Repository 'ensembl_get_genetree'
hg clone https://toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_genetree

Changeset 2:950d9d11b6fb (2016-12-21)
Previous changeset 1:98aba0efe77a (2016-12-12) Next changeset 3:181e12d6ac96 (2017-03-24)
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_genetree.py
get_genetree.xml
get_sequences.py
test-data/genetree.json
test-data/genetree.phyloxml
removed:
tool_dependencies.xml
b
diff -r 98aba0efe77a -r 950d9d11b6fb get_feature_info.py
--- a/get_feature_info.py Mon Dec 12 07:47:26 2016 -0500
+++ b/get_feature_info.py Wed Dec 21 15:16:35 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 98aba0efe77a -r 950d9d11b6fb get_genetree.py
--- a/get_genetree.py Mon Dec 12 07:47:26 2016 -0500
+++ b/get_genetree.py Wed Dec 21 15:16:35 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 98aba0efe77a -r 950d9d11b6fb get_genetree.xml
--- a/get_genetree.xml Mon Dec 12 07:47:26 2016 -0500
+++ b/get_genetree.xml Wed Dec 21 15:16:35 2016 -0500
[
@@ -1,4 +1,4 @@
-<tool id="get_genetree" name="Get gene tree by Ensembl ID" version="0.1.1">
+<tool id="get_genetree" name="Get gene tree by Ensembl ID" version="0.1.2">
     <description>using REST API</description>
     <macros>
         <xml name="sequence_conditional">
@@ -21,7 +21,8 @@
         </xml>
     </macros>
     <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[
@@ -108,7 +109,7 @@
             <param name="sequence_selector" value="protein" />
             <param name="aligned" value="0" />
             <param name="cigar" value="0" />
-            <output name="output" file="genetree.json" ftype="json" />
+            <output name="output" file="genetree.json" ftype="json" compare="sim_size" />
         </test>
         <test>
             <param name="input_type" value="gene_tree_id" />
@@ -117,7 +118,7 @@
             <param name="sequence_selector" value="protein" />
             <param name="aligned" value="0" />
             <param name="cigar" value="0" />
-            <output name="output" file="genetree.json" ftype="json" />
+            <output name="output" file="genetree.json" ftype="json" compare="sim_size" />
         </test>
         <test>
             <param name="input_type" value="gene_tree_id" />
b
diff -r 98aba0efe77a -r 950d9d11b6fb get_sequences.py
--- a/get_sequences.py Mon Dec 12 07:47:26 2016 -0500
+++ b/get_sequences.py Wed Dec 21 15:16:35 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 98aba0efe77a -r 950d9d11b6fb test-data/genetree.json
--- a/test-data/genetree.json Mon Dec 12 07:47:26 2016 -0500
+++ b/test-data/genetree.json Wed Dec 21 15:16:35 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 98aba0efe77a -r 950d9d11b6fb test-data/genetree.phyloxml
--- a/test-data/genetree.phyloxml Mon Dec 12 07:47:26 2016 -0500
+++ b/test-data/genetree.phyloxml Wed Dec 21 15:16:35 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 98aba0efe77a -r 950d9d11b6fb tool_dependencies.xml
--- a/tool_dependencies.xml Mon Dec 12 07:47:26 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>