Mercurial > repos > earlhaminst > ensembl_get_genetree

annotate get_feature_info.py @ 5:675fd774314e 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 07:49:30 -0400
parents 0602dcf02768
children 0618e3bd5138
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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 feature
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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2 # information using the Ensembl REST API.
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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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5 import json
98aba0efe77a 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
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0602dcf02768 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
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7 from itertools import islice
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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
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9 import requests
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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
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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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14 parser.add_option('-e', '--expand', type='choice', choices=['0', '1'],
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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15 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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16 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.')
98aba0efe77a 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('-f', '--format', 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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19 choices=['full', 'condensed'], default='full',
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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20 help='Specify the formats to emit from this endpoint')
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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21 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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22 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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23 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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675fd774314e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit ed32f2e6d8174873cefcbe141084f857f84b0586"
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26 server = 'http://rest.ensembl.org'
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27 ext = 'lookup/id'
98aba0efe77a 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': 'application/json', 'Accept': 'application/json'}
98aba0efe77a 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 ['format', 'expand'])
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0602dcf02768 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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32 first = True
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34 print('{')
0602dcf02768 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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36 with open(options.input) as f:
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0602dcf02768 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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37 while True:
0602dcf02768 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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38 ids = [line.strip() for line in islice(f, 50)]
0602dcf02768 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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39 if not ids:
0602dcf02768 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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40 break
0602dcf02768 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
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41 if not first:
0602dcf02768 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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42 print(",")
0602dcf02768 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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43 data = {'ids': ids}
0602dcf02768 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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44 r = requests.post(urljoin(server, ext), params=params, headers=headers,
0602dcf02768 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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45 data=json.dumps(data))
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47 if not r.ok:
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48 r.raise_for_status()
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50 print(r.text[1:-1])
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52 first = False
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54 print('}')