comparison create_features_from_gff3.py @ 0:6002cc0df04e draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd

0:6002cc0df04e

#!/usr/bin/env python
import argparse
from webapollo import WebApolloInstance, featuresToFeatureSchema
from BCBio import GFF
import logging
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
    parser.add_argument('apollo', help='Complete Apollo URL')
    parser.add_argument('username', help='WA Admin Username')
    parser.add_argument('password', help='WA Admin Password')

    parser.add_argument('cn', help='Organism Common Name')
    parser.add_argument('email', help='User Email')
    parser.add_argument('gff3', type=file, help='GFF3 file')
    args = parser.parse_args()

    wa = WebApolloInstance(args.apollo, args.username, args.password)
    # User must have an account
    gx_user = wa.users.loadUsers(email=args.email)
    if len(gx_user) == 0:
        raise Exception("Unknown user. Please register first")

    # TODO: Check user perms on org.

    org = wa.organisms.findOrganismByCn(args.cn)
    wa.annotations.setSequence(args.cn, org['id'])

    for rec in GFF.parse(args.gff3):
        featureData = featuresToFeatureSchema(rec.features)
        wa.annotations.addFeature(
            {
                'features': featureData
            }, trustme=True
        )