Mercurial > repos > earlhaminst > ensembl_get_feature_info

annotate get_sequences/get_sequences.py @ 0:874c067e4527 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 14:29:29 -0400
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874c067e4527 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 sequences using
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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2 # the Ensembl REST API.
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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3 import json
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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4 import optparse
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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5 from itertools import islice
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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6 from urlparse import urljoin
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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8 import requests
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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10 parser = optparse.OptionParser()
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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11 parser.add_option('-i', '--input', help='List of Ensembl IDs')
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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13 parser.add_option('-s', '--species', type='choice',
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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14 choices=['ensembl', 'ensemblgenomes'], default='ensembl',
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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15 help='Specify the genome databases for vertebrates and other eukaryotic species')
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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17 parser.add_option('-t', '--type', type='choice',
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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18 choices=['genomic', 'cds', 'cdna', 'protein'],
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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19 default='genomic', help='Type of sequence')
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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20 parser.add_option('--expand_3prime', type='int', default=0,
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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21 help='Expand the sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type')
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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22 parser.add_option('--expand_5prime', type='int', default=0,
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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23 help='Expand the sequence upstream of the sequence by this many basepairs. Only available when using genomic sequence type')
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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24 options, args = parser.parse_args()
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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25 if options.input is None:
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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26 raise Exception('-i option must be specified')
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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27
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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28 server = 'http://rest.%s.org' % options.species
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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29 ext = 'sequence/id'
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
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874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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31 headers = {'Content-Type': 'text/x-fasta', 'Accept': 'text/x-fasta'}
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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32 params = dict((k, getattr(options, k)) for k in ['type', 'expand_3prime', 'expand_5prime'])
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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33 with open(options.input) as f:
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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34 # Need to split the file in chunks of 50 lines because of the limit imposed by Ensembl
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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35 while True:
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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36 ids = [line.strip() for line in islice(f, 50)]
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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37 if not ids:
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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38 break
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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39 data = {'ids': ids}
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
parents:
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40 r = requests.post(urljoin(server, ext), params=params, headers=headers,
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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41 data=json.dumps(data))
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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42
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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43 if not r.ok:
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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44 r.raise_for_status()
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
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45
874c067e4527 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
earlhaminst
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46 print r.text