Mercurial > repos > earlhaminst > ensembl_get_genetree

annotate get_feature_info/get_feature_info.py @ 0:f0018341e9f6 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
author earlhaminst
date Thu, 11 Aug 2016 14:29:07 -0400
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f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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1 # A simple tool to connect to the Ensembl server and retrieve feature
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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2 # information using the Ensembl REST API.
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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3 import json
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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4 import optparse
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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5 from urlparse import urljoin
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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7 import requests
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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9 parser = optparse.OptionParser()
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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10 parser.add_option('-i', '--input', help='List of Ensembl IDs')
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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11 parser.add_option('-e', '--expand', type='choice', choices=['0', '1'],
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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12 default='0',
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-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.')
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
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f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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15 parser.add_option('-s', '--species', type='choice',
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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16 choices=['ensembl', 'ensemblgenomes'], default='ensembl',
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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17 help='Specify the genome databases for vertebrates and other eukaryotic species')
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
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f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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19 parser.add_option('-f', '--format', type='choice',
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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20 choices=['full', 'condensed'], default='full',
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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21 help='Specify the formats to emit from this endpoint')
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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22 options, args = parser.parse_args()
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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23 if options.input is None:
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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24 raise Exception('-i option must be specified')
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
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f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
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f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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27 server = 'http://rest.%s.org' % options.species
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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28 ext = 'lookup/id'
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
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f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
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30 headers = {'Content-Type': 'application/json', 'Accept': 'application/json'}
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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31 params = dict((k, getattr(options, k)) for k in ['format', 'expand'])
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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32 with open(options.input) as f:
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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33 ids = [line.strip() for line in f]
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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34 data = {'ids': ids}
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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35 r = requests.post(urljoin(server, ext), params=params, headers=headers,
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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36 data=json.dumps(data))
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
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f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
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38 if not r.ok:
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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39 r.raise_for_status()
f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
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f0018341e9f6 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
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41 print r.text