Mercurial > repos > eric-rasche > apollo

annotate create_features_from_gff3.py @ 2:c8e16c8eff98 draft

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planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 6944305517dcccad3e6b37f8aba0b43ccb004540
author eric-rasche
date Tue, 03 May 2016 13:48:11 -0400
parents 6002cc0df04e
children
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
1 #!/usr/bin/env python
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
2 import argparse
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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3 from webapollo import WebApolloInstance, featuresToFeatureSchema
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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4 from BCBio import GFF
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
5 import logging
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
6 logging.basicConfig(level=logging.INFO)
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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7 log = logging.getLogger(__name__)
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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8
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
9
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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10 if __name__ == '__main__':
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
11 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
12 parser.add_argument('apollo', help='Complete Apollo URL')
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
13 parser.add_argument('username', help='WA Admin Username')
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
14 parser.add_argument('password', help='WA Admin Password')
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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16 parser.add_argument('cn', help='Organism Common Name')
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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17 parser.add_argument('email', help='User Email')
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
18 parser.add_argument('gff3', type=file, help='GFF3 file')
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
19 args = parser.parse_args()
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
21 wa = WebApolloInstance(args.apollo, args.username, args.password)
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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22 # User must have an account
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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23 gx_user = wa.users.loadUsers(email=args.email)
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
24 if len(gx_user) == 0:
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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25 raise Exception("Unknown user. Please register first")
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
27 # TODO: Check user perms on org.
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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29 org = wa.organisms.findOrganismByCn(args.cn)
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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30 wa.annotations.setSequence(args.cn, org['id'])
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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32 for rec in GFF.parse(args.gff3):
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
33 featureData = featuresToFeatureSchema(rec.features)
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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34 wa.annotations.addFeature(
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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35 {
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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36 'features': featureData
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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37 }, trustme=True
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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38 )