Mercurial > repos > gga > apollo_list_organism

comparison delete_features.py @ 0:1f2e360f7554 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:48:05 -0400
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-1:000000000000 0:1f2e360f7554
1 #!/usr/bin/env python
2 from __future__ import print_function
3
4 import argparse
5 import logging
6 import random
7
8 from webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance, retry
9 logging.basicConfig(level=logging.INFO)
10 log = logging.getLogger(__name__)
11
12
13 if __name__ == '__main__':
14 parser = argparse.ArgumentParser(description='Sample script to delete all features from an organism')
15 WAAuth(parser)
16 parser.add_argument('email', help='User Email')
17 parser.add_argument('--type', help='Feature type filter')
18 OrgOrGuess(parser)
19
20 args = parser.parse_args()
21
22 wa = WebApolloInstance(args.apollo, args.username, args.password)
23 # User must have an account
24 gx_user = AssertUser(wa.users.loadUsers(email=args.email))
25
26 # Get organism
27 org_cn = GuessOrg(args, wa)
28 if isinstance(org_cn, list):
29 org_cn = org_cn[0]
30
31 # TODO: Check user perms on org.
32 org = wa.organisms.findOrganismByCn(org_cn)
33
34 sequences = wa.organisms.getSequencesForOrganism(org['id'])
35 for sequence in sequences['sequences']:
36 log.info("Processing %s %s", org['commonName'], sequence['name'])
37 # Call setSequence to tell apollo which organism we're working with
38 wa.annotations.setSequence(sequence['name'], org['id'])
39 # Then get a list of features.
40 features = wa.annotations.getFeatures()
41 # For each feature in the features
42 for feature in sorted(features['features'], key=lambda x: random.random()):
43 if args.type:
44 if args.type == 'tRNA':
45 if feature['type']['name'] != 'tRNA':
46 continue
47
48 elif args.type == 'terminator':
49 if feature['type']['name'] != 'terminator':
50 continue
51
52 elif args.type == 'mRNA':
53 if feature['type']['name'] != 'mRNA':
54 continue
55
56 else:
57 raise Exception("Unknown type")
58
59 # We see that deleteFeatures wants a uniqueName, and so we pass
60 # is the uniquename field in the feature.
61 def fn():
62 wa.annotations.deleteFeatures([feature['uniquename']])
63 print('Deleted %s [type=%s]' % (feature['uniquename'], feature['type']['name']))
64
65 if not retry(fn, limit=3):
66 print('Error %s' % feature['uniquename'])