Mercurial > repos > earlhaminst > ensembl_get_genetree

annotate get_sequences.py @ 2:950d9d11b6fb draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 099d38157cec200f0a343579ca9babcd8acb266f
author earlhaminst
date Wed, 21 Dec 2016 15:16:35 -0500
parents 98aba0efe77a
children 675fd774314e
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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 sequences using
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 # the Ensembl REST API.
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950d9d11b6fb planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 099d38157cec200f0a343579ca9babcd8acb266f
earlhaminst
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3 from __future__ import print_function
950d9d11b6fb planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 099d38157cec200f0a343579ca9babcd8acb266f
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earlhaminst
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5 import json
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
earlhaminst
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6 import optparse
98aba0efe77a 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
98aba0efe77a 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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950d9d11b6fb planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 099d38157cec200f0a343579ca9babcd8acb266f
earlhaminst
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10 from six.moves.urllib.parse import urljoin
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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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12 parser = optparse.OptionParser()
98aba0efe77a 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')
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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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
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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
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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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19 parser.add_option('-t', '--type', type='choice',
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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20 choices=['genomic', 'cds', 'cdna', 'protein'],
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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21 default='genomic', help='Type of sequence')
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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22 parser.add_option('--expand_3prime', type='int', default=0,
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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23 help='Expand the sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type')
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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24 parser.add_option('--expand_5prime', type='int', 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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25 help='Expand the sequence upstream of the sequence by this many basepairs. Only available when using genomic sequence type')
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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26 options, args = parser.parse_args()
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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27 if options.input is None:
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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28 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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30 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
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31 ext = 'sequence/id'
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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33 headers = {'Content-Type': 'text/x-fasta', 'Accept': 'text/x-fasta'}
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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34 params = dict((k, getattr(options, k)) for k in ['type', 'expand_3prime', 'expand_5prime'])
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35 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
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36 # Need to split the file in chunks of 50 lines because of the limit imposed by Ensembl
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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37 while True:
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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38 ids = [line.strip() for line in islice(f, 50)]
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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39 if not ids:
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40 break
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41 data = {'ids': ids}
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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42 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
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43 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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45 if not r.ok:
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46 r.raise_for_status()
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47
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48 print(r.text)