| Previous changeset 1:396f0f54d115 (2016-12-12) Next changeset 3:3a78d1f0bfb6 (2017-02-22) |
|
Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 099d38157cec200f0a343579ca9babcd8acb266f |
|
modified:
get_feature_info.py get_feature_info.xml get_genetree.py get_sequences.py test-data/genetree.json test-data/genetree.phyloxml |
|
removed:
tool_dependencies.xml |
| b |
| diff -r 396f0f54d115 -r 840ea71e6318 get_feature_info.py --- a/get_feature_info.py Mon Dec 12 07:47:09 2016 -0500 +++ b/get_feature_info.py Wed Dec 21 15:16:22 2016 -0500 |
| b |
| @@ -1,10 +1,12 @@ # A simple tool to connect to the Ensembl server and retrieve feature # information using the Ensembl REST API. +from __future__ import print_function + import json import optparse -from urlparse import urljoin import requests +from six.moves.urllib.parse import urljoin parser = optparse.OptionParser() parser.add_option('-i', '--input', help='List of Ensembl IDs') @@ -38,4 +40,4 @@ if not r.ok: r.raise_for_status() -print r.text +print(r.text) |
| b |
| diff -r 396f0f54d115 -r 840ea71e6318 get_feature_info.xml --- a/get_feature_info.xml Mon Dec 12 07:47:09 2016 -0500 +++ b/get_feature_info.xml Wed Dec 21 15:16:22 2016 -0500 |
| [ |
| @@ -1,7 +1,8 @@ -<tool id="get_feature_info" name="Get features by Ensembl ID" version="0.1.1"> +<tool id="get_feature_info" name="Get features by Ensembl ID" version="0.1.2"> <description>using REST API</description> <requirements> - <requirement type="package" version="2.7">requests</requirement> + <requirement type="package" version="2.12.4">requests</requirement> + <requirement type="package" version="1.10.0">six</requirement> </requirements> <command> <![CDATA[ |
| b |
| diff -r 396f0f54d115 -r 840ea71e6318 get_genetree.py --- a/get_genetree.py Mon Dec 12 07:47:09 2016 -0500 +++ b/get_genetree.py Wed Dec 21 15:16:22 2016 -0500 |
| b |
| @@ -1,9 +1,11 @@ # A simple tool to connect to the Ensembl server and retrieve genetree using # the Ensembl REST API. +from __future__ import print_function + import optparse -from urlparse import urljoin import requests +from six.moves.urllib.parse import urljoin parser = optparse.OptionParser() parser.add_option('--id_type', type='choice', default='gene_id', @@ -55,4 +57,4 @@ if not r.ok: r.raise_for_status() -print r.text +print(r.text) |
| b |
| diff -r 396f0f54d115 -r 840ea71e6318 get_sequences.py --- a/get_sequences.py Mon Dec 12 07:47:09 2016 -0500 +++ b/get_sequences.py Wed Dec 21 15:16:22 2016 -0500 |
| b |
| @@ -1,11 +1,13 @@ # A simple tool to connect to the Ensembl server and retrieve sequences using # the Ensembl REST API. +from __future__ import print_function + import json import optparse from itertools import islice -from urlparse import urljoin import requests +from six.moves.urllib.parse import urljoin parser = optparse.OptionParser() parser.add_option('-i', '--input', help='List of Ensembl IDs') @@ -43,4 +45,4 @@ if not r.ok: r.raise_for_status() - print r.text + print(r.text) |
| b |
| diff -r 396f0f54d115 -r 840ea71e6318 test-data/genetree.json --- a/test-data/genetree.json Mon Dec 12 07:47:09 2016 -0500 +++ b/test-data/genetree.json Wed Dec 21 15:16:22 2016 -0500 |
| [ |
| b'@@ -1,1 +1,1 @@\n-{"tree":{"events":{"type":"speciation"},"branch_length":0,"children":[{"events":{"type":"speciation"},"branch_length":0.149761,"children":[{"events":{"type":"speciation"},"branch_length":0.148891,"children":[{"events":{"type":"speciation"},"branch_length":0.124852,"children":[{"events":{"type":"speciation"},"branch_length":0.18545,"children":[{"events":{"type":"speciation"},"branch_length":0.023103,"children":[{"events":{"type":"speciation"},"branch_length":0.202291,"children":[{"sequence":{"mol_seq":{"seq":"QLARDMQDMRIRKKKRQTIRPLPGSLFQKKSSGVARIPFKAAVNGKPPARYTAKPLCGLGVPLNVLEITSETAESFRFSLQHFVKLESLIDKGGIQLADGGWLIPTNDGTAGKEEFYRALCDTPGVDPKLMSEEWVYNHYRWIVWKQASMERSFPEEMGSLCLTPEQVLLQLKYRYDIEVDHSRRPALRKIMEKDDTAAKTLVLCVCGVVFRGSSPKNKSFGDISTPGADPKVENPCAVVWLTDGWYSIKAQLDGPLTSMLHRGRLPVGGKLIIHGAQLVGSENACSPLEAPVSLMLKICANSSRPARWDSKLGFHRDPRPFLLPVSSLYSSGGPVGCVDIIILRSYPILWMERKPEGGTVFRSGRAEEKEARRYNIHKEKAMEILFDKIKAEFEKEEKGNRKPQCRRTINGQNITSLQDGEELYEAVGDDPAFLEAHLTEKQVEVLQNYKRLVMEKQQAELQDRYRRAVESAEDGVGGCPKRDVAPVWRLCIADSMGHSGRVYQLSLWRPPSELQALLKEGCRYKVYNLTTLDSKKQGGNATVQLTATKKTQFEHLQGSEEWLSKHFQPRVATNFVRLQDPEFNPLCSEVDLTGYVITIIDGQGFSPAFYLADGKQNFVKVRCFSSFAQSGLEDVIKPRVLLALSNLQLRGQSTSPTPVVYAGDLTVFSTNPKEVHLQESFSQLKTLVQGQENFFVHAEEKLSQLMSDGLSAIASPAGQIQTPASTVKRRGDMTDVSSNIMVINKTSKVTCQQPGRSHRFSTPINRNSTAHSSAERNPSTIKKRKALDYLSHIPSPPPLSCLSTLSSPSVKKIFIPPRRTEIPGTLKTVKTPNQKPSNTPVDDQWVNDEELAMIDTQAL","is_aligned":0},"location":"scaffold_19:196046-199577","id":[{"source":"EnsEMBL","accession":"ENSTRUP00000015030"}]},"branch_length":0.069516,"id":{"source":"EnsEMBL","accession":"ENSTRUG00000006177"},"confidence":{},"taxonomy":{"scientific_name":"Takifugu rubripes","common_name":"Fugu","id":31033}},{"sequence":{"mol_seq":{"seq":"VSFSSDTPRKPKAGSLSSEFTDRFLAQEALDCTKALLEDERLVDDPHMTGECLHRCPQFSLLVNLFVKPHTAVLIPEQPPLKRRLLEEFDRTDGSSRGSALNPEKCSPNGIMGDRRVFKCSVSFQPNITTPHRICSQKAERPVSFLSRRSGTNYVETSLPNTTPTKVSALRDSNEARLQKSNFIPPFIKNVKLDTPNSKTASTFVPPFKKSRNSSKTEEEEPKHHFIPPFTNPCATSSTKKHTAGHLHNVELARDMQGMRIRKKKRQTILPLPGSLFLKKSSGVTRIPLKSAVNGKPPARYTPKQLYGLGVPLNVLEITSETAGSFRFSLQQFVKLESLTDKGGIQLADGGWLIPRNDGTAGKEEFYRALCDTTGVDPKLISEEWVYNHYRWIVWKQASMERSFPEQLGSLCLTPEQVLLQLKYRYDIEVDQSRRPALRKIMERDDTAAKTLILCVCGVVSRGSSPQKQGLGGVAAPSSDPQVENPFAVVWLTDGWYSIKAQLDGPLTSMLNRGRLPVGGKLIIHGAQLVGSQDACSPLEAPESIMLKIFANSSRRARWDAKLGFYRDPRPFLLPVSSLYNSGGPVGCVDIIILRSYPTLWMERKPEGGTVFRSGRAEEKEARRYNVHKEKAMEILFDKIQAEFEKEERDNRKPRSRRRTIGDQDIKSLQDGEELYEAVGDDPAYLEAHLTEQQAETLQNYKRLLIEKKQAELQDRYRRAVETAEDGTGSCPKRDVAPVWRLSIADFMEKPGSVYQLNIWRPPSELQSLLKEGCRYKVYNLTTTDSKKQGGNTTVQLSGTKKTQFEDLQASEELLSTYFQPRVSATFIDLQDPEFHSLCGEVDLTGYVISIIDGQGFSPAFYLTDGKQNFVKVRCFSSFAQSGLEDVIKPSVLLALSNLQLRGQATSPTPVLYAGDLTVFSTNPKEVHLQESFSQLKTLVQ","is_aligned":0},"location":"16:4700614-4705074","id":[{"source":"EnsEMBL","accession":"ENSTNIP00000002435"}]},"branch_length":0.114058,"id":{"source":"EnsEMBL","accession":"ENSTNIG00000016261"},"confidence":{},"taxonomy":{"scientific_name":"Tetraodon nigroviridis","common_name":"Tetraodon","id":99883}}],"confidence":{"bootstrap":100},"taxonomy":{"scientific_name":"Tetraodontidae","common_name":"Puffers","timetree_mya":69.8,"id":31031}},{"sequence":{"mol_seq":{"seq":"LPNVELAQDMQDMRIRKKKRQTIRPLPGSLFLTKTSGVTRIPLKAALVFLLQLYRHGVHQHVCEISSETAESFRFNLKQFIKREALLDGGGVQLADGGWLIPSKDGTAGKEEFYRALCDTPGVDPKLISDGWVDNHYRWVVWKQASMERSFPETMGGLCLTPEQVLLQLKYRYDVEVDHSRRPALRRITERDDTAAKTLVLCVCGVVSRSFDDSKTPRGADAGGGNPSAVVWLTDGWYAIRAQLDEPLTAMLRNGRVAVGSKLIVHGAQLVGSQEACSPLEAPEALMLKICANSSRPVRWDAKLGFHKDPRPFLLPLSCLYSSGGQVGCVDMIVLRSYPIQWMERKPEGGVVFRSVRAEEKEAKRFNGLKQKAMEILFAKIQDEFEKEDKGRTCDFTTQAISRQAIAGLQAGEELCEAVGEDPAHLEALLSEQQVETLNTYRRCVMEKKQAQLHDRFQRALESAEASEGSCPKREVTPVWRLGVADSRDQRGRVYQLNLWRPSSDLQALLKEGRRYKVYNLTTSDGKKHNGSSNVQLTGTKKTQFQDLQASREWLSTRFQPRVSACFVDLQNPEFQSLCGEVDLTGFVIQIVDGQGFSPAFYLADGELNFVKVRCFSSFAQSGLEDLVKPRVLLSLSNLQLRGQSASPTPVVYAGDLTVFSANPKDAHLQESLSQNKNLRQSQENFFLIAEETLSRLVQSDGRRPLSSPALHTRTPALATSMIQDTTASVKCVLLMQGASQQLVRSRGTFTPVSRKPPAANCSTEKDAGSVKRRRALNYLSHIPSPPPLLNLGSVASPCVNKTFNPPRRSGTPSTLKTVQTPAHKAQKVDSLVEDEWVNDEELAMIDTQAL","is_ali'..b'FSTARGAKLKVSEKALEQARMFLNDVDSIGESQTPKLVPRSSGKHDVSMQSTRLQKTKDLCRGETSIKISQPDSGVANQISNGADITTFNSENVFQEQKSGNAAKEVCEKISPSETSMPQPQQGYGFQTASGKGVSVLPSALKKAKAIFKDCDSNIDNLQSTNMEERKTKLDVEIVKQTNALISNSKSVTFSDVEEFKTDLINNLDQEAPQKEVCELKGLQSEFSNLISSNGNCGFSTASGKKVSVSAEALQRAKDVLFESVDGFSCANVYKKTNQVVDIQLDSSSSGKHKGFCTAGGKKVAFSATGLQKAKNLFRGCEEESLTTEQNCKGLSNVLMLACNGVSLIPEPGNSSGNNVGFSTAGGRKMDISVTALQKANNLFKDCEEESLASRSLAHQGFTTASGKNVFVSEKALSEVRAVFAGCDETSFSLELKKLSVNNVGFSTAGGKKVTISDTSLQRTMNLFQDCEEESLGSRSLKHQGCKGFTTASGKNVTVSEKALSEVRAVFAGCDEASFSHEPKNISGNKIGFSTTVEKMTTALEMPNNNNNFKDCEEESLASRNLMHQACKGFTTASGKNVTVSETALNEVKAVFAGCDEATFDLEPKKSLGSNIGFSTAGGKKVTISSTALQRAQTLFKDCEEEKEVFESEKAPLPTKSFHARSEDIVDGNLKFDQTNKKNPRLSTASGKVVSVTKVSLEETSTFFREFDNQNTATDNQLLLRDSSKHYPQHKDRQTKATLHPKAARNEPAHLDLHSLDFNSCTDTQQIYFEQEAMACTKALLEDDDLIESAGLISSEDIDNKRRPSFSDVQTIESVDQNRKRKRQVDGSSVADSGQPPLKRQLLSEFDRTLHAKTSGLTPLKSCPNGTLKDRRVFKYNVHLKPYVTSPVLFPVNQQSNNIEEHCSTESVQKRCNSDHMGGVFNPPFQKNMNPPTSNSQDASKVSSGIVLSFNVVNQEENPNSKEMDQIMAISKSHCDRGKQNCNEKNQDSKSKSSSSVQSIPLKIGNFDEKDMIALQESLQLARDMQDMRLRKKKRQTIRPVPGSLYLAKTSGVSRKSLRDAVGCTCPSQYTQDELSQHGVHHKVLEITSENAESFRFDCSDYFTCEHLMESGALQLADGGWLVPDSKGTVGKEEFFSALCDTPGVDPKLISDVWVFNHYRWIIWKRASMERTFPNLIGGLCLTPEQVLLQLKFRYDVEVDHSQRSALRRIMERDDTPAKTLVLCVCGIVQTCQNPEKTMKDDKSPSAKMESCVIWLTDGWYSIKSLLDPPLSAMLNKGRLKIGDKIVTSGAELVGSQEACPPLEAPESLMLKISANSTRRARWDTKLGYYRDPRPIRLLLSSLYASGGLVSCVNLLVLRSYPTQWMEKKPNSVFIFRNDRAEDREARKHSNSKHKSLDLLISKIQTQFEKEMEGKKKKRAQRRTFSRHEIETLQDGDELYEAMEQDAAVETRLSHKQMEAVSKYRCCREEKRQAELQERVQKAVMEAQEAEGGCPNRDVTPVWKLSVIDASDMQSNCVYTLNIWRPTRELQGLLTEGHRYRAYHLASSEGKKRSGVAHIQLTATKKTLFQDIEVSPEWLHQHFRARECVRFRELQNPHFSSPCGEVDIVGYIVSIEGKQGHCPVLHLVDENFDLVTVRTYSSLEQLAVEELVKPRALVAICNLQVRVLSGPVPSLYAGEQALFSINPKESYLQEAMAHLKTFAQNYEQFFNLAEEKVSDVVPSGVLGSFQSPRTPGVQPFPKMNGTVTPQQKSSIFSPFTPLNRRTPASTSNSEVKDSKNLKRRRGLDYLSRIPSPPPLIPLKTRASPCINKTFNPPRKSVTPKPPQNECSPASRPPAGEEKWVHDEELAMIDTQALVDGLMND","is_aligned":0},"location":"15:32054010-32070540","name":"brca2-001","id":[{"source":"EnsEMBL","accession":"ENSDARP00000099674"}]},"branch_length":0.529522,"id":{"source":"EnsEMBL","accession":"ENSDARG00000079015"},"confidence":{},"taxonomy":{"scientific_name":"Danio rerio","common_name":"Zebrafish","id":7955}}],"confidence":{"bootstrap":34},"taxonomy":{"scientific_name":"Otophysi","common_name":"Teleost fishes","timetree_mya":152.9,"id":186626}}],"confidence":{"bootstrap":9},"taxonomy":{"scientific_name":"Clupeocephala","common_name":"Teleost fishes","timetree_mya":265.5,"id":186625}},{"sequence":{"mol_seq":{"seq":"MIQNLDFARGMQEMRIRKKKRQTIRPLPGSLCLTKTSGVSRVSLRAAVGGKSPAQHTQQQLYVCGVNRCVLEISSENAESFRFSCRDHFGIEFFSAGNGVQLADGGCLIPDNKGTAGKEEFYRALCDTPGVDPKLISESWVYNHYRWIVWKRAAMERAFPLEMGSRCLTPEQVLLQLKYRYDLEIDNSQRSALRKIMERDDTPAKTLVLCVCRIVSMGSLQAHDTPGNKALPYAKAKTDGPVGVIEVTDGWYAIKALLDAPLTAILRKGRLAVGGKIVTHGADLIGCQDACSPLEAPEALMLKICANSTRLARWDTKLGFHRDPRPFHVPLSSLFSNGGRVGCVDVVVLRTYPIQWMEKKADGVFVFRGDRAEEREARRHNENKQKTMEALFAKIQSEFEKEQEGKKKSNRRQRFSHQEIQALQEGEELYEATESDPVCLEACLSEQQLMTLNNYRRALNERKQTKLQEEFQKAIRSAQDRENSCPERDVTPVWKLLVVDCKNLQNNTAYFLNIWRPSTEVCSLLKEGCRYKIYQLATSETKRRIGNAAVQLTAMKKTQFEQLQVPPELLCQLYASREAVSFRSLLSPRFQPVCGEVDLVGYVISITGKQGGAPVVYLVNENRDFVAVKCWVGLSQLALEDIVQPRALLAVSNVQARPSPAAAVPTAYAAELSVFSANPKETHLQAACTLLRSAAQGIECFFEAAEEKLSKLIKEDFPCQSLKDLSSIPKTPIMKPDVQRESSNLMISFILLLPSPQVPGRSPQQSLCAFEHLTPTCGKPPLHAGRSDDKGPKSLKRKRGLIYLSRIPSPPPLAPLRSPCVNKTFQPPRRCASPLAAARGKEECRSPGPAPEAGGEWVKDEELAQINTQDL","is_aligned":0},"location":"LG3:13357730-13380925","id":[{"source":"EnsEMBL","accession":"ENSLOCP00000009962"}]},"branch_length":0.204682,"id":{"source":"EnsEMBL","accession":"ENSLOCG00000008205"},"confidence":{},"taxonomy":{"scientific_name":"Lepisosteus oculatus","common_name":"Spotted gar","id":7918}}],"confidence":{"bootstrap":87},"taxonomy":{"scientific_name":"Neopterygii","common_name":"Ray-finned fishes","timetree_mya":333.8,"id":41665}}],"confidence":{},"taxonomy":{"scientific_name":"Euteleostomi","common_name":"Bony vertebrates","timetree_mya":441,"id":117571}},"rooted":1,"id":"ENSGT00390000003602","type":"gene tree"}\n' |
| b |
| diff -r 396f0f54d115 -r 840ea71e6318 test-data/genetree.phyloxml --- a/test-data/genetree.phyloxml Mon Dec 12 07:47:09 2016 -0500 +++ b/test-data/genetree.phyloxml Wed Dec 21 15:16:22 2016 -0500 |
| b |
| b'@@ -4,302 +4,121 @@\n <phylogeny rooted="true" type="gene tree">\n <clade branch_length="0">\n <taxonomy>\n+ <id>117571</id>\n <scientific_name>Euteleostomi</scientific_name>\n- <id>117571</id>\n <common_name>Bony vertebrates</common_name>\n </taxonomy>\n- <clade branch_length="0.149761">\n- <confidence type="bootstrap">92</confidence>\n+ <clade branch_length="0.169242">\n+ <confidence type="bootstrap">3</confidence>\n <taxonomy>\n- <scientific_name>Neopterygii</scientific_name>\n- <id>41665</id>\n- <common_name>Ray-finned fishes</common_name>\n+ <id>8287</id>\n+ <scientific_name>Sarcopterygii</scientific_name>\n+ <common_name>Lobe-finned fish</common_name>\n </taxonomy>\n- <clade branch_length="0.148891">\n- <confidence type="bootstrap">33</confidence>\n+ <clade branch_length="0.117496">\n+ <confidence type="bootstrap">3</confidence>\n <taxonomy>\n- <scientific_name>Clupeocephala</scientific_name>\n- <id>186625</id>\n- <common_name>Teleost fishes</common_name>\n+ <id>32523</id>\n+ <scientific_name>Tetrapoda</scientific_name>\n+ <common_name>Tetrapods</common_name>\n </taxonomy>\n- <clade branch_length="0.181209">\n- <confidence type="bootstrap">46</confidence>\n+ <clade branch_length="0.115666">\n+ <confidence type="bootstrap">99</confidence>\n <taxonomy>\n- <scientific_name>Otophysi</scientific_name>\n- <id>186626</id>\n- <common_name>Teleost fishes</common_name>\n+ <id>32524</id>\n+ <scientific_name>Amniota</scientific_name>\n+ <common_name>Amniotes</common_name>\n </taxonomy>\n- <clade branch_length="0.421267">\n- <name>ENSAMXG00000013027</name>\n+ <clade branch_length="0.090766">\n+ <confidence type="bootstrap">26</confidence>\n <taxonomy>\n- <id>7994</id>\n- <scientific_name>Astyanax mexicanus</scientific_name>\n- <common_name>Cave fish</common_name>\n- </taxonomy>\n- <sequence>\n- <accession source="Ensembl">ENSAMXP00000013440</accession>\n- <name>brca2-201</name>\n- <location>KB882257.1:1212119-1232402</location>\n- <mol_seq is_aligned="0">MIEDFFHQIETEELGPLSSDWFKELTAKASKDESFPGAVEHEASSRTEDGTFRAPQETPALESQMSSTPRLFRVRGPLSPDSVLGRSPNPAFQQQGMQTPLSTLPWTDSSPCLFGSAKESQRFEEDSEPLKKHDYFGLLDTPKSSLVQDSSAKRISESLGAQLHPDLSWSSNFNTPGAMSPTVILTKKDAQPSPVSFLKDKEVIIVRKLFPSLSKGTESTSEITSTAHNNASLTEENAQTKGPDESFDNVEGLWRQTVPDAINDSDVRDTVESVLDGAEDVLSIFFSNSSSALRRVKSKERTKKRVNGVSKDVKPAALATQHYTDRTGTATEAKSPPKNKDFSQWSPLSLSQVSDAKAKQDCTSDLANKHLNFESVNSDSGEDALKDSITQLGQFNTCEVEKQKSSPDSYPEKSQLRSSLLAASPALTFSRKPRKFVYQVQSPFPPTKENDLTGKHYREPFLTAENKKHIKDDPQTSDTVGDCLVHPKEPPVKQGNPGALNVDHGLDMTQLCNAFAEDFTQEIRSDAIKIDEVQTKAESVLHSDDGAEHLEFPANHKEASALAEESINLTSRSRMENTLSESLKHENGYPAVFNDVSGLSSSCNDGADKYLYSGFKTANNKLIHVPPEAVMKAKATFEDFVDLEEIRSDGLNTGSGTALNSSVVSTWSSERYSHALNKPEREPTGNLLHGSLDVASGCTSTSYLPKTNDSGFKTASNRSITISSVNLEKAKDIFKELEVENLYKTDICPSSNSAELEIQVMKNAKVPKLDIKRNVDGNYVLTASQKADVTELCSMLEDADSQYEFTQFRQAKPCSKSMESSRSEREWDPEILSGIDFDDSFNCDTERQLPRKWPVRPDLPTQNGPVSNSMKNGKETPKAELSLNDYRLSLRSDGREMAKTPAVQTNTSEGNEPVCVGFKTARGNSVRISEKNLTKARSLFADLEDCVGKIGLKSDHNSVTAQVTTKQTKHNQNSHNKDDVCKQICSTENPEDQDNPQGTKQNEKPDLLVDTRHCGFSTAGGKELKVSESSLLKAKKLLNKVSDQCEAVPSIKAPPNRVTTLKVANINLQPSVCSNSKVSENVFPHNLKMSCKSLTGNSKDQMFRNSESHHRLSEIEQQTTAKYQSTKSIQSSGFKMASGKGVSFSSSAIEKSRAIFRDLDSLIAEDGSNETKSMDENAKLHDEAERSQCKFANGFKMASGKGVSFSEGAFLKSKAFFKDCDADYPDHSQGKGDQSSVMDNCGFKALVGNTVHLPEIDSPNKEIVGLKDEATVLNKYVEKEFVPTSAPEILQFTSGCGFSTASGKMVSVSAEALQKAKAVLDDSSAASPCEIKADVSEEKNKKGVPKTDTYIPGRSLGFSTASGRKVAISDRALEKAKNLFASCEVEDLANNGITLNSAQTKPLGSEQTRCLGFSTASGKGVAVSEKTLKEAKAVFAGCEDILETADVHKPLKTGRVVEEKDKGSLNQSLTNREFQTCESA'..b'LTASQKADVTELCSLLEEANSQYEFTQYKSTNIGSHNRTTEKEWDPDILNDIDFDDSFSCDVVKGKHPSKTNASSVNTSDLISFRSDLKEKQNGTVVLSVTEESALVDGMRSILSKSSDNSHFHTFGFKTAKGKAISVSEKSLNKAKHFFEEDYKEATFTGVINQEHFKTESSVKTCISTENNNAQTKQDVRLSCGEVNAAHNMINWQEAGNAGTEPNCLRDKTDVVCVDSNIHFGFSTARGAKLKVSEKALEQARMFLNDVDSIGESQTPKLVPRSSGKHDVSMQSTRLQKTKDLCRGETSIKISQPDSGVANQISNGADITTFNSENVFQEQKSGNAAKEVCEKISPSETSMPQPQQGYGFQTASGKGVSVLPSALKKAKAIFKDCDSNIDNLQSTNMEERKTKLDVEIVKQTNALISNSKSVTFSDVEEFKTDLINNLDQEAPQKEVCELKGLQSEFSNLISSNGNCGFSTASGKKVSVSAEALQRAKDVLFESVDGFSCANVYKKTNQVVDIQLDSSSSGKHKGFCTAGGKKVAFSATGLQKAKNLFRGCEEESLTTEQNCKGLSNVLMLACNGVSLIPEPGNSSGNNVGFSTAGGRKMDISVTALQKANNLFKDCEEESLASRSLAHQGFTTASGKNVFVSEKALSEVRAVFAGCDETSFSLELKKLSVNNVGFSTAGGKKVTISDTSLQRTMNLFQDCEEESLGSRSLKHQGCKGFTTASGKNVTVSEKALSEVRAVFAGCDEASFSHEPKNISGNKIGFSTTVEKMTTALEMPNNNNNFKDCEEESLASRNLMHQACKGFTTASGKNVTVSETALNEVKAVFAGCDEATFDLEPKKSLGSNIGFSTAGGKKVTISSTALQRAQTLFKDCEEEKEVFESEKAPLPTKSFHARSEDIVDGNLKFDQTNKKNPRLSTASGKVVSVTKVSLEETSTFFREFDNQNTATDNQLLLRDSSKHYPQHKDRQTKATLHPKAARNEPAHLDLHSLDFNSCTDTQQIYFEQEAMACTKALLEDDDLIESAGLISSEDIDNKRRPSFSDVQTIESVDQNRKRKRQVDGSSVADSGQPPLKRQLLSEFDRTLHAKTSGLTPLKSCPNGTLKDRRVFKYNVHLKPYVTSPVLFPVNQQSNNIEEHCSTESVQKRCNSDHMGGVFNPPFQKNMNPPTSNSQDASKVSSGIVLSFNVVNQEENPNSKEMDQIMAISKSHCDRGKQNCNEKNQDSKSKSSSSVQSIPLKIGNFDEKDMIALQESLQLARDMQDMRLRKKKRQTIRPVPGSLYLAKTSGVSRKSLRDAVGCTCPSQYTQDELSQHGVHHKVLEITSENAESFRFDCSDYFTCEHLMESGALQLADGGWLVPDSKGTVGKEEFFSALCDTPGVDPKLISDVWVFNHYRWIIWKRASMERTFPNLIGGLCLTPEQVLLQLKFRYDVEVDHSQRSALRRIMERDDTPAKTLVLCVCGIVQTCQNPEKTMKDDKSPSAKMESCVIWLTDGWYSIKSLLDPPLSAMLNKGRLKIGDKIVTSGAELVGSQEACPPLEAPESLMLKISANSTRRARWDTKLGYYRDPRPIRLLLSSLYASGGLVSCVNLLVLRSYPTQWMEKKPNSVFIFRNDRAEDREARKHSNSKHKSLDLLISKIQTQFEKEMEGKKKKRAQRRTFSRHEIETLQDGDELYEAMEQDAAVETRLSHKQMEAVSKYRCCREEKRQAELQERVQKAVMEAQEAEGGCPNRDVTPVWKLSVIDASDMQSNCVYTLNIWRPTRELQGLLTEGHRYRAYHLASSEGKKRSGVAHIQLTATKKTLFQDIEVSPEWLHQHFRARECVRFRELQNPHFSSPCGEVDIVGYIVSIEGKQGHCPVLHLVDENFDLVTVRTYSSLEQLAVEELVKPRALVAICNLQVRVLSGPVPSLYAGEQALFSINPKESYLQEAMAHLKTFAQNYEQFFNLAEEKVSDVVPSGVLGSFQSPRTPGVQPFPKMNGTVTPQQKSSIFSPFTPLNRRTPASTSNSEVKDSKNLKRRRGLDYLSRIPSPPPLIPLKTRASPCINKTFNPPRKSVTPKPPQNECSPASRPPAGEEKWVHDEELAMIDTQALVDGLMND</mol_seq>\n+ </sequence>\n+ <property datatype="xsd:string" ref="Compara:genome_db_name" applies_to="clade">danio_rerio</property>\n+ </clade>\n+ </clade>\n+ </clade>\n+ <clade branch_length="0.204682">\n+ <name>ENSLOCG00000008205</name>\n+ <taxonomy>\n+ <id>7918</id>\n+ <scientific_name>Lepisosteus oculatus</scientific_name>\n+ <common_name>Spotted gar</common_name>\n+ </taxonomy>\n+ <sequence>\n+ <accession source="Ensembl">ENSLOCP00000009962</accession>\n+ <location>LG3:13357730-13380925</location>\n+ <mol_seq is_aligned="0">MIQNLDFARGMQEMRIRKKKRQTIRPLPGSLCLTKTSGVSRVSLRAAVGGKSPAQHTQQQLYVCGVNRCVLEISSENAESFRFSCRDHFGIEFFSAGNGVQLADGGCLIPDNKGTAGKEEFYRALCDTPGVDPKLISESWVYNHYRWIVWKRAAMERAFPLEMGSRCLTPEQVLLQLKYRYDLEIDNSQRSALRKIMERDDTPAKTLVLCVCRIVSMGSLQAHDTPGNKALPYAKAKTDGPVGVIEVTDGWYAIKALLDAPLTAILRKGRLAVGGKIVTHGADLIGCQDACSPLEAPEALMLKICANSTRLARWDTKLGFHRDPRPFHVPLSSLFSNGGRVGCVDVVVLRTYPIQWMEKKADGVFVFRGDRAEEREARRHNENKQKTMEALFAKIQSEFEKEQEGKKKSNRRQRFSHQEIQALQEGEELYEATESDPVCLEACLSEQQLMTLNNYRRALNERKQTKLQEEFQKAIRSAQDRENSCPERDVTPVWKLLVVDCKNLQNNTAYFLNIWRPSTEVCSLLKEGCRYKIYQLATSETKRRIGNAAVQLTAMKKTQFEQLQVPPELLCQLYASREAVSFRSLLSPRFQPVCGEVDLVGYVISITGKQGGAPVVYLVNENRDFVAVKCWVGLSQLALEDIVQPRALLAVSNVQARPSPAAAVPTAYAAELSVFSANPKETHLQAACTLLRSAAQGIECFFEAAEEKLSKLIKEDFPCQSLKDLSSIPKTPIMKPDVQRESSNLMISFILLLPSPQVPGRSPQQSLCAFEHLTPTCGKPPLHAGRSDDKGPKSLKRKRGLIYLSRIPSPPPLAPLRSPCVNKTFQPPRRCASPLAAARGKEECRSPGPAPEAGGEWVKDEELAQINTQDL</mol_seq>\n+ </sequence>\n+ <property datatype="xsd:string" ref="Compara:genome_db_name" applies_to="clade">lepisosteus_oculatus</property>\n+ </clade>\n+ </clade>\n </clade>\n <property datatype="xsd:string" ref="Compara:gene_tree_stable_id" applies_to="phylogeny">ENSGT00390000003602</property>\n </phylogeny>\n' |
| b |
| diff -r 396f0f54d115 -r 840ea71e6318 tool_dependencies.xml --- a/tool_dependencies.xml Mon Dec 12 07:47:09 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="requests" version="2.7"> - <repository changeset_revision="7e330b122c8c" name="package_python_2_7_requests_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |