Mercurial > repos > gga > apollo_delete_organism

comparison create_features_from_gff3.py @ 13:6ea838bf1f2f draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7bf18c69becc57152efdadedf7ebd0bcfa382a15"
author gga
date Mon, 29 Jun 2020 09:15:25 -0400
parents dd63c6e11a95
children
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12:64c887661f4f 13:6ea838bf1f2f
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 import argparse 2 import argparse
3 import json
3 import logging 4 import logging
4 5
5 from apollo import accessible_organisms 6 from apollo import accessible_organisms
6 from apollo.util import GuessOrg, OrgOrGuess 7 from apollo.util import GuessOrg, OrgOrGuess
7 8
14 15
15 if __name__ == '__main__': 16 if __name__ == '__main__':
16 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services') 17 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
17 parser.add_argument('email', help='User Email') 18 parser.add_argument('email', help='User Email')
18 parser.add_argument('--source', help='URL where the input dataset can be found.') 19 parser.add_argument('--source', help='URL where the input dataset can be found.')
20 parser.add_argument('--use_name', action='store_true', help='Use the given name instead of generating one.')
21 parser.add_argument('--disable_cds_recalculation', action='store_true', help='Disable CDS recalculation and instead use the one provided.')
19 OrgOrGuess(parser) 22 OrgOrGuess(parser)
20 23
21 parser.add_argument('gff3', type=argparse.FileType('r'), help='GFF3 file') 24 parser.add_argument('gff3', type=argparse.FileType('r'), help='GFF3 file')
22 args = parser.parse_args() 25 args = parser.parse_args()
23 26
40 43
41 orgs = accessible_organisms(gx_user, [org_cn], 'WRITE') 44 orgs = accessible_organisms(gx_user, [org_cn], 'WRITE')
42 if not orgs: 45 if not orgs:
43 raise Exception("You do not have write permission on this organism") 46 raise Exception("You do not have write permission on this organism")
44 47
45 wa.annotations.load_gff3(org_cn, args.gff3, args.source) 48 load_result = wa.annotations.load_gff3(org_cn, args.gff3, args.source, use_name=args.use_name, disable_cds_recalculation=args.disable_cds_recalculation)
49 print(json.dumps(load_result, indent=2))