Mercurial > repos > earlhaminst > ensembl_get_sequences

annotate get_genetree.py @ 5:0fa1d1cc417d draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit ed32f2e6d8174873cefcbe141084f857f84b0586"
author earlhaminst
date Thu, 31 Oct 2019 07:50:07 -0400
parents 4b7261f484bb
children 7af66c2b3831
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e5dd4bd78bbc 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 genetree using
e5dd4bd78bbc 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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earlhaminst
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5 import optparse
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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7 import requests
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earlhaminst
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8 from six.moves.urllib.parse import urljoin
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e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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10 parser = optparse.OptionParser()
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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11 parser.add_option('--id_type', type='choice', default='gene_id',
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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12 choices=['gene_id', 'gene_tree_id'], help='Input type')
e5dd4bd78bbc 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='Ensembl ID')
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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14 parser.add_option('--format', type='choice',
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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15 choices=['json', 'orthoxml', 'phyloxml', 'nh'],
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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16 default='json', help='Output format')
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17 parser.add_option('-s', '--sequence', type='choice',
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18 choices=['protein', 'cdna', 'none'], default='protein',
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19 help='The type of sequence to bring back. Setting it to none results in no sequence being returned')
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e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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21 parser.add_option('-a', '--aligned', type='choice', choices=['0', '1'],
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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22 default='0', help='Return the aligned string if true. Otherwise, return the original sequence (no insertions)')
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23 parser.add_option('-c', '--cigar_line', type='choice', choices=['0', '1'],
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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24 default='0',
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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25 help='Return the aligned sequence encoded in CIGAR format')
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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26 parser.add_option('--nh_format', type='choice',
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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27 choices=['full', 'display_label_composite', 'simple', 'species', 'species_short_name', 'ncbi_taxon', 'ncbi_name', 'njtree', 'phylip'],
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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28 default='simple',
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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29 help='The format of a NH (New Hampshire) request')
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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30 options, args = parser.parse_args()
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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31 if options.input is None:
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32 raise Exception('-i option must be specified')
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34 server = 'http://rest.ensembl.org'
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e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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36 if options.id_type == 'gene_id':
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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37 ext = 'genetree/member/id'
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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38 elif options.id_type == 'gene_tree_id':
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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39 ext = 'genetree/id'
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e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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41 if options.format == 'json':
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42 content_type = 'application/json'
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43 elif options.format == 'orthoxml':
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44 content_type = 'text/x-orthoxml+xml'
e5dd4bd78bbc planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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45 elif options.format == 'phyloxml':
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46 content_type = 'text/x-phyloxml+xml'
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47 elif options.format == 'nh':
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48 content_type = 'text/x-nh'
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49 headers = {'Content-Type': content_type}
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50 params = dict((k, getattr(options, k)) for k in ['sequence', 'aligned', 'cigar_line', 'nh_format'])
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51 r = requests.get(urljoin(server, '/'.join([ext, options.input])), params=params, headers=headers)
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53 if not r.ok:
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54 r.raise_for_status()
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56 print(r.text)