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annotate create_features_from_gff3.py @ 20:d87bd3f2654e draft default tip

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b
author gga
date Wed, 11 Jan 2023 11:45:03 +0000
parents f5fa6d32498c
children
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a5ebd72b4369 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 json
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4 import logging
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6 from apollo import accessible_organisms
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7 from apollo.util import GuessOrg, OrgOrGuess
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9 from arrow.apollo import get_apollo_instance
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11 from webapollo import UserObj, handle_credentials
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12 logging.basicConfig(level=logging.INFO)
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13 log = logging.getLogger(__name__)
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a5ebd72b4369 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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16 if __name__ == '__main__':
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17 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
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18 parser.add_argument('email', help='User Email')
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19 parser.add_argument('--source', help='URL where the input dataset can be found.')
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20 parser.add_argument('--use_name', action='store_true', help='Use the given name instead of generating one.')
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21 parser.add_argument('--disable_cds_recalculation', action='store_true', help='Disable CDS recalculation and instead use the one provided.')
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22 OrgOrGuess(parser)
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24 parser.add_argument('gff3', type=argparse.FileType('r'), help='GFF3 file')
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25 args = parser.parse_args()
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27 wa = get_apollo_instance()
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28 # User must have an account
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29 gx_user = UserObj(**wa.users._assert_or_create_user(args.email))
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30 handle_credentials(gx_user)
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32 # Get organism
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33 org_cn = GuessOrg(args, wa)
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34 if isinstance(org_cn, list):
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35 org_cn = org_cn[0]
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37 all_orgs = wa.organisms.get_organisms()
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38 if 'error' in all_orgs:
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39 all_orgs = []
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40 all_orgs = [org['commonName'] for org in all_orgs]
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41 if org_cn not in all_orgs:
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42 raise Exception("Could not find organism %s" % org_cn)
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44 orgs = accessible_organisms(gx_user, [org_cn], 'WRITE')
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45 if not orgs:
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46 raise Exception("You do not have write permission on this organism")
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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)
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49 print(json.dumps(load_result, indent=2))