annotate get_sequences.py @ 7:d6bb417dc831 draft default tip

"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 17c65045b726d0695814bfe761e534f6521786f1"
author earlhaminst
date Tue, 20 Oct 2020 15:06:54 +0000
parents 70e4134eb0ed
children
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396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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1 # A simple tool to connect to the Ensembl server and retrieve sequences using
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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2 # the Ensembl REST API.
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earlhaminst
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3 from __future__ import print_function
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5 import json
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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6 import optparse
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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7 from itertools import islice
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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9 import requests
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10 from six.moves.urllib.parse import urljoin
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12 parser = optparse.OptionParser()
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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13 parser.add_option('-i', '--input', help='List of Ensembl IDs')
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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15 parser.add_option('-t', '--type', type='choice',
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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16 choices=['genomic', 'cds', 'cdna', 'protein'],
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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17 default='genomic', help='Type of sequence')
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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18 parser.add_option('--expand_3prime', type='int', default=0,
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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19 help='Expand the sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type')
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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20 parser.add_option('--expand_5prime', type='int', default=0,
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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21 help='Expand the sequence upstream of the sequence by this many basepairs. Only available when using genomic sequence type')
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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22 options, args = parser.parse_args()
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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23 if options.input is None:
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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24 raise Exception('-i option must be specified')
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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d6bb417dc831 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 17c65045b726d0695814bfe761e534f6521786f1"
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26 server = 'https://rest.ensembl.org'
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27 ext = 'sequence/id'
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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29 headers = {'Content-Type': 'text/x-fasta', 'Accept': 'text/x-fasta'}
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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30 params = dict((k, getattr(options, k)) for k in ['type', 'expand_3prime', 'expand_5prime'])
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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31 with open(options.input) as f:
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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32 # Need to split the file in chunks of 50 lines because of the limit imposed by Ensembl
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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33 while True:
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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34 ids = [line.strip() for line in islice(f, 50)]
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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35 if not ids:
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36 break
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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37 data = {'ids': ids}
396f0f54d115 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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38 r = requests.post(urljoin(server, ext), params=params, headers=headers,
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d6bb417dc831 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 17c65045b726d0695814bfe761e534f6521786f1"
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39 data=json.dumps(data), allow_redirects=False)
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41 if not r.ok:
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42 r.raise_for_status()
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44 print(r.text)