Mercurial > repos > gga > apollo_fetch_jbrowse
comparison delete_organism.py @ 0:c6d7f19953a6 draft
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 05:47:25 -0400 |
| parents | |
| children | 1a2976c6b161 |
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| -1:000000000000 | 0:c6d7f19953a6 |
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| 1 #!/usr/bin/env python | |
| 2 from __future__ import print_function | |
| 3 | |
| 4 import argparse | |
| 5 import logging | |
| 6 | |
| 7 from webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance | |
| 8 logging.basicConfig(level=logging.INFO) | |
| 9 log = logging.getLogger(__name__) | |
| 10 | |
| 11 | |
| 12 if __name__ == '__main__': | |
| 13 parser = argparse.ArgumentParser(description='Sample script to completely delete an organism') | |
| 14 WAAuth(parser) | |
| 15 parser.add_argument('email', help='User Email') | |
| 16 OrgOrGuess(parser) | |
| 17 | |
| 18 args = parser.parse_args() | |
| 19 | |
| 20 wa = WebApolloInstance(args.apollo, args.username, args.password) | |
| 21 # User must have an account | |
| 22 gx_user = AssertUser(wa.users.loadUsers(email=args.email)) | |
| 23 | |
| 24 # Get organism | |
| 25 org_cn = GuessOrg(args, wa) | |
| 26 if isinstance(org_cn, list): | |
| 27 org_cn = org_cn[0] | |
| 28 | |
| 29 # TODO: Check user perms on org. | |
| 30 org = wa.organisms.findOrganismByCn(org_cn) | |
| 31 | |
| 32 # Call setSequence to tell apollo which organism we're working with | |
| 33 wa.annotations.setSequence(org['commonName'], org['id']) | |
| 34 # Then get a list of features. | |
| 35 features = wa.annotations.getFeatures() | |
| 36 # For each feature in the features | |
| 37 for feature in features['features']: | |
| 38 # We see that deleteFeatures wants a uniqueName, and so we pass | |
| 39 # is the uniquename field in the feature. | |
| 40 print(wa.annotations.deleteFeatures([feature['uniquename']])) |