Mercurial > repos > earlhaminst > ensembl_get_genetree

comparison get_feature_info.py @ 1:98aba0efe77a draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
author earlhaminst
date Mon, 12 Dec 2016 07:47:26 -0500
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children 950d9d11b6fb
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0:f0018341e9f6 1:98aba0efe77a
1 # A simple tool to connect to the Ensembl server and retrieve feature
2 # information using the Ensembl REST API.
3 import json
4 import optparse
5 from urlparse import urljoin
6
7 import requests
8
9 parser = optparse.OptionParser()
10 parser.add_option('-i', '--input', help='List of Ensembl IDs')
11 parser.add_option('-e', '--expand', type='choice', choices=['0', '1'],
12 default='0',
13 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.')
14
15 parser.add_option('-s', '--species', type='choice',
16 choices=['ensembl', 'ensemblgenomes'], default='ensembl',
17 help='Specify the genome databases for vertebrates and other eukaryotic species')
18
19 parser.add_option('-f', '--format', type='choice',
20 choices=['full', 'condensed'], default='full',
21 help='Specify the formats to emit from this endpoint')
22 options, args = parser.parse_args()
23 if options.input is None:
24 raise Exception('-i option must be specified')
25
26
27 server = 'http://rest.%s.org' % options.species
28 ext = 'lookup/id'
29
30 headers = {'Content-Type': 'application/json', 'Accept': 'application/json'}
31 params = dict((k, getattr(options, k)) for k in ['format', 'expand'])
32 with open(options.input) as f:
33 ids = [line.strip() for line in f]
34 data = {'ids': ids}
35 r = requests.post(urljoin(server, ext), params=params, headers=headers,
36 data=json.dumps(data))
37
38 if not r.ok:
39 r.raise_for_status()
40
41 print r.text