Mercurial > repos > gga > apollo_export

annotate create_features_from_gff3.py @ 12:257230cd202f draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 6d9302680b01ce11a8f2ee744942296243d5d004"
author gga
date Fri, 24 Apr 2020 08:55:57 -0400
parents c3b5bc8b4080
children b763acecfb57
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b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 #!/usr/bin/env python
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2 import argparse
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3 import logging
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5 from apollo import accessible_organisms
c3b5bc8b4080 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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6 from apollo.util import GuessOrg, OrgOrGuess
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8 from arrow.apollo import get_apollo_instance
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10 from webapollo import UserObj, handle_credentials
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11 logging.basicConfig(level=logging.INFO)
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12 log = logging.getLogger(__name__)
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15 if __name__ == '__main__':
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16 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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17 parser.add_argument('email', help='User Email')
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18 parser.add_argument('--source', help='URL where the input dataset can be found.')
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19 OrgOrGuess(parser)
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21 parser.add_argument('gff3', type=argparse.FileType('r'), help='GFF3 file')
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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22 args = parser.parse_args()
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24 wa = get_apollo_instance()
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25 # User must have an account
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26 gx_user = UserObj(**wa.users._assert_or_create_user(args.email))
c3b5bc8b4080 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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27 handle_credentials(gx_user)
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29 # Get organism
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30 org_cn = GuessOrg(args, wa)
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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31 if isinstance(org_cn, list):
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32 org_cn = org_cn[0]
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34 all_orgs = wa.organisms.get_organisms()
c3b5bc8b4080 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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35 if 'error' in all_orgs:
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36 all_orgs = []
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37 all_orgs = [org['commonName'] for org in all_orgs]
c3b5bc8b4080 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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38 if org_cn not in all_orgs:
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39 raise Exception("Could not find organism %s" % org_cn)
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41 orgs = accessible_organisms(gx_user, [org_cn], 'WRITE')
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42 if not orgs:
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43 raise Exception("You do not have write permission on this organism")
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45 wa.annotations.load_gff3(org_cn, args.gff3, args.source)