Mercurial > repos > earlhaminst > ensembl_get_sequences

comparison get_feature_info.py @ 5:0fa1d1cc417d draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit ed32f2e6d8174873cefcbe141084f857f84b0586"
author earlhaminst
date Thu, 31 Oct 2019 07:50:07 -0400
parents 3b686142e9c2
children 7af66c2b3831
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4:3b686142e9c2 5:0fa1d1cc417d
13 parser.add_option('-i', '--input', help='List of Ensembl IDs') 13 parser.add_option('-i', '--input', help='List of Ensembl IDs')
14 parser.add_option('-e', '--expand', type='choice', choices=['0', '1'], 14 parser.add_option('-e', '--expand', type='choice', choices=['0', '1'],
15 default='0', 15 default='0',
16 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.') 16 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.')
17 17
18 parser.add_option('-s', '--species', type='choice',
19 choices=['ensembl', 'ensemblgenomes'], default='ensembl',
20 help='Specify the genome databases for vertebrates and other eukaryotic species')
21
22 parser.add_option('-f', '--format', type='choice', 18 parser.add_option('-f', '--format', type='choice',
23 choices=['full', 'condensed'], default='full', 19 choices=['full', 'condensed'], default='full',
24 help='Specify the formats to emit from this endpoint') 20 help='Specify the formats to emit from this endpoint')
25 options, args = parser.parse_args() 21 options, args = parser.parse_args()
26 if options.input is None: 22 if options.input is None:
27 raise Exception('-i option must be specified') 23 raise Exception('-i option must be specified')
28 24
29 25
30 server = 'http://rest.%s.org' % options.species 26 server = 'http://rest.ensembl.org'
31 ext = 'lookup/id' 27 ext = 'lookup/id'
32 28
33 headers = {'Content-Type': 'application/json', 'Accept': 'application/json'} 29 headers = {'Content-Type': 'application/json', 'Accept': 'application/json'}
34 params = dict((k, getattr(options, k)) for k in ['format', 'expand']) 30 params = dict((k, getattr(options, k)) for k in ['format', 'expand'])
35 31