Mercurial > repos > earlhaminst > ensembl_get_genetree

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