| Next changeset 1:98aba0efe77a (2016-12-12) |
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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty |
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added:
get_feature_info/get_feature_info.py get_genetree/get_genetree.py get_genetree/get_genetree.xml get_sequences/get_sequences.py test-data/genetree.json test-data/genetree.phyloxml test-data/input.txt test-data/out.json test-data/sequences.fasta tool_dependencies.xml |
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| diff -r 000000000000 -r f0018341e9f6 get_feature_info/get_feature_info.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_feature_info/get_feature_info.py Thu Aug 11 14:29:07 2016 -0400 |
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| @@ -0,0 +1,41 @@ +# A simple tool to connect to the Ensembl server and retrieve feature +# information using the Ensembl REST API. +import json +import optparse +from urlparse import urljoin + +import requests + +parser = optparse.OptionParser() +parser.add_option('-i', '--input', help='List of Ensembl IDs') +parser.add_option('-e', '--expand', type='choice', choices=['0', '1'], + default='0', + help='Expands the search to include any connected features. e.g. If the object is a gene, its transcripts, translations and exons will be returned as well.') + +parser.add_option('-s', '--species', type='choice', + choices=['ensembl', 'ensemblgenomes'], default='ensembl', + help='Specify the genome databases for vertebrates and other eukaryotic species') + +parser.add_option('-f', '--format', type='choice', + choices=['full', 'condensed'], default='full', + help='Specify the formats to emit from this endpoint') +options, args = parser.parse_args() +if options.input is None: + raise Exception('-i option must be specified') + + +server = 'http://rest.%s.org' % options.species +ext = 'lookup/id' + +headers = {'Content-Type': 'application/json', 'Accept': 'application/json'} +params = dict((k, getattr(options, k)) for k in ['format', 'expand']) +with open(options.input) as f: + ids = [line.strip() for line in f] +data = {'ids': ids} +r = requests.post(urljoin(server, ext), params=params, headers=headers, + data=json.dumps(data)) + +if not r.ok: + r.raise_for_status() + +print r.text |
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| diff -r 000000000000 -r f0018341e9f6 get_genetree/get_genetree.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_genetree/get_genetree.py Thu Aug 11 14:29:07 2016 -0400 |
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| @@ -0,0 +1,58 @@ +# A simple tool to connect to the Ensembl server and retrieve genetree using +# the Ensembl REST API. +import optparse +from urlparse import urljoin + +import requests + +parser = optparse.OptionParser() +parser.add_option('--id_type', type='choice', default='gene_id', + choices=['gene_id', 'gene_tree_id'], help='Input type') +parser.add_option('-i', '--input', help='Ensembl ID') +parser.add_option('--format', type='choice', + choices=['json', 'orthoxml', 'phyloxml', 'nh'], + default='json', help='Output format') +parser.add_option('-s', '--sequence', type='choice', + choices=['protein', 'cdna', 'none'], default='protein', + help='The type of sequence to bring back. Setting it to none results in no sequence being returned') + +parser.add_option('-g', '--species', type='choice', + choices=['ensembl', 'ensemblgenomes'], default='ensembl', + help='Specify the genome databases for vertebrates and other eukaryotic species') + +parser.add_option('-a', '--aligned', type='choice', choices=['0', '1'], + default='0', help='Return the aligned string if true. Otherwise, return the original sequence (no insertions)') +parser.add_option('-c', '--cigar_line', type='choice', choices=['0', '1'], + default='0', + help='Return the aligned sequence encoded in CIGAR format') +parser.add_option('--nh_format', type='choice', + choices=['full', 'display_label_composite', 'simple', 'species', 'species_short_name', 'ncbi_taxon', 'ncbi_name', 'njtree', 'phylip'], + default='simple', + help='The format of a NH (New Hampshire) request') +options, args = parser.parse_args() +if options.input is None: + raise Exception('-i option must be specified') + +server = 'http://rest.%s.org' % options.species + +if options.id_type == 'gene_id': + ext = 'genetree/member/id' +elif options.id_type == 'gene_tree_id': + ext = 'genetree/id' + +if options.format == 'json': + content_type = 'application/json' +elif options.format == 'orthoxml': + content_type = 'text/x-orthoxml+xml' +elif options.format == 'phyloxml': + content_type = 'text/x-phyloxml+xml' +elif options.format == 'nh': + content_type = 'text/x-nh' +headers = {'Content-Type': content_type} +params = dict((k, getattr(options, k)) for k in ['sequence', 'aligned', 'cigar_line', 'nh_format']) +r = requests.get(urljoin(server, '/'.join([ext, options.input])), params=params, headers=headers) + +if not r.ok: + r.raise_for_status() + +print r.text |
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| diff -r 000000000000 -r f0018341e9f6 get_genetree/get_genetree.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_genetree/get_genetree.xml Thu Aug 11 14:29:07 2016 -0400 |
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| @@ -0,0 +1,146 @@ +<tool id="get_genetree" name="Get gene tree by Ensembl ID" version="0.1.1"> + <description>using REST API</description> + <macros> + <xml name="sequence_conditional"> + <conditional name="sequence"> + <param name="sequence_selector" type="select" label="Sequence type" help="The type of sequences to bring back. If 'None', no sequence is returned"> + <option value="protein" selected="true">Protein</option> + <option value="cdna">cDNA</option> + <option value="none">None</option> + </param> + <when value="protein"> + <param name="aligned" type="boolean" truevalue="1" falsevalue="0" label="Return the aligned sequences instead of the original ones" help="The original sequences contain no insertions" /> + <yield /> + </when> + <when value="cdna"> + <param name="aligned" type="boolean" truevalue="1" falsevalue="0" label="Return the aligned sequences instead of the original ones" help="The original sequences contain no insertions" /> + <yield /> + </when> + <when value="none" /> + </conditional> + </xml> + </macros> + <requirements> + <requirement type="package" version="2.7">requests</requirement> + </requirements> + <command> +<![CDATA[ +python $__tool_directory__/get_genetree.py +--id_type $input_type +-i "$input" +-g $species_selector +--format ${output_format.output_format_selector} +#if $output_format.output_format_selector == 'json' + -s ${output_format.sequence.sequence_selector} + #if $output_format.sequence.sequence_selector != 'none' + -a ${output_format.sequence.aligned} + -c ${output_format.sequence.cigar} + #end if +#elif $output_format.output_format_selector == 'phyloxml' + -s ${output_format.sequence.sequence_selector} + #if $output_format.sequence.sequence_selector != 'none' + -a ${output_format.sequence.aligned} + #end if +#else + --nh_format $output_format.nh_format +#end if +> "$output" +]]> + </command> + + <inputs> + <param name="input_type" type="select" label="Input type"> + <option value="gene_id" selected="true">Ensembl gene ID</option> + <option value="gene_tree_id">Ensembl genetree ID</option> + </param> + <param name="input" type="text" label="Ensembl ID"> + <validator type="empty_field" /> + </param> + <param name="species_selector" type="select" label="Select Species"> + <option value="ensembl" selected="true">Vertebrates</option> + <option value="ensemblgenomes">Other species</option> + </param> + <conditional name="output_format"> + <param name="output_format_selector" type="select" label="Output format"> + <option value="json" selected="true">JSON</option> + <!-- <option value="orthoxml">OrthoXML</option> --> + <option value="phyloxml">phyloXML</option> + <option value="nh">Newick</option> + </param> + <when value="json"> + <expand macro="sequence_conditional"> + <param name="cigar" type="boolean" truevalue="1" falsevalue="0" label="Output the sequences also in CIGAR format" /> + </expand> + </when> + <when value="phyloxml"> + <expand macro="sequence_conditional" /> + </when> + <when value="nh"> + <param name="nh_format" type="select" label="NH format" help="The format of a NH (New Hampshire) request"> + <option value="simple" selected="true">simple</option> + <option value="full">full</option> + <option value="display_label_composite">display_label_composite</option> + <option value="species">species</option> + <option value="species_short_name">species_short_name</option> + <option value="ncbi_taxon">ncbi_taxon</option> + <option value="ncbi_name">ncbi_name</option> + <option value="njtree">njtree</option> + <option value="phylip">phylip</option> + </param> + </when> + </conditional> + </inputs> + + <outputs> + <data name="output" format="json" label="$(tool.name) on ${input_type} ${input}"> + <change_format> + <when input="output_format.output_format_selector" value="phyloxml" format="phyloxml" /> + <when input="output_format.output_format_selector" value="nh" format="nhx" /> + </change_format> + </data> + </outputs> + + <tests> + <test> + <param name="input_type" value="gene_id" /> + <param name="input" value="ENSGALP00000027524" /> + <param name="output_format_selector" value="json" /> + <param name="sequence_selector" value="protein" /> + <param name="aligned" value="0" /> + <param name="cigar" value="0" /> + <output name="output" file="genetree.json" ftype="json" /> + </test> + <test> + <param name="input_type" value="gene_tree_id" /> + <param name="input" value="ENSGT00390000003602" /> + <param name="output_format_selector" value="json" /> + <param name="sequence_selector" value="protein" /> + <param name="aligned" value="0" /> + <param name="cigar" value="0" /> + <output name="output" file="genetree.json" fype="json" /> + </test> + <test> + <param name="input_type" value="gene_tree_id" /> + <param name="input" value="ENSGT00390000003602" /> + <param name="output_format_selector" value="phyloxml" /> + <param name="sequence_selector" value="protein" /> + <param name="aligned" value="0" /> + <output name="output" file="genetree.phyloxml" ftype="phyloxml" compare="sim_size" /> + </test> + </tests> + + <help> +<![CDATA[ +**What it does** + +Retrieve a gene tree from Ensembl using its REST API. + +Uses the `"GET genetree/id"`_ and `"GET genetree/member/id"`_ API endpoint. + +.. _"GET genetree/id": http://rest.ensembl.org/documentation/info/genetree +.. _"GET genetree/member/id": http://rest.ensembl.org/documentation/info/genetree_member_id +]]> + </help> + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r f0018341e9f6 get_sequences/get_sequences.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_sequences/get_sequences.py Thu Aug 11 14:29:07 2016 -0400 |
| [ |
| @@ -0,0 +1,46 @@ +# A simple tool to connect to the Ensembl server and retrieve sequences using +# the Ensembl REST API. +import json +import optparse +from itertools import islice +from urlparse import urljoin + +import requests + +parser = optparse.OptionParser() +parser.add_option('-i', '--input', help='List of Ensembl IDs') + +parser.add_option('-s', '--species', type='choice', + choices=['ensembl', 'ensemblgenomes'], default='ensembl', + help='Specify the genome databases for vertebrates and other eukaryotic species') + +parser.add_option('-t', '--type', type='choice', + choices=['genomic', 'cds', 'cdna', 'protein'], + default='genomic', help='Type of sequence') +parser.add_option('--expand_3prime', type='int', default=0, + help='Expand the sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type') +parser.add_option('--expand_5prime', type='int', default=0, + help='Expand the sequence upstream of the sequence by this many basepairs. Only available when using genomic sequence type') +options, args = parser.parse_args() +if options.input is None: + raise Exception('-i option must be specified') + +server = 'http://rest.%s.org' % options.species +ext = 'sequence/id' + +headers = {'Content-Type': 'text/x-fasta', 'Accept': 'text/x-fasta'} +params = dict((k, getattr(options, k)) for k in ['type', 'expand_3prime', 'expand_5prime']) +with open(options.input) as f: + # Need to split the file in chunks of 50 lines because of the limit imposed by Ensembl + while True: + ids = [line.strip() for line in islice(f, 50)] + if not ids: + break + data = {'ids': ids} + r = requests.post(urljoin(server, ext), params=params, headers=headers, + data=json.dumps(data)) + + if not r.ok: + r.raise_for_status() + + print r.text |
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| diff -r 000000000000 -r f0018341e9f6 test-data/genetree.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genetree.json Thu Aug 11 14:29:07 2016 -0400 |
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| b'@@ -0,0 +1,1 @@\n+{"tree":{"events":{"type":"speciation"},"branch_length":0,"children":[{"events":{"type":"speciation"},"branch_length":0.153275,"children":[{"events":{"type":"speciation"},"branch_length":0.155187,"children":[{"events":{"type":"speciation"},"branch_length":0.133192,"children":[{"events":{"type":"speciation"},"branch_length":0.201095,"children":[{"events":{"type":"speciation"},"branch_length":0.015782,"children":[{"events":{"type":"speciation"},"branch_length":0.217419,"children":[{"sequence":{"mol_seq":{"seq":"QLARDMQDMRIRKKKRQTIRPLPGSLFQKKSSGVARIPFKAAVNGKPPARYTAKPLCGLGVPLNVLEITSETAESFRFSLQHFVKLESLIDKGGIQLADGGWLIPTNDGTAGKEEFYRALCDTPGVDPKLMSEEWVYNHYRWIVWKQASMERSFPEEMGSLCLTPEQVLLQLKYRYDIEVDHSRRPALRKIMEKDDTAAKTLVLCVCGVVFRGSSPKNKSFGDISTPGADPKVENPCAVVWLTDGWYSIKAQLDGPLTSMLHRGRLPVGGKLIIHGAQLVGSENACSPLEAPVSLMLKICANSSRPARWDSKLGFHRDPRPFLLPVSSLYSSGGPVGCVDIIILRSYPILWMERKPEGGTVFRSGRAEEKEARRYNIHKEKAMEILFDKIKAEFEKEEKGNRKPQCRRTINGQNITSLQDGEELYEAVGDDPAFLEAHLTEKQVEVLQNYKRLVMEKQQAELQDRYRRAVESAEDGVGGCPKRDVAPVWRLCIADSMGHSGRVYQLSLWRPPSELQALLKEGCRYKVYNLTTLDSKKQGGNATVQLTATKKTQFEHLQGSEEWLSKHFQPRVATNFVRLQDPEFNPLCSEVDLTGYVITIIDGQGFSPAFYLADGKQNFVKVRCFSSFAQSGLEDVIKPRVLLALSNLQLRGQSTSPTPVVYAGDLTVFSTNPKEVHLQESFSQLKTLVQGQENFFVHAEEKLSQLMSDGLSAIASPAGQIQTPASTVKRRGDMTDVSSNIMVINKTSKVTCQQPGRSHRFSTPINRNSTAHSSAERNPSTIKKRKALDYLSHIPSPPPLSCLSTLSSPSVKKIFIPPRRTEIPGTLKTVKTPNQKPSNTPVDDQWVNDEELAMIDTQAL","is_aligned":0},"location":"scaffold_19:196046-199577","name":"brca2-201","id":[{"source":"EnsEMBL","accession":"ENSTRUP00000015030"}]},"branch_length":0.072273,"id":{"source":"EnsEMBL","accession":"ENSTRUG00000006177"},"confidence":{},"taxonomy":{"scientific_name":"Takifugu rubripes","id":31033}},{"sequence":{"mol_seq":{"seq":"VSFSSDTPRKPKAGSLSSEFTDRFLAQEALDCTKALLEDERLVDDPHMTGECLHRCPQFSLLVNLFVKPHTAVLIPEQPPLKRRLLEEFDRTDGSSRGSALNPEKCSPNGIMGDRRVFKCSVSFQPNITTPHRICSQKAERPVSFLSRRSGTNYVETSLPNTTPTKVSALRDSNEARLQKSNFIPPFIKNVKLDTPNSKTASTFVPPFKKSRNSSKTEEEEPKHHFIPPFTNPCATSSTKKHTAGHLHNVELARDMQGMRIRKKKRQTILPLPGSLFLKKSSGVTRIPLKSAVNGKPPARYTPKQLYGLGVPLNVLEITSETAGSFRFSLQQFVKLESLTDKGGIQLADGGWLIPRNDGTAGKEEFYRALCDTTGVDPKLISEEWVYNHYRWIVWKQASMERSFPEQLGSLCLTPEQVLLQLKYRYDIEVDQSRRPALRKIMERDDTAAKTLILCVCGVVSRGSSPQKQGLGGVAAPSSDPQVENPFAVVWLTDGWYSIKAQLDGPLTSMLNRGRLPVGGKLIIHGAQLVGSQDACSPLEAPESIMLKIFANSSRRARWDAKLGFYRDPRPFLLPVSSLYNSGGPVGCVDIIILRSYPTLWMERKPEGGTVFRSGRAEEKEARRYNVHKEKAMEILFDKIQAEFEKEERDNRKPRSRRRTIGDQDIKSLQDGEELYEAVGDDPAYLEAHLTEQQAETLQNYKRLLIEKKQAELQDRYRRAVETAEDGTGSCPKRDVAPVWRLSIADFMEKPGSVYQLNIWRPPSELQSLLKEGCRYKVYNLTTTDSKKQGGNTTVQLSGTKKTQFEDLQASEELLSTYFQPRVSATFIDLQDPEFHSLCGEVDLTGYVISIIDGQGFSPAFYLTDGKQNFVKVRCFSSFAQSGLEDVIKPSVLLALSNLQLRGQATSPTPVLYAGDLTVFSTNPKEVHLQESFSQLKTLVQ","is_aligned":0},"location":"16:4700614-4705074","name":"brca2-201","id":[{"source":"EnsEMBL","accession":"ENSTNIP00000002435"}]},"branch_length":0.113355,"id":{"source":"EnsEMBL","accession":"ENSTNIG00000016261"},"confidence":{},"taxonomy":{"scientific_name":"Tetraodon nigroviridis","id":99883}}],"confidence":{"bootstrap":100},"taxonomy":{"scientific_name":"Tetraodontidae","id":31031}},{"sequence":{"mol_seq":{"seq":"LPNVELAQDMQDMRIRKKKRQTIRPLPGSLFLTKTSGVTRIPLKAALVFLLQLYRHGVHQHVCEISSETAESFRFNLKQFIKREALLDGGGVQLADGGWLIPSKDGTAGKEEFYRALCDTPGVDPKLISDGWVDNHYRWVVWKQASMERSFPETMGGLCLTPEQVLLQLKYRYDVEVDHSRRPALRRITERDDTAAKTLVLCVCGVVSRSFDDSKTPRGADAGGGNPSAVVWLTDGWYAIRAQLDEPLTAMLRNGRVAVGSKLIVHGAQLVGSQEACSPLEAPEALMLKICANSSRPVRWDAKLGFHKDPRPFLLPLSCLYSSGGQVGCVDMIVLRSYPIQWMERKPEGGVVFRSVRAEEKEAKRFNGLKQKAMEILFAKIQDEFEKEDKGRTCDFTTQAISRQAIAGLQAGEELCEAVGEDPAHLEALLSEQQVETLNTYRRCVMEKKQAQLHDRFQRALESAEASEGSCPKREVTPVWRLGVADSRDQRGRVYQLNLWRPSSDLQALLKEGRRYKVYNLTTSDGKKHNGSSNVQLTGTKKTQFQDLQASREWLSTRFQPRVSACFVDLQNPEFQSLCGEVDLTGFVIQIVDGQGFSPAFYLADGELNFVKVRCFSSFAQSGLEDLVKPRVLLSLSNLQLRGQSASPTPVVYAGDLTVFSANPKDAHLQESLSQNKNLRQSQENFFLIAEETLSRLVQSDGRRPLSSPALHTRTPALATSMIQDTTASVKCVLLMQGASQQLVRSRGTFTPVSRKPPAANCSTEKDAGSVKRRRALNYLSHIPSPPPLLNLGSVASPCVNKTFNPPRRSGTPSTLKTVQTPAHKAQKVDSLVEDEWVNDEELAMIDTQAL","is_aligned":0},"location":"groupI:13362884-13366744","name'..b'LQLDCLKCESTDVKHTPQKETINDNSKCNESSLSELSMKGFQTASGRNIMMSESSIQKARNIFAEEHEDSFTLRCNIQNTIQIPQPVNEPTQFPYVNLGPKPTTTSGWQEKNILRRSTEKGFMPGFCTAGGKKVSVSDNSLAKAHKLFQEECTFSKEGKLDEVKQNKLMNSEPLSLLTCESVLKQSDGFIEDISTSRNALEIRPELYPEGMCSNRASNGSGNNSEFTAGEGISININQSSLLTTGNVLKNLPSESSGHDVYSVTEHLSTVVKVKRYNDSGHFVNQNLAECNDNHVLSTQKNTANISNRNEDCTSLAPLSFSTASGKSVTVSHDSLQKARLMLSEAANDVTVDTSKQEAAYITPAIRKTEAEKEQNTVDDSDRVNANTFSFSTASGKKVNISGNSLKQVRAVCLSSDPKETSAALFNVEKSVFNEDVKDVSLLQPNVTMPKAVSFSTASGKTVQLSDESLKKARVIFSEIDTCPLMQQQTNESTVEEIVIGGGMTKSKQMPLTTEKVETTRKNNGTFGFNTASGKQVSVSESALQKVKDIFQEFDDPDNYEQNKSLVRLPVSSKIKESTPGTKRLVQTAGSSYKNDNLQCKAGNLRTFQDKQAGKKSLTYSEAAISPIESSVPIYEMQVMLKHTNNQACKYQPRVEVPLQDQRWQNILEIELPATCAPAFRETHNILFFGDLQHSTHFDICSLYSGKNPAVKHQLASHSKMQTLVISGRDSSGTLTLQFTLRIVILHTVNNQYSLNKQLFTFSSALRQVTCIPTQAHLHSKVKIFHQSLPIKSPDVASDSTSKSYSPTAAKETINCSSASKIPAKKFVPPFKKTVATLADNQSNSVQNGSSDGLIESIVYPKEDKVETICSSKDQFDDSDILQMTSNLRCSKDLQEMRIRKKLRQKIKPHPGSLYRLKMSHVKRISLQSAVAERCPTLYSREQLYRYGIVKNHIGVSSENALSFQFHCSNYFTKELLLSGNGVQLADGGWLIPTEQGNAGKEEIYRAFCDTPGVDPKLISAEWVHNHYRWIVWKLAAMEVRFPKTFACRCLTPERVLLQLKYRYDVEIDKSQRSAIKKIMERDDSPAKTLVLCIAKIISQGTRLPNACSNKTEPADSKESSAVIEVTDSWYGIKVLLDPCLTALLHKGRLFIGQKLIVHGAELIGSDDACSPLEAPESLMLKIAANSTRPVRWHTKLGYFKDPRPFCLHLSSLLSEGGVVGCVDVVIQRIYPMQWMEKMANGLYVFRNDRAEEREAEKHSANQQKKLEMLFSKIQAEFEQREVTCNRRKGLRRRSLNAQQMQTLQDGAEIYEAIQNESDPGYLESYLSAEQLKALNHHRQLLNDKKQALIQAEFRKAIECSEQDANGCTRRDVTPVWKLRIADYRNYETDAAYILNIWRPLPDVLSLLKEGCRYKMYHLAASTSKGKSLAADLQLTATKKTRFQQLQLSESILEQIYSPREVTDFSRFQEPLFSAPYAEVDLVGLIISIYKKTGAAPVVYISDESHNIVALKFWTDLGQLGLEEITKPRTYISASNLRWRSDCIEGIPTLYVGDLANISSNPKESHLQRAIQKLKLSVQNVQDFWNSSQTALMKTLQINSTDTTECSKNPTTPTWKSDVSARSGYLTPLHHSGKRLLNSVHTSDPQTENPGCSKEIQLKTCKKRKALDFLNRIPSPPPVTPVRPFVSPSLQKAFRPPRSCSVQKLGPETKGNTENVQGTTPECTKDLAKLEGEFVADEELAMINTQALLLGLEEEKKKTEQKTSRTAGKMTAHESPIENASPVPAQEQQTEEALNIPVGNSEKSYLCLRKRKRK","is_aligned":0},"location":"GL172716.1:1071058-1096238","name":"brca2-201","id":[{"source":"EnsEMBL","accession":"ENSXETP00000060681"}]},"branch_length":0.774548,"id":{"source":"EnsEMBL","accession":"ENSXETG00000017011"},"confidence":{},"taxonomy":{"scientific_name":"Xenopus tropicalis","id":8364}}],"confidence":{"bootstrap":1},"taxonomy":{"scientific_name":"Tetrapoda","id":32523}},{"sequence":{"mol_seq":{"seq":"MEWEAVESVKALMRDDELTDAGLDASKDSLNRACRRQSGGNFRARKRMRLEQVSADEPPVKRQLLAEFDRTVENGHKSLQKPLICTPNGTLKDRRKFMYSVPLKPVVCGPWSNNSKTGQQVTKPSITLPGRGVETFQPKNHIAPSPVYDPPSNRRGPVFAPPFHGATFRGLQKPSASHTSSKTAKTFVPPFKMKASASHTVHFSSKVINTCEKILENLVYLKPSLASCNIFQSLEEMTANLQCARDLQEMRLRKKQRQNIRPQPGSLYLAKTSGVARVSLKAATGNQCPSSYSTEQLYVHGVGKSTLKVRSENAESFQFSCSDYFGKDVLLAGNGLKLADGGWLIPSDKGMVGKEEFYRALCDTPGVAPKLISESWVYNHYRWIVWKLAAMEAAFPKEFGNRCLTPERVLLQLKYRYDIEVDKCRRSTVKKIMERDDTAAKTLVLCISKLISVEDRFKQTKNKNEKGAEEARKEAVAGVIETTDGWYGIKVLLDPPLTVLVQRGRLSVGCKIITHGAEIIGSQDACTPLEAPECLMLKISANSTRPACWSAKLGFHRDPRPFPLPLASLFNDGGLVGCVDVVVVRLYPIQWMEKKSDGIFVFRNDRAEEREAQRQVENQQRKMESLFAKIQTEFEQKYEAKSKRRGQKAQKFSKQEIQALQDGAELNEAIENSMDPGYFEACLREEQLKVLHGHRQMLNEKKQAEFQAEFKKALESAEQEGKSCCKRGVTPVWKLRIVDYRKPSAAEYILNIWRPLADLHSLLKEGNRYRIYQLLASQSKGRTTTADIQLTATKKTQYQQFQSFPELISELYSPRKAVKFNMLMDPTFRPAYAEVDLVGYTISIEGKPGVAPVVYLSDESHNFVAIKVWTALNQLAVEDIVKPFSLIAASNLQWRSDSRSIIPMLYAGDLSIFSSNPKEGHLQEAFNQRRTAIQENISGTYLPPEKKNLHQESYKSCQYNTLNVLMNGNIHTQSPVLSRVHMGTSCAFLFLLPSPYPESKHTSPLITMKAGVKSMTFPGSAKLMPQASENQELDTPKNRKKKAALDYLCRIPSPPALTPIRSFVSSSLQKAFHPPRSCVKLQSGENPVVPTVGNNAVLGIQSKKDEGPAAFNEEDSVADEELAMINTQAFLVGLRRDKRPSLLDKTASLKGHVPSERFLEEKLLSVLKEQASSNSERNATSLENKSCDKSRTCVKPCEHSNDSIAEETSEIIPGCHGGESAVENQSKNSSLCHKKLQQKKRRKYY","is_aligned":0},"location":"JH127744.1:299190-332700","name":"BRCA2-201","id":[{"source":"EnsEMBL","accession":"ENSLACP00000008815"}]},"branch_length":0.318609,"id":{"source":"EnsEMBL","accession":"ENSLACG00000007788"},"confidence":{},"taxonomy":{"scientific_name":"Latimeria chalumnae","id":7897}}],"confidence":{"bootstrap":1},"taxonomy":{"scientific_name":"Sarcopterygii","id":8287}}],"confidence":{},"taxonomy":{"scientific_name":"Euteleostomi","id":117571}},"rooted":1,"id":"ENSGT00390000003602","type":"gene tree"}\n' |
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| diff -r 000000000000 -r f0018341e9f6 test-data/genetree.phyloxml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genetree.phyloxml Thu Aug 11 14:29:07 2016 -0400 |
| b |
| b'@@ -0,0 +1,1347 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+\n+<phyloxml xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.phyloxml.org">\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+ </taxonomy>\n+ <clade branch_length="0.153275">\n+ <confidence type="bootstrap">95</confidence>\n+ <taxonomy>\n+ <id>41665</id>\n+ <scientific_name>Neopterygii</scientific_name>\n+ </taxonomy>\n+ <clade branch_length="0.155187">\n+ <confidence type="bootstrap">19</confidence>\n+ <taxonomy>\n+ <id>186625</id>\n+ <scientific_name>Clupeocephala</scientific_name>\n+ </taxonomy>\n+ <clade branch_length="0.133192">\n+ <confidence type="bootstrap">18</confidence>\n+ <taxonomy>\n+ <id>123368</id>\n+ <scientific_name>Acanthomorphata</scientific_name>\n+ </taxonomy>\n+ <clade branch_length="0.374304">\n+ <name>ENSGMOG00000009699</name>\n+ <taxonomy>\n+ <id>8049</id>\n+ <scientific_name>Gadus morhua</scientific_name>\n+ </taxonomy>\n+ <sequence>\n+ <accession source="Ensembl">ENSGMOP00000010385</accession>\n+ <name>brca2-201</name>\n+ <location>GeneScaffold_2233:16156-29802</location>\n+ <mol_seq is_aligned="0">LARDLQDMRLRKKKRQTVRPLPGSLFLAKASGGARIPLRAALRQLYQHGVHQPVWTVTAENAESFRLSFRRFFRWGSSVSRGVQLADGGWLVPRDDWTLGKEEFYRALCDSPGVDVKLLSQEWAYNHYRWVVWKLASMERSFPLTMASLWLNPEQILLQLKYRYDVEVDHSRRPALRKITERDDAAAKTLVLCVCGVVPGADQQPQGSHAPPPGVVWLTDGWYAIKAQLDAPLTAMLRRGGAGGKLVVYGAELVGSQDGCSPLEAPEGLMLKIGANSCRRARWDAKLGFQRDPRPFLLRLSSLFSTGGAVGCVDLLILRSYPVLWMEKKQDGVFVFRSGRAEEREARRFDDHNNKTMEALYAKIQADIQREDKGSARERNSGEELYEAFENDPAYLEACLNDQQLEVLQSYRRSVLEKRQAGLQERCRRALEQAQESQGGCPRRDVTPVWKLCVVDARAPPGYMLNVWRPPADLQAQLKEGARYRVYNLSVTAGKKRNPGASVQLTATSKTHFQEVQVGQDWLSDHFQARQAVHFQELQRPEVQSACGEVDLVGYVVTTADTHGTSPVVYLVDGDLNLVKVRCFSSLLQWGLEELVKPATLLALSNLQLSARRATTLPVLYASDLTAFSSNPREAHLQSSHSNADRXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXRRRALDYLSRMPSPPPLGPLGSLASPACVKKTFNPPRRSTTPAAVATTRQTPAHGPRVGPWQEEEWENDEGLAQIDTQVL</mol_seq>\n+ </sequence>\n+ <property datatype="xsd:string" ref="Compara:genome_db_name" applies_to="clade">gadus_morhua</property>\n+ </clade>\n+ <clade branch_length="0.201095">\n+ <taxonomy>\n+ <id>1489872</id>\n+ <scientific_name>Percomorphaceae</scientific_name>\n+ </taxonomy>\n+ <clade branch_length="0.015782">\n+ <confidence type="bootstrap">38</confidence>\n+ <taxonomy>\n+ <id>1489922</id>\n+ <scientific_name>Eupercaria</scientific_name>\n+ </taxonomy>\n+ <clade branch_length="0.159219">\n+ <name>ENSGACG00000011490</name>\n+ <taxonomy>\n+ <id>69293</id>\n+ <scientific_name>Gasterosteus aculeatus</scientific_name>\n+ </taxonomy>\n+ <sequence>\n+ <accession source="Ensembl">ENSGACP00000015199</accession>\n+ <name>brca2-201</name>\n+ <location>groupI:13362884-13366744</location>\n+ <mol_seq is_aligned="0">LPNVELAQDMQDMRIRKKKRQTIRPLPGSLFLTKTSGVTRIPLKAALVFLLQLYRHGVHQHVCEISSETAESFRFNLKQFIKREALLDGGGVQLADGGWLIPSKDGTAGKEEFYRALCDTPGVDPKLISDGWVDNHYRWVVWKQASMERSFPETMGGLCLTPEQVLLQLKYRYDVEVDHSRRPALRRITERDDTAAKTLVLCVCGVVSRSFDDSKTPRGADAGGGNPSAVVWLTDGWYAIRAQLDEPLTAMLRNGRVAVGSKLIVHGAQLVGSQEACSPLEAPEALMLKICANSSRPVRWDAKLGFHKDPRPFLLPLSCLYSSGGQVGCVDMIVLRSYPIQWMERKPEGGVVFRSVRAEEKEAKRFNGLKQKAMEILFAKIQDEFEKEDKGRTCDFT'..b'name>ENSXETG00000017011</name>\n+ <taxonomy>\n+ <id>8364</id>\n+ <scientific_name>Xenopus tropicalis</scientific_name>\n+ </taxonomy>\n+ <sequence>\n+ <accession source="Ensembl">ENSXETP00000060681</accession>\n+ <name>brca2-201</name>\n+ <location>GL172716.1:1071058-1096238</location>\n+ <mol_seq is_aligned="0">MAAPQLGKSVFYDLFSTHCSHSDLGPISLNWFEELTAEALPYKSRTCEDHECSLDDLHENNIKTPKLKSSIYSQLDSTPVIFKERLLSPLFASSLTELDKRQNATDNGNNVRLEKSNCTQMQHQASEVFSPSSRCLNESPAVIKEIFKTPLRNKYLHKTPQCDWKPDICSSLFCTPKLMKNQTGCIKESLGAEVDPEMSWSSSLATPPSPTVIIAHANDQPSGNKHAAIVQSLFPNCENMEANNLPPPETGTQNEDRQICAGLEKPGSCSASKTVPEASAISSRAAWKKTVANTVKDEEVSRTVENALEGMEDVLSIFFASEKTPGLRKLKNSTQARRKVESIKSQKCQVSLFKAEEGESILVPLDEHHKCDHEMLMKPEQDYKMNAVNQKIAKETTPYEWSQLNICELDITQSQDSTLHAANLCCEDITVNKSDTCNITEAEKQEEVNEPSTDNVLSNKVGKESTLNVNCINADLNNMASSSNNSVHSLNLSQCEKMDSSEISNSEVGCITKLTTHPAKITTGELSSVDDCAKKPQERVTISTSFSTLKKQSKFMYSVNTVLTGHIASNTSIATRRSLNSHLSSDEPKPHIKENQNEPESNAKYYSNGLQKPVFLEKENDNKGISLCKTISDGQNTSEGARAPDYFEERVPETKDRCKATLSIREKVVATANCFARKQLETDYPEDASAQHEALQFHAKQYVSCSMLNSNVSNDMQIKPQVLTQACDFRSSAENLVEKTKNQLRRNEDQSFSSTGIGKKPASGEKLVGDCNEGSFLHVKQEISAAQALVGNGYETRDTPDVTSDHTRSVISNHGKSLWEEETALTELPVPEILSKTFKGFKTASNKKIHISDKNIVKGCDLFKEIEFGIGDAKPCNEENKEPLKKTPFDVPGYETNLKGFKTASNKEINVSENKFAKGRLLFKDIEEESGQTTAIMAKDNELFIKPASSNKPDIFKSTCIKGMNPSENLDSMPPKKGDVQQSAGLKHSDQIDVFGFDDPPAKGNVQTLGYFNMSASETDFKGFKTASNKDIIISESTLAKGKLIFEDIEDTRYSETGRTIDCKAKGGALSTSNLVMHNTMCKNEPSTSENTNDKAPKRAKVQTPMAENSHLKEPSSDKNAMDAANHQMTLKASAYSPKAASSALPRYKKKPISTTKTSFQLNEHLTESQQAEISELSSILENADSQFDFTQFRKVPSVTEKQNSTEGGSESQNLNNSDVWKDVDFNDSFAAGRDHSEGMEAIPSSPGIKELPSAGECCSKETHDSMPDFVTLAPKQGFLVKQNERLFAGFNLASGKQVNIDNDVLKKAAELFNDIDNDKELLSHAKEESRKSNIKHSSKLINNENCGKTEHTSEHLVCQSNVSLPFIKTLGKNATILVSGNEKSQNQELQLDCLKCESTDVKHTPQKETINDNSKCNESSLSELSMKGFQTASGRNIMMSESSIQKARNIFAEEHEDSFTLRCNIQNTIQIPQPVNEPTQFPYVNLGPKPTTTSGWQEKNILRRSTEKGFMPGFCTAGGKKVSVSDNSLAKAHKLFQEECTFSKEGKLDEVKQNKLMNSEPLSLLTCESVLKQSDGFIEDISTSRNALEIRPELYPEGMCSNRASNGSGNNSEFTAGEGISININQSSLLTTGNVLKNLPSESSGHDVYSVTEHLSTVVKVKRYNDSGHFVNQNLAECNDNHVLSTQKNTANISNRNEDCTSLAPLSFSTASGKSVTVSHDSLQKARLMLSEAANDVTVDTSKQEAAYITPAIRKTEAEKEQNTVDDSDRVNANTFSFSTASGKKVNISGNSLKQVRAVCLSSDPKETSAALFNVEKSVFNEDVKDVSLLQPNVTMPKAVSFSTASGKTVQLSDESLKKARVIFSEIDTCPLMQQQTNESTVEEIVIGGGMTKSKQMPLTTEKVETTRKNNGTFGFNTASGKQVSVSESALQKVKDIFQEFDDPDNYEQNKSLVRLPVSSKIKESTPGTKRLVQTAGSSYKNDNLQCKAGNLRTFQDKQAGKKSLTYSEAAISPIESSVPIYEMQVMLKHTNNQACKYQPRVEVPLQDQRWQNILEIELPATCAPAFRETHNILFFGDLQHSTHFDICSLYSGKNPAVKHQLASHSKMQTLVISGRDSSGTLTLQFTLRIVILHTVNNQYSLNKQLFTFSSALRQVTCIPTQAHLHSKVKIFHQSLPIKSPDVASDSTSKSYSPTAAKETINCSSASKIPAKKFVPPFKKTVATLADNQSNSVQNGSSDGLIESIVYPKEDKVETICSSKDQFDDSDILQMTSNLRCSKDLQEMRIRKKLRQKIKPHPGSLYRLKMSHVKRISLQSAVAERCPTLYSREQLYRYGIVKNHIGVSSENALSFQFHCSNYFTKELLLSGNGVQLADGGWLIPTEQGNAGKEEIYRAFCDTPGVDPKLISAEWVHNHYRWIVWKLAAMEVRFPKTFACRCLTPERVLLQLKYRYDVEIDKSQRSAIKKIMERDDSPAKTLVLCIAKIISQGTRLPNACSNKTEPADSKESSAVIEVTDSWYGIKVLLDPCLTALLHKGRLFIGQKLIVHGAELIGSDDACSPLEAPESLMLKIAANSTRPVRWHTKLGYFKDPRPFCLHLSSLLSEGGVVGCVDVVIQRIYPMQWMEKMANGLYVFRNDRAEEREAEKHSANQQKKLEMLFSKIQAEFEQREVTCNRRKGLRRRSLNAQQMQTLQDGAEIYEAIQNESDPGYLESYLSAEQLKALNHHRQLLNDKKQALIQAEFRKAIECSEQDANGCTRRDVTPVWKLRIADYRNYETDAAYILNIWRPLPDVLSLLKEGCRYKMYHLAASTSKGKSLAADLQLTATKKTRFQQLQLSESILEQIYSPREVTDFSRFQEPLFSAPYAEVDLVGLIISIYKKTGAAPVVYISDESHNIVALKFWTDLGQLGLEEITKPRTYISASNLRWRSDCIEGIPTLYVGDLANISSNPKESHLQRAIQKLKLSVQNVQDFWNSSQTALMKTLQINSTDTTECSKNPTTPTWKSDVSARSGYLTPLHHSGKRLLNSVHTSDPQTENPGCSKEIQLKTCKKRKALDFLNRIPSPPPVTPVRPFVSPSLQKAFRPPRSCSVQKLGPETKGNTENVQGTTPECTKDLAKLEGEFVADEELAMINTQALLLGLEEEKKKTEQKTSRTAGKMTAHESPIENASPVPAQEQQTEEALNIPVGNSEKSYLCLRKRKRK</mol_seq>\n+ </sequence>\n+ <property datatype="xsd:string" ref="Compara:genome_db_name" applies_to="clade">xenopus_tropicalis</property>\n+ </clade>\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+</phyloxml>\n' |
| b |
| diff -r 000000000000 -r f0018341e9f6 test-data/input.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.txt Thu Aug 11 14:29:07 2016 -0400 |
| b |
| @@ -0,0 +1,2 @@ +ENSG00000157764 +ENSG00000248378 |
| b |
| diff -r 000000000000 -r f0018341e9f6 test-data/out.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.json Thu Aug 11 14:29:07 2016 -0400 |
| [ |
| @@ -0,0 +1,1 @@ +{"ENSG00000157764":{"source":"ensembl_havana","object_type":"Gene","logic_name":"ensembl_havana_gene","version":12,"species":"homo_sapiens","description":"B-Raf proto-oncogene, serine/threonine kinase [Source:HGNC Symbol;Acc:HGNC:1097]","display_name":"BRAF","assembly_name":"GRCh38","biotype":"protein_coding","end":140924764,"seq_region_name":"7","db_type":"core","strand":-1,"id":"ENSG00000157764","start":140719327},"ENSG00000248378":{"source":"havana","object_type":"Gene","logic_name":"havana","version":1,"species":"homo_sapiens","display_name":"RP11-5N11.5","assembly_name":"GRCh38","biotype":"lincRNA","end":31744451,"seq_region_name":"5","db_type":"core","strand":-1,"id":"ENSG00000248378","start":31743988}} |
| b |
| diff -r 000000000000 -r f0018341e9f6 test-data/sequences.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sequences.fasta Thu Aug 11 14:29:07 2016 -0400 |
| b |
| b'@@ -0,0 +1,3435 @@\n+>ENSG00000157764 chromosome:GRCh38:7:140719327:140924764:-1\n+CGCCTCCCTTCCCCCTCCCCGCCCGACAGCGGCCGCTCGGGCCCCGGCTCTCGGTTATAA\n+GATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAA\n+CGGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGA\n+CCCTGCCATTCCGGAGGAGGTGAGTGCTGGCGCCACCCTGCCGCCCTCCCGACTCCGGGC\n+TCGGCGGCTGGCTGGTGTTTATTTTGGAAAGAGGCGGCGGTGGGGGCTTGATGCCCTCAG\n+CCACCTTCTCGGGCCAGCTCCGCGGGCTGGGAGGTGGGCATCGCCCCCGTGTCCCTCTCC\n+GTCATGCAGCGCCTTCCTACGTAAACACACACAATGGCCCGGGGGGTTTCCCTGGCCCCC\n+ACCCCAGATGTGGGGATTGGGGCAGCGGTGGTTGAGCGGGAGGCTATCAATAGGGGGCGA\n+AACTCAGGGTTGGTCCGAGAAGGTCACGATTGGCTGAAGTATCCAGCTCTGCATCTCTGT\n+GGGGTGGGGGCGGCGGCGGCCTCGACGTGGAGGATATAGGTTAGTTGCTGGGGCTGAGAC\n+AACAGCCCGAGTTACTGTCGCGTGTAATTCTTACATGGTCGTGGGGATGATGGGGCTCAT\n+CATTTCCTCTCTCCTCTCCCGGACTGCCCCCCTTCTCAGTCCGCTGCCCTTTTTCACTTT\n+TCTATTTGGGGATTTCTCTTCACCTGTTTTACCCAGCAAATTATTTTGATTTAGTCTTTA\n+CTTTTTCAATCCTAAATCGCAGTTTCCGATGCCTTTTCTGGTCTCTGGTCCTCTGTTCCT\n+AATGTTTGTCAGCGCTCTGTCGCTGATTGGTAACCCCCATTCTATTCCCATCTACCGCCC\n+GCTCATTTTCCAGTTGTCGGACCTGCCTGCCTTCTAACCCCAGCTCCCACTTAAGAGCAT\n+TTTTGCACTTCTCTTACCCTGGTCCTCTTGAGGCTCTGTACTTGATCTCACCACTCCCTA\n+ACATTGTTGTCTGTTGTTATCTTCACAAATCCTCCTGGACACTTTGGAGCTACTTGTTTT\n+CTGAGCCCAGAAGCTGTCAAGATTCCATCAGGTTTCACTTGGCTCTTTTCGCGCTTGCAC\n+TACTGGCACTTTTTGGCTAGTCGTCCATTGTGCATTCACACCTCTTTATTCCTACCCATT\n+TTTATAGGTCTGATTGATTTCTTAGTGTTGTCCTCCTTTTTGTCCTATTTTTTTCCTTTT\n+CCTTTTTCCTCTCCAGTCCTTGCTTCTCTCAGCCTGTTTTTGCATTAGTCAGCCTCTTAG\n+CACTGTGTCAAATTATTTACGTTTTTTTATTACATAAAATTTATTACAAATATTTGGTAT\n+TTTATTACAGAAAATAATACTTTATTATGCTTTACAAATAAGATATGGTATAATAATTGT\n+GGTTTACAGTTATTGATTAGGTAATGTGACTTACTCTGTTGACTTTGCTCGAAGTTCTCT\n+TTGCTACTTACTATTAACATCTAATTTCTCAATTCTCATAACATCTCATTCTCTCTGCAA\n+TTTTTTTTTTGCATCATCATCTTTGGAAATTCATCCAATATGCTTGCTTTATTCAGCATC\n+AGCTTGTTTATGATAATGTTTGTTTTCTACTCTTTATATCATCTTTGTTACATGCCCAAA\n+ATGTGTTCTGTACCATCATTTGATCTGTTCTAAAATTTCTCATTTTTAAGTTTCTTAAAA\n+TCATTCCACTTTTCAGTATGCATTTTTGCTTAGATCAGTTTCCTCTCATATCTGTTCCTT\n+TCCCCCAGCTTCTTGATTTCTAAGGAGAAAGCTCTTCTCTACTTCAATTTCCTAGTTTAT\n+TCTGTTTCCCTTGTTTCCAGTTACCATTCATTTTGCCTTGTTTCCTGGCTTTTGGTACTT\n+AACTTTCTGAAGCTTCCTCTTTTCTTCTCCACACCTCCACGTTCCTTCTTATTTATAAAC\n+ATCTTTGTTTCCTTTGACATGGAAATTTATTTTTAGGATACATTGTTTTTAATGGATAAA\n+TACTAGGGGTCACATCTGCTGTCTGTTTTCTCCAGGAATCGGATATGCCTTTGTCTTAAC\n+CAGGCACAGGTGCCTCTGGATTTTATTTTACTCTGTAATAGATGTGTAGTTTTGTTGAAT\n+TGTATCTTGTTTGAAGACTACTACAGAGTGGAACAATGAGTGAAGTAATAAGTAGGGGTT\n+ATGAAATTGTAATTCTCTGATTATAAAATTGTTTATCTTGGGAACTTTGCTGCAGAGTTA\n+TTAGAACCGTTTGCAATTCTGTAAAGAAGGCTTTTGTGAAGTAAAATCTCTACCCTTCTA\n+TTTTATTTGAAAGGGCCAGATTGTTTGGAACTGTACCCCCTGAAGAGTCTGATTTAGTAA\n+GTGAGAGCGAGGGCCATGGATTTCTGTATTTGGCACATGTCTTGAGCAGTTCCCATGTAC\n+CAATCCTTGAGAACCTCTAGGCTAGCTGAATTTAAGTATAAATTGCCAGTAATTGGAAAG\n+CATATTCATATCTTCTGAAACTATAAGGATACTCTCATTTTACTTGGTTAAAAAACAAGT\n+GTTTCCTACTGTCCTCTTTACCCAGGTTTTAATGTTTAGTGGTGAACAGTAGTTTTCCCT\n+CTACATTTTTTTCTGAACTGATAATAAATGTATTTGGCTGGGAGGGTGACATTGATTAAA\n+AAATGTATCTCTTGAATGTAAATATCAGTATTACAGATGATAAAATAAATTCCTCCAAGA\n+AATAATTTTAAATTTGAAGTTGATATTCAGTGGAAACTGAAATGTGCTGTGGTCTTTTAT\n+TTGAAGTCTTCCTTACATTCACTTAAAGGGATCTTTTACTGCAAATTACATGGAAAGAAT\n+GAAAAGGTTTGCTTGTGTGTAATGACACATTTTATTCTGAAGATTTATTTTACCTAACAG\n+TAAAATGTAGGTTTTTTTTTTTTAAATAAAAGTTTCCCAGAGGGAAATTTCATCTAAAAA\n+AAAAGTCTGATTTCAAAGGGAAAGCAAGTCATTATCAAAAATTAGAAAACTATAAGTACA\n+AAAAGTAAAAAATCATCAGTAATTTTGCCACTAAGATATTATTACTATAGACATTTTGGT\n+GTATTCCATCTGTTCTTTTTTAATGCTTTTATAACACTATGTAGTTTTGTATTTTAAAAA\n+ACTTAAAGCAAAAATTTCTACGTATTATTAGACATACTGTGATTTATTTAACTAATCATT\n+TTTTTGGGGTGTTAGGTTGTTTTTAATTTTTTACTGCCATCAAACATCTTGAACATAGGA\n+TGTAGATTTTAGTCTTTAAAATATGTTGGGGAATGAACAAATTTCACATCCTGTATTTGT\n+AGTATTAATACTTTGTAGGTGCTCAAAATAGAATATTCTGGTAAATGATTAGTGCTTATT\n+AAATATTTATCAAATGAATGTACTTGTACTTTTGGCATTAAACATTAACATCTGACCATT\n+TATATTTACCTGATTTTTTTTCTATGGCCATATGGTATGAAATAGTGTATGGTATAAATT\n+AACCATATGGTATAATAAATACATTTTTTTAAGTGTGATACCAGAGTGATATTTATTAAC\n+TGTTCTTCCTGTGCTGTTTCTGTAGAAGGGAGCTTCTCACAATTGCATTAGAATTACAAT\n+TTTATTATGTTCTGTTTTCAAGATCTCTGATCGTCAGTCTTAAACTGTTTAATTATAATA\n+ATGTATTGACTAGGGAATATTCTGGGATATAATCTCCTTTATAATGAGGTCCACTGTATT\n+AAAATACATCTT'..b'GAGGGTAGAATGATTACTCTTTTTGCAAGATTCTCTTCTTTGTCCAAGT\n+TGGCATTGTTAGTGCTAGGAATACCAGCACCTTGAGACGAGCAGATTCCAACCATTAGGC\n+TATAAACACCATAGCCAGAGATGGAAGGTTTACTGTGAGTATGAACAGCAAATAGCTTAC\n+AGGTCATGAGTTGAAATGGTGTAGGTGAGGCTCTAGAAAAATACCTTGACAATTTGCCAA\n+ATGATCTTACTGTGCCTTCATGATGCAATAAAAAAGCTAACATTTTAGCAGAAATCAGTG\n+ATTTGTGAAGAGAGCAGCCACTCTGGTTTAACTCAGCTGTGTTAATAATTTTTAGAGTGC\n+AATTTAGACTGCATAGGTAAATGCACTAAAGAGTTTATAGCCAAAATCACATTTAACAAT\n+GAGAAAACACACAGGTAAATTTTCAGTGAACAAAATTATTTTTTTAAAGCACATAATCCC\n+TAGTATAGTCAGATATATTTATCACATAGAGCAACTAGGTTGCAAATATAGTTCAGTGAC\n+ATTTCTAGAGAAACTTTTTCTACTCCCATAGGCTCTTCAAAGCATGGAACTTTTATACAA\n+CAGAAATGTTGACAGAAATTGCTGTAGTTTAGGGTTGAAGTACTGTATGATGGGCAGCAA\n+TCATGTATTAACTTAGAAGGGGAAATTGAAATATAGGACCGAATTTGGTTTTATCAGTTT\n+CCAGAGTACTGCTGCCAACCTAGACACTGATTTTTCAGAGTTTGAAATGTAAATTTCTTC\n+CCGGGACTTGATTGCACATGAAGCTGGACTGCGTTAGTCATCCTGTCCCAAAGCGCTGTG\n+GGGGCCAGGGTGGAGGTCTCAAGGCATCCTTTATGACCTGGCCATTGGATGTAAAAGAAA\n+ACATATTCCATGCTGTGGTTCTTGTATCTTGTTTCATTCCTCACCATTGAAAGAGAAAGT\n+CCATGTATTGTCTCCAGCACATCCTTGAAATGTTATACTGGGATGGATTACTGATGCCCA\n+TCGGTAGTTGAGCCCCAGAAGAGGGTAGTAGCATCTCTGCCTCAGGTGATGATTTGTAGC\n+TTGGCCAGAGGAGAGCGGAGTCACCAGTATATCTGTGGTCCATGTTGCTAGCTCTGGTAA\n+AATTAAAAATACTGGTAAGATGTTTGTTTTATTAGTACACTAGACAGTAAGCTCTGTTTT\n+GTTGTTTTCAAATAACCTATTTTCACTTTTGTTTGGGCAAAGACATTTAAATTGAAATTC\n+AATTCTAATTTTTGTTAATTGTGGAAAGGGTAATTAACAGTTCCTATCAGGTATTTTTAA\n+TGTGGAAAAGGACAGAAACCCAACTCCTAAAATCTTAAATTAAGGTAACAGTGCTTTAAA\n+AAAAAAAAATGCATGGGGCAATTAGTCGGCAACTCAATGAGTGACTAAAGTACTTTTATT\n+TAACATCCACAACTTCAACTGTTAAGTTTTATTAATTACTAAATCAGCTTTATTAAAATG\n+TTGACATTTATTTAGCTATTTTGAATAATTATAGTGACTTGACGAGTGTGTATGAGGACA\n+CAGCCAATGTAAGCCAGTGTATCCATTTTTTAGAGGTGCATTTTTTTTTAAAGAATTCTG\n+TAGATAGAAGTGCTCTGAAAACAACTAAAATATGTTTATTCATGGTAGTATCAAAAAATG\n+TTTGTACAAACCATCTGCTTCTCCCGGCCAGCCGAGTTCATTCTCCAGCACCGTGACCGC\n+TGGTTCTCATGTACAGCACATATGCGGGAGAGTTGGCAGAAAATTTGTGAAGAGATGCCG\n+CAAAGGAAGGGTCTGTTGACGGGTGGGATTGGGGGTTTTGATGAAGTTGCTTAGTCCTGG\n+TTTTGTTTTGAAAATTACTGCGTTGCATTTTTGTGTTAAGTTTTTGAACCCACGTGTGTT\n+TTGGTGGAGTATGAGTTGGAAGTCACTGCAAACTAGCATAAACAACAAAGCTCACAGAGT\n+AGGCACAGATGTAGAGAACAGAGACCAAAATGGGGTGAGGTGGCAGTAAATCTAGGATAG\n+GGAAAAATTAATGTGAGGGTGGGAAATAAACTGTAATTACCTGAAATCAAATGTAAGAGT\n+GCAATAAGTATGCTTTTTATTCTAAGCTGTGAACGGTTTTTTTAAGAATCATTCCTTCCT\n+AATACATTTGTGTATGTTCCATAGCTGATTAAAACCAGCTATATCAACATATAATGCCTT\n+TTTATTCATGTTAATGACCAACGTAAGTGGCTAGCCTTTATGTCTTATTTATCTTCATGT\n+TATGTTAGTTTACATACAGGGGTGTATGTCTCTGTGCTGTCCCCTTCTCCTGCCTTCATT\n+TTAAAATGCATCCATGGGTCCTCCGTGTTTCCTTTGGCCATGCCACATATATAGACTCAG\n+TTTGGCCTTCATGATATCGCCTGATTTTTGAGGACTGTATCACAGTGATATGTATTTGTG\n+GTAATCTCATTTGTTGGTTGTACATCTGATCCTTTCCTCAACATGGCAATTGCTGCCTTT\n+CCTAAGATAGGATCATACAACTGATCAGGGGATTGAATTTGATCATTCATCAACATGTGT\n+CTCTGAATTTTATTCAGTAGTTGTCATTGCTCTTTGGTTTAGACCAAGAAAAAGGAAATC\n+CCCCCTTTTCATGTATTCCTTGGTTTGAGGACATGACTCCTGTAAGGGAGAGGAAAGGGA\n+GATGCTTCCTGTTTGAACTGCAGTGAATTCACGGTTCCTGTTTCACCACTCCAAACCTTA\n+TGGCGACTCACACACACATTCCTCTTTTCTGTTACTGCCAAAGGTTCGGGTTTAGTACAC\n+TTCAGTTCCACTCAAGCATTGAAAAGGTTCTCGTGGAGTCTGGGGCGTGCCCAGTGAAAA\n+GATGGGGACTTTTTAATTGTCCACAGACCTCTCTATACCTGCTTTGCAAAAATTACAATG\n+GAGTAACTATTTTTAAAGCTTATTTTTCAATTCATAAAAAAGACATTTATTTTCAGTCAA\n+ATGGATGATGTCTCCCTCTTTTCCCCTATTCTCAATGTTTGCTTGAATCTTTTATTATTT\n+TTTTTAATTCTCCCCCATACCCACTTCCTGATACTTTGGTTCTCTTTCCTGCTCAGGTCC\n+CTTCATTTGTACTTTGGAGTTTTTCTCATGTAAATTTGTATAACAGAAAATATTGTTCAG\n+TTTGGATAGAAAGCATGGAGAATAAAAAAAGATAGCTGAAATTCAGATTGAAGAAATTTA\n+TTTCTGTGTAAAGTTATTTAAAAACTGTATTATATAAAAGGCAAAAAAAGTTCTATGTAC\n+TTGATGTGAATATGCGAATACTGCTATAATAAAGATTGACTGCATGGAGAAGTCTTCA\n+>ENSG00000248378 chromosome:GRCh38:5:31743988:31744451:-1\n+TTGGAAGTGAATTAAGACCCTCTCTTGGATACCAGCTGTGAAAGAACGGACTTTTTTTAC\n+CTAGTAAGGATGTGACAGACCTGCTCCTGACCCTTCTTTGTTAGTGGCCAGTAAATATAC\n+GCAAGGCAAAGTCCCACCCTAGTTTTGAAAAAAGCCAAACTAACAACTCTGCCCAATTTC\n+AAGGAACCGATATAATTTTCAGTACATGAGTGTGATTTAGAAATGGAAACAACATCAGAG\n+CAGGGTTAAATCAACAACCAAGCCATAGACCTTAAAAGGACCAGACTTCATGGTTCAATG\n+ATGCCAAGAAAAAGATTCCACCTATAAACTCTTTAGAAAGTAACCACCTCAGAAAGTTCC\n+AGACAAACCAGTTCTGCTTTGCAGATCAGCCCTGTATAAAGCTCTTACCACATTAGTAAG\n+AAGTTACTTGTGCTTTGGTTACAAACAGGCACAATTAAAGGGAA\n+\n' |
| b |
| diff -r 000000000000 -r f0018341e9f6 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Aug 11 14:29:07 2016 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?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> |