872927465 83 312 313 0.9067524115755627 +sp|P0C881|R10B1_HUMAN HOG:D0661287.1a.2b.5a.2a.1a Homo sapiens 6421.796319570017 865 1.0 0.999999812279352 6 871 871 1.0 +sp|P12104|FABPI_HUMAN HOG:D0641313.1b Primates 1273.974731265406 127 1.0 0.999978724993224 127 133 133 1.0 +sp|P19622|HME2_HUMAN HOG:D0632442.1b Primates 2532.2810698546 327 1.0 0.999977786389984 327 334 335 1.0 +sp|P20813|CP2B6_HUMAN HOG:D0671285.6ah.265a.202b.82b Hominoidea 3965.2155397202205 486 1.0 0.9999944309541087 84 492 492 1.0 +sp|P22626|ROA2_HUMAN HOG:D0679329.10fdq.3086r.2380b.1642a.1109f.653b Primates 3180.0277293941886 340 1.0 0.9999884551801466 340 354 342 1.0 +sp|P25929|NPY1R_HUMAN HOG:D0635707.1a Primates 3839.2856592128996 379 1.0 0.9999819788177898 379 385 384 1.0 +sp|P26599|PTBP1_HUMAN HOG:D0671471.2a.1a.1d.3b.6e.3a.5b.4a Primates 4179.095968916793 524 1.0 0.9999607038110139 524 532 532 1.0 +sp|P42224|STAT1_HUMAN HOG:D0661771.1b Primates 6776.242926772081 745 1.0 0.9999539145809104 745 751 744 1.0 +sp|P42695|CNDD3_HUMAN HOG:D0671844.4b Primates 11211.682296353 1493 1.0 0.9998243873337745 1493 1499 1499 1.0 +sp|P47929|LEG7_HUMAN HOG:D0641111.10b Simiiformes 1219.0569952460728 131 1.0 0.9999955259912221 14 137 137 1.0 +sp|P51693|APLP1_HUMAN HOG:D0660679.1a Primates 5056.8124129922835 645 1.0 0.9999476259392016 645 651 640 1.0 +sp|P57678|GEMI4_HUMAN HOG:D0639146 Primates 8562.495763610617 1053 1.0 0.999890621435752 1053 1059 1059 1.0 +sp|P78417|GSTO1_HUMAN HOG:D0699874.1a.3c.8a.18a.27b.15b.3b Simiiformes 2208.5054830237655 236 1.0 0.9999911458427683 46 242 242 1.0 +sp|P80188|NGAL_HUMAN HOG:D0615744.1a.2b Primates 1741.721242422051 193 1.0 0.999961454693606 193 199 199 1.0 +sp|Q05195|MAD1_HUMAN HOG:D0638507.1c Primates 2231.948352172975 216 1.0 0.9999906139675988 216 222 222 1.0 +sp|Q13077|TRAF1_HUMAN HOG:D0615660 Primates 3704.3470383386293 411 1.0 0.9999673678940186 411 417 417 1.0 +sp|Q14765|STAT4_HUMAN HOG:D0632400 Primates 6767.325687112324 743 1.0 0.9999589830384069 743 749 749 1.0 +sp|Q15019|SEPT2_HUMAN HOG:D0671290.6j.36c.7b.14b.13a.11a.6a Primates 3489.280783000945 356 1.0 0.9999813530822964 356 362 364 1.0 +sp|Q15468|STIL_HUMAN HOG:D0645362.3b Primates 9834.974240963404 1282 1.0 0.9998483842899468 1282 1288 1279 1.0 +sp|Q3BBV2|NBPF8_HUMAN HOG:D0608047.2a Catarrhini 3950.290666607274 608 0.8373227747284284 0.420437306441702 111 870 662 1.0 |
| b |
| diff -r 000000000000 -r ce13b4c42256 test-data/output.omq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.omq Wed Feb 21 19:27:16 2024 +0000 |
| b |
| b'@@ -0,0 +1,17792 @@\n+>Single\n+HOG:D0900595.1b.1a.4b.2b.2a\n+HOG:D0639405.1a.1a\n+HOG:D0637239.1g.14a\n+HOG:D0671844.4b\n+HOG:D0630383\n+HOG:D0671285.6ah.265a.202b.82b\n+HOG:D0615657.2b.1b.1a\n+HOG:D0630531\n+HOG:D0613610\n+HOG:D0616795\n+HOG:D0639146\n+HOG:D0641111.10b\n+HOG:D0615744.1a.2b\n+HOG:D0645362.3b\n+HOG:D0660679.1a\n+HOG:D0680682.1a.1b.3b.3a.9b.14a.10a\n+HOG:D0615660\n+HOG:D0685997.6b.12a.16b.7a.3a.4e.4a\n+HOG:D0639114.1b.8b\n+HOG:D0638507.1c\n+HOG:D0679329.10fdq.3086r.2380b.1642a.1109f.653b\n+HOG:D0622973\n+HOG:D0699874.1a.3c.8a.18a.27b.15b.3b\n+HOG:D0615645.1b\n+HOG:D0641313.1b\n+HOG:D0692878.1e.7a.24a\n+HOG:D0632442.1b\n+HOG:D0632400\n+HOG:D0671290.6j.36c.7b.14b.13a.11a.6a\n+HOG:D0645798.6a\n+HOG:D0658980.4g.16b.11b\n+HOG:D0661771.1b\n+HOG:D0671137.5c.35d.18b.8b.4a\n+HOG:D0635707.1a\n+>Lost\n+HOG:D0659433\n+HOG:D0629714\n+HOG:D0671843.2c.4a.1b\n+HOG:D0682523.9a.13a.3b.3a\n+HOG:D0671716.6a\n+HOG:D0680844.11b.12b.26a\n+HOG:D0660683.1b.5a\n+HOG:D0660683.1b.5b\n+HOG:D0667470.5a\n+HOG:D0692362.1g.6a.4a\n+HOG:D0692362.1g.6b.6b\n+HOG:D0679525.7a\n+HOG:D0630327.1a.2b\n+HOG:D0673139.1a.2a\n+HOG:D0673139.1b.3d.4c.4a\n+HOG:D0673139.1c\n+HOG:D0618878.3b\n+HOG:D0610946\n+HOG:D0629901.3b\n+HOG:D0687720.7c.12b\n+HOG:D0686017.2a.3b.4a\n+HOG:D0610601.2c\n+HOG:D0610601.2f.4a\n+HOG:D0605270\n+HOG:D0613984\n+HOG:D0629819.1b\n+HOG:D0616680\n+HOG:D0658626.1a.2a.3b\n+HOG:D0658626.1c.4b\n+HOG:D0605460\n+HOG:D0618713\n+HOG:D0631532\n+HOG:D0658713.4h.11b\n+HOG:D0658713.4t.17b\n+HOG:D0631604.3b\n+HOG:D0637188\n+HOG:D0667973.1b.1b.8a.3b\n+HOG:D0667973.1b.1c\n+HOG:D0612581.5b\n+HOG:D0679870.4c.6a.7a.5b\n+HOG:D0614620\n+HOG:D0687764.4e\n+HOG:D0687764.4k.14b.21b\n+HOG:D0687764.4m.15a.23a.22a.24b\n+HOG:D0687764.4m.15a.23a.22g\n+HOG:D0687764.4o.18a\n+HOG:D0687764.4p\n+HOG:D0685981.3a.7c.6a\n+HOG:D0630540\n+HOG:D0621397\n+HOG:D0637078.2c.5b\n+HOG:D0613865\n+HOG:D0679860.9a.37e.43a.14a.8b\n+HOG:D0679860.9a.37e.43a.14b.9g.15a.12a.7b\n+HOG:D0679860.9a.37h.44b\n+HOG:D0615573\n+HOG:D0620005.3a\n+HOG:D0623327.11b.2b\n+HOG:D0611657\n+HOG:D0672525.1a.5a.1a\n+HOG:D0644557.3a\n+HOG:D0615989\n+HOG:D0629739.3b\n+HOG:D0608617\n+HOG:D0660768.1a.3b\n+HOG:D0679453.4b\n+HOG:D0680122.9a.30b\n+HOG:D0613888.2a\n+HOG:D0622296.2b.7a.1b.5b\n+HOG:D0622296.2b.7a.1b.5a\n+HOG:D0671510.2b.11a.5b\n+HOG:D0608868.1a\n+HOG:D0685365.1c\n+HOG:D0643268.2d\n+HOG:D0620131\n+HOG:D0679893.30e.9c.7a.9a.1b.1b\n+HOG:D0619886\n+HOG:D0644291\n+HOG:D0681717.2a.5a\n+HOG:D0635572\n+HOG:D0607932\n+HOG:D0659044.1b.1a.3a\n+HOG:D0628990.4b\n+HOG:D0680001.8e.4b.8e.28a.25b\n+HOG:D0680001.8e.4b.8e.28a.25e.27b.18b.9b\n+HOG:D0646321.2a.1y.19b.6a.1b\n+HOG:D0639074.1b.2b\n+HOG:D0613884\n+HOG:D0631500\n+HOG:D0661878\n+HOG:D0629561.5b\n+HOG:D0658818.1d.5a.5b\n+HOG:D0658818.1d.5d.12a\n+HOG:D0619253\n+HOG:D0681337.23b\n+HOG:D0629779.1a\n+HOG:D0630236\n+HOG:D0629128.1b\n+HOG:D0671157.2b.6b.14a.8b.9b\n+HOG:D0639149.1b\n+HOG:D0658651.6b\n+HOG:D0701127.4g.7d.4b.4b\n+HOG:D0701127.4g.7e.6c.12b.20a.5c.1a\n+HOG:D0701127.4g.7e.6c.12b.20d.9b.4c.12a.8a\n+HOG:D0630789\n+HOG:D0618191.1b\n+HOG:D0900523.11b.61ao\n+HOG:D0900523.11b.61az\n+HOG:D0900523.11b.61bd.221b.209b\n+HOG:D0900523.11b.61by.239b.234b.118a\n+HOG:D0900523.11b.61by.239b.234b.118d.62b\n+HOG:D0900523.11b.61by.239b.234b.118d.62c.30a\n+HOG:D0900523.11b.61by.239c.240b\n+HOG:D0900523.11b.61bz.241a.242a.121b.65b.39a\n+HOG:D0900523.11b.61bz.241a.242a.121b.65b.39b\n+HOG:D0900523.11b.61bz.241a.242b.123b.66b.43b.31c\n+HOG:D0629259.7a\n+HOG:D0634477\n+HOG:D0635866.1b\n+HOG:D0682920.3a.3b.7a.17b.21b\n+HOG:D0618862\n+HOG:D0618528.1a\n+HOG:D0679603.4b.4b.9b.11a.23a.9a\n+HOG:D0613632.1a\n+HOG:D0686259.3b.5c.4a.8b\n+HOG:D0613514\n+HOG:D0680123.10d.54c.45e.53b.31b\n+HOG:D0680123.10e.55b.47b\n+HOG:D0680123.10e.55b.47c\n+HOG:D0671678.2c.1a.2b\n+HOG:D0671678.2c.1a.2c\n+HOG:D0611184.2b.6d.4d\n+HOG:D0611184.2b.6d.4a\n+HOG:D0611184.2b.6d.4b\n+HOG:D0611184.2b.6e.5b\n+HOG:D0626800\n+HOG:D0630070.4a\n+HOG:D0614354.1c.8a\n+HOG:D0606829.2e.5a\n+HOG:D0672669.2a.8b.2b\n+HOG:D0680445.10a.10a.7a.17b.28a\n+HOG:D0637205.1a\n+HOG:D0607813\n+HOG:D0615998.1b.4a\n+HOG:D0620069.2ad\n+HOG:D0620069.2br.7b\n+HOG:D0620069.2dv.10c\n+HOG:D0679692.2a.1a.1b.1c.2b\n+HOG:D0685743.15b\n'..b'37.15c.15b.16a\n+HOG:D0704039.1a.2a.6a.6b\n+HOG:D0673667.1a.3a.4a.3a\n+HOG:D0673667.1a.3a.4b.7b\n+HOG:D0673667.1a.3c.6b.8b\n+HOG:D0683130.2b.4d.26a.6f.1a\n+HOG:D0630335.1b\n+HOG:D0680549.2b.2a\n+HOG:D0680549.2b.2b.5a\n+HOG:D0635480.1a.3b.4b\n+HOG:D0671393.8a.7c.6a.4c\n+HOG:D0671393.8a.7e.12a.12a.1a.2d\n+HOG:D0671393.8a.7e.12a.12a.1a.2b\n+HOG:D0642352.2e\n+HOG:D0629032.1a\n+HOG:D0631925\n+HOG:D0628671\n+HOG:D0620301\n+HOG:D0629993\n+HOG:D0639503\n+HOG:D0629278.5b\n+HOG:D0621217\n+HOG:D0621184\n+HOG:D0610846\n+HOG:D0637121.1b\n+HOG:D0637121.1c.9b\n+HOG:D0704000.6b.5a.12c\n+HOG:D0672172.1a\n+HOG:D0672172.1c.8c.6b\n+HOG:D0672172.1c.8g\n+HOG:D0672172.1c.8i.14e.9a.4b\n+HOG:D0672172.1c.8i.14h\n+HOG:D0672172.1c.8i.14i.16b.8b.6b.2a.3a\n+HOG:D0672172.1c.8i.14m\n+HOG:D0621329.5a\n+HOG:D0633394.1a.1b.1a.3b.5b\n+HOG:D0629273\n+HOG:D0672140.1b.3b.4b\n+HOG:D0905873.10j.43a.55a\n+HOG:D0905873.10j.43d.59b.53a.19b.10a\n+HOG:D0905873.10j.43d.59b.53c.20a\n+HOG:D0905873.10j.43d.59b.53c.20b\n+HOG:D0905873.10m.52a\n+HOG:D0905873.10n\n+HOG:D0680203\n+HOG:D0618421\n+HOG:D0635887.2a\n+HOG:D0901213.2b\n+HOG:D0630181.2a.4c\n+HOG:D0609526\n+HOG:D0611003.3a\n+HOG:D0680415.1a.9b.10b.3a.10a\n+HOG:D0622385.12a.2b\n+HOG:D0642013.2a.3a.1a\n+HOG:D0629263\n+HOG:D0618511\n+HOG:D0667514.1b.4a.5b\n+HOG:D0667514.1b.4b.11a\n+HOG:D0899962.1b.6f.22e.22a.22b.25a.6c.5a.1a\n+HOG:D0615869.1c\n+HOG:D0604028\n+HOG:D0629053\n+HOG:D0699046.3a.9a\n+HOG:D0637294.1b\n+HOG:D0621743\n+HOG:D0693619.2a.2a.2b\n+HOG:D0629525.3b\n+HOG:D0702129.17a.7b\n+HOG:D0617159\n+HOG:D0629405.1a.5a\n+HOG:D0658526.1b.2a.1a.5b\n+HOG:D0658526.1e\n+HOG:D0671507.5a\n+HOG:D0671507.5b.13a.5a\n+HOG:D0671183.5e.11d.5f.7c\n+HOG:D0671183.5e.11d.5f.7d.12a.3b\n+HOG:D0671183.5e.11d.5f.7g.17a\n+HOG:D0671183.5g.14n.28b\n+HOG:D0671183.5j.18a.31b.46b\n+HOG:D0671183.5j.18d.33a.62b.59c\n+HOG:D0671183.5j.18d.33a.62b.59a.30a\n+HOG:D0671183.5j.18d.33a.62b.59a.30c\n+HOG:D0671183.5o.30b.41e.72b.69a.34a.16b.6a.2a\n+HOG:D0668239\n+HOG:D0610443\n+HOG:D0667821.1a.2b.7b\n+HOG:D0625626\n+HOG:D0605573\n+HOG:D0662261.1b.3a\n+HOG:D0679774.6c.6c.9a.2b.25b.28e.19k.5a.3a.1a.2b.2c\n+HOG:D0688830.1b.1c.1a.11b\n+HOG:D0619055.2a\n+HOG:D0622492\n+HOG:D0672154.1a.1b.4a.2b.2b\n+HOG:D0672154.1e.8a.7b\n+HOG:D0635850.4a.2a.1c\n+HOG:D0639727\n+HOG:D0612770\n+HOG:D0629061\n+HOG:D0661162.1c.5b.1b.2b\n+HOG:D0661162.1c.5b.1b.2c.15a\n+HOG:D0661162.1k\n+HOG:D0620086\n+HOG:D0606606\n+HOG:D0603966\n+HOG:D0612498\n+HOG:D0629897\n+HOG:D0630223.1a\n+HOG:D0690057.4b.4a\n+HOG:D0628773.1b\n+HOG:D0603933\n+HOG:D0667592.1a.2b.2b\n+HOG:D0667592.1b.3a\n+HOG:D0628685\n+HOG:D0632166.1d\n+HOG:D0635474\n+HOG:D0682945.5a\n+HOG:D0690992.1b\n+HOG:D0672517.2b.1b\n+HOG:D0672517.2d.2a\n+HOG:D0679472.8b.20b.21a.22b.40b.28b.22a.7a.4c.3b.3a\n+HOG:D0679472.8b.20b.21b.26c.41a.30b\n+HOG:D0639082.2a.5b.1a.1a\n+HOG:D0639082.2b\n+HOG:D0630648\n+HOG:D0612779\n+HOG:D0608996\n+HOG:D0668804.1a.3a.4c.6a.8b\n+HOG:D0668804.1a.3a.4c.6c.11b\n+HOG:D0668804.1a.3a.4e.7a.14c.17b.8d\n+HOG:D0613770\n+HOG:D0680920.4b.13c.28b.44c.40a\n+HOG:D0680976.5a.13b.13a\n+HOG:D0680976.5a.13b.13f\n+HOG:D0680976.5d.24b.24c.13a.17a.13b\n+HOG:D0614777\n+HOG:D0681338.16b\n+HOG:D0680945.3b.16a.8a.2a.1b\n+HOG:D0668331.1b.2b.3d.9c\n+HOG:D0637135\n+HOG:D0614366\n+HOG:D0668036.2d.5a.2a\n+HOG:D0668036.2d.5e.6a\n+HOG:D0668036.2d.5e.6c\n+HOG:D0620286.1a\n+HOG:D0651107.1a.1b.2a\n+HOG:D0645921.5b\n+HOG:D0621678\n+HOG:D0616745\n+HOG:D0629536.6a\n+HOG:D0655462.1c\n+HOG:D0621421.4a\n+HOG:D0635646.1b\n+HOG:D0615602\n+HOG:D0630209.3a\n+HOG:D0671783.1a.7b\n+HOG:D0671783.1a.7c.5a\n+HOG:D0671783.1c\n+HOG:D0621616.4b.2b\n+HOG:D0623496.1b\n+HOG:D0614184.2a.2b\n+HOG:D0622595.2b.3a\n+HOG:D0620553.1b\n+HOG:D0611011.2b.5a.5b\n+HOG:D0641340.1a.1a.1a.3a\n+HOG:D0641340.1b\n+HOG:D0629702\n+HOG:D0679551.10e.63b.79b\n+HOG:D0679551.10e.63c\n+HOG:D0679551.10t\n+HOG:D0679551.10z.74b.104a.77a.48a\n+HOG:D0679551.10z.74b.104a.77d.51a\n+HOG:D0679551.10z.74d.105a\n+HOG:D0679551.10z.74f.111d\n+HOG:D0679551.10z.74f.111f.86a\n+HOG:D0610805.1a\n+>Duplicated\n+>Underspecific\n+HOG:D0671471.2a.1a.1d.3b.6e.3a.5b.4a.2e\n+>Overspecific_S\n+HOG:D0617450.2b.4a\n+HOG:D0607131.3b\n+HOG:D0661287.1a.2b.5a.2a\n+HOG:D0615771.2e.5a\n+>Overspecific_D\n' |
| b |
| diff -r 000000000000 -r ce13b4c42256 test-data/output.pdf |
| b |
| Binary file test-data/output.pdf has changed |
| b |
| diff -r 000000000000 -r ce13b4c42256 test-data/output.png |
| b |
| Binary file test-data/output.png has changed |
| b |
| diff -r 000000000000 -r ce13b4c42256 test-data/output.sum --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.sum Wed Feb 21 19:27:16 2024 +0000 |
| [ |
| @@ -0,0 +1,15 @@ +#The selected clade was Hominidae +#Number of conserved HOGs is: 17786 +#Results on conserved HOGs is: +#S:Single:S, D:Duplicated[U:Unexpected,E:Expected],M:Missing +S:39,D:0[U:0,E:0],M:17747 +S:0.22%,D:0.00%[U:0.00%,E:0.00%],M:99.78% +#On the whole proteome, there are 44 proteins +#Of which: +#A:Consistent (taxonomically)[P:Partial hits,F:Fragmented], I: Inconsistent (taxonomically)[P:Partial hits,F:Fragmented], C: Likely Contamination[P:Partial hits,F:Fragmented], U: Unknown +A:43[P:0,F:0],I:1[P:0,F:0],C:0[P:0,F:0],U:0 +A:97.73%[P:0.00%,F:0.00%],I:2.27%[P:0.00%,F:0.00%],C:0.00%[P:0.00%,F:0.00%],U:0.00% +#From HOG placement, the detected species are: +#Clade NCBI taxid Number of associated proteins Percentage of proteome's total +Homo sapiens 9606 44 100.00% + |
| b |
| diff -r 000000000000 -r ce13b4c42256 test-data/output.tax --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.tax Wed Feb 21 19:27:16 2024 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>Sampled +Hominidae +>Closest +Homo sapiens |
| b |
| diff -r 000000000000 -r ce13b4c42256 test-data/output.ump --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.ump Wed Feb 21 19:27:16 2024 +0000 |
| b |
| @@ -0,0 +1,54 @@ +>Consistent_Full +sp|P25929|NPY1R_HUMAN +sp|P0C629|O10J4_HUMAN +sp|D6RGX4|F90AP_HUMAN +sp|A0JD32|TV382_HUMAN +sp|Q05195|MAD1_HUMAN +sp|A5D6W6|FITM1_HUMAN +sp|O75347|TBCA_HUMAN +sp|O43598|DNPH1_HUMAN +sp|P20813|CP2B6_HUMAN +sp|P26599|PTBP1_HUMAN +sp|Q15468|STIL_HUMAN +sp|P80188|NGAL_HUMAN +sp|O95274|LYPD3_HUMAN +sp|O15547|P2RX6_HUMAN +sp|A6NH00|OR2T8_HUMAN +sp|P42224|STAT1_HUMAN +sp|O75078|ADA11_HUMAN +sp|P03999|OPSB_HUMAN +tr|A0A2R8YED5|A0A2R8YED5_HUMAN +sp|Q15019|SEPT2_HUMAN +sp|O95210|STBD1_HUMAN +sp|P0C881|R10B1_HUMAN +sp|P57678|GEMI4_HUMAN +sp|Q3BBV2|NBPF8_HUMAN +sp|P78417|GSTO1_HUMAN +sp|P42695|CNDD3_HUMAN +sp|P51693|APLP1_HUMAN +sp|Q14765|STAT4_HUMAN +sp|B3EWG5|FM25C_HUMAN +sp|P47929|LEG7_HUMAN +sp|P00491|PNPH_HUMAN +sp|P12104|FABPI_HUMAN +sp|Q13077|TRAF1_HUMAN +sp|O14901|KLF11_HUMAN +sp|O15079|SNPH_HUMAN +sp|O94913|PCF11_HUMAN +sp|O15400|STX7_HUMAN +sp|P22626|ROA2_HUMAN +sp|P19622|HME2_HUMAN +sp|O00451|GFRA2_HUMAN +sp|P09544|WNT2_HUMAN +sp|P09466|PAEP_HUMAN +sp|O14817|TSN4_HUMAN +>Consistent_Partial +>Consistent_Fragment +>Inconsistent_Full +sp|O95415|BRI3_HUMAN +>Inconsistent_Partial +>Inconsistent_Fragment +>Contamination_Full +>Contamination_Partial +>Contamination_Fragment +>Unknown |
| b |
| diff -r 000000000000 -r ce13b4c42256 test-data/output_detailed_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_detailed_summary.txt Wed Feb 21 19:27:16 2024 +0000 |
| b |
| @@ -0,0 +1,63 @@ +COMPLETENESS ASSESSMENT +------------ +#This benchmark gives an estimate of the completeness of the gene set based on the presence or not of conserved genes of the target lineage. +#Conserved genes are defined using Hierarchical Orthologous Groups (HOGs) defined at a certain taxonomic clade, which is a proxy for the ancestral gene repertoire of this clade. HOGs are considered conserved if they have at least one gene in >80% of the extant species. +#Because representatives of these groups are expected to be present in the target species repertoire, the proportion of missing HOGs proxies the proportion of missing genes in the total gene repertoire of the target proteome. +#Ancestral genes used for this benchmark were in single copy in the selected ancestral lineage, but no assumption is made regarding their propensity to duplicate - they are not universal single copy genes. This benchmark reports the proportion of those genes that are found in multiple copies in target proteomes, and whether it corresponds to a known duplication event in descendants of this gene family (Expected) or not (Unexpected). + +The clade used was: Hominidae +Number of conserved HOGs: 17786 + +#Results on conserved HOGs: +Single: 39 (0.22%) +Duplicated: 0 (0.00%) +Duplicated, Unexpected: 0 (0.00%) +Duplicated, Expected: 0 (0.00%) +Missing: 17747 (99.78%) + + +CONSISTENCY ASSESSMENT +------------------------- +#This benchmark gives the proportion of annotated protein-coding genes in the query proteome that likely correspond to an actual protein-coding gene by comparing to the known gene families of the selected ancestral lineage. + +##High-level categories +#Genes in the "Consistent" category correspond to a gene family known to exist in the selected lineage. Genes in the "Inconsistent" or “Contaminants'' categories correspond to known gene families from different lineages. Such genes are deemed contaminants if more genes than expected by chance correspond to the same species. They are deemed Inconsistent if they correspond to other species seemingly at random. Genes are classified in the “Unknown” category if they do not share enough similarity with known gene families: they may be orphan genes or erroneous protein sequences. + +##Subcategories +#Partial hit proteins are those that share similarity with proteins in known gene families on only part of their sequence: they can indicate poorly defined gene models, structurally divergent genes, or erroneous annotation. +#Fragmented proteins are those whose length is smaller than the proteins from the gene families they share similarity with (<50% median length): they are likely fragmentend sequences or erroneous annotations. + +Number of proteins in the whole proteome: 44 + +#Consistent lineage placements +Total Consistent: 43 (97.73%) +Consistent, partial hits: 0 (0.00%) +Consistent, fragmented: 0 (0.00%) + +#Inconsistent lineage placements +Total Inconsistent: 1 (2.27%) +Inconsistent, partial hits: 0 (0.00%) +Inconsistent, fragmented: 0 (0.00%) + +#Contaminants +Total Contaminants: 0 (0.00%) +Contaminants, partial hits: 0 (0.00%) +Contaminants, fragmented: 0 (0.00%) + +#Unknown +Total Unknown: 0 (0.00%) + + +SPECIES COMPOSITION +------------------- +#This benchmark gives an estimate of the species composition of the dataset, according to HOGs placement. It reports the clades most consistent with the taxonomic distribution of gene families where coding-genes for the query proteomes were placed. The species to which most of the proteins in the query proteome are consistent with is called "Main species." The others are potential contaminants. +#This section also lists the numbers of proteins that can be associated to each of these clades, based on the taxonomic placement of the gene families they share similarity with. + + +##Detected species + +#Main species +Clade: Homo sapiens +Number of associated query proteins: 44 (100.00%) + + |
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| diff -r 000000000000 -r ce13b4c42256 test-data/test.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.fasta Wed Feb 21 19:27:16 2024 +0000 |
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| @@ -0,0 +1,22 @@ +>sp|Q8IYX0|ZN679_HUMAN Zinc finger protein 679 OS=Homo sapiens OX=9606 GN=ZNF679 PE=1 SV=2 +MAKRPGSPGSREMGLLTFRDVVIEFSLEEWQCLDHAQQNLYRDVMLENYRNLVSLGIAVS +KPDLITCLEQNKEPWNIKRNEMVTKHPVMCSHFTQDLPPELGIKDSLQKVIPRRYGKSGH +DNLQVKTCKSMGECEVQKGGCNEVNQCLSTTQNKIFQTHKCVKVFGKFSNSNRHKTRHTG +KKHFKCKKYGKSFCMVSQLHQHQIIHTRENSYQCEECGKPFNCSSTLSKHKRIHTGEKPY +RCEECGKAFTWSSTLTKHRRIHTGEKPYTCEECGQAFSRSSTLANHKRIHTGEKPYTCEE +CGKAFSLSSSLTYHKRIHTGEKPYTCEECGKAFNCSSTLKKHKIIHTGEKPYKCKECGKA +FAFSSTLNTHKRIHTGEEPYKCEECDKAFKWSSSLANHKSMHTGEKPYKCE +>sp|Q8IZE3|PACE1_HUMAN Protein-associating with the carboxyl-terminal domain of ezrin OS=Homo sapiens OX=9606 GN=SCYL3 PE=1 SV=3 +MGSENSALKSYTLREPPFTLPSGLAVYPAVLQDGKFASVFVYKRENEDKVNKAAKHLKTL +RHPCLLRFLSCTVEADGIHLVTERVQPLEVALETLSSAEVCAGIYDILLALIFLHDRGHL +THNNVCLSSVFVSEDGHWKLGGMETVCKVSQATPEFLRSIQSIRDPASIPPEEMSPEFTT +LPECHGHARDAFSFGTLVESLLTILNEQVSADVLSSFQQTLHSTLLNPIPKCRPALCTLL +SHDFFRNDFLEVVNFLKSLTLKSEEEKTEFFKFLLDRVSCLSEELIASRLVPLLLNQLVF +AEPVAVKSFLPYLLGPKKDHAQGETPCLLSPALFQSRVIPVLLQLFEVHEEHVRMVLLSH +IEAYVEHFTQEQLKKVILPQVLLGLRDTSDSIVAITLHSLAVLVSLLGPEVVVGGERTKI +FKRTAPSFTKNTDLSLEDSPMCVVCSHHSQISPILENPFSSIFPKCFFSGSTPINSKKHI +QRDYYNTLLQTGDPFSQPIKFPINGLSDVKNTSEDSENFPSSSKKSEEWPDWSEPEEPEN +QTVNIQIWPREPCDDVKSQCTTLDVEESSWDDCEPSSLDTKVNPGGGITATKPVTSGEQK +PIPALLSLTEESMPWKSSLPQKISLVQRGDDADQIEPPKVSSQERPLKVPSELGLGEEFT +IQVKKKPVKDPEMDWFADMIPEIKPSAAFLILPELRTEMVPKKDDVSPVMQFSSKFAAAE +ITEGEAEGWEEEGELNWEDNNW \ No newline at end of file |
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| diff -r 000000000000 -r ce13b4c42256 tool-data/omamer.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/omamer.loc.sample Wed Feb 21 19:27:16 2024 +0000 |
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| @@ -0,0 +1,9 @@ + +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of OMAMer databases. +# +# the columns are: +#value description version /path/to/data +# +#for example +#Primates-v2.0 Primates 2.0.2 /path/to/data |
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| diff -r 000000000000 -r ce13b4c42256 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Feb 21 19:27:16 2024 +0000 |
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| @@ -0,0 +1,6 @@ +<tables> + <table name="omamer" comment_char="#"> + <columns>value, name, version, path</columns> + <file path="tool-data/omamer.loc"/> + </table> +</tables> |
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| diff -r 000000000000 -r ce13b4c42256 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Feb 21 19:27:16 2024 +0000 |
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| @@ -0,0 +1,6 @@ +<tables> + <table name="omamer" comment_char="#"> + <columns>value, name, version, path</columns> + <file path="${__HERE__}/test-data/omamer.loc"/> + </table> +</tables> \ No newline at end of file |
