annotate create_features_from_gff3.py @ 12:257230cd202f draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 6d9302680b01ce11a8f2ee744942296243d5d004"

#!/usr/bin/env python
import argparse
import logging

from apollo import accessible_organisms
from apollo.util import GuessOrg, OrgOrGuess

from arrow.apollo import get_apollo_instance

from webapollo import UserObj, handle_credentials
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('email', help='User Email')
    parser.add_argument('--source', help='URL where the input dataset can be found.')
    OrgOrGuess(parser)

    parser.add_argument('gff3', type=argparse.FileType('r'), help='GFF3 file')
    args = parser.parse_args()

    wa = get_apollo_instance()
    # User must have an account
    gx_user = UserObj(**wa.users._assert_or_create_user(args.email))
    handle_credentials(gx_user)

    # Get organism
    org_cn = GuessOrg(args, wa)
    if isinstance(org_cn, list):
        org_cn = org_cn[0]

    all_orgs = wa.organisms.get_organisms()
    if 'error' in all_orgs:
        all_orgs = []
    all_orgs = [org['commonName'] for org in all_orgs]
    if org_cn not in all_orgs:
        raise Exception("Could not find organism %s" % org_cn)

    orgs = accessible_organisms(gx_user, [org_cn], 'WRITE')
    if not orgs:
        raise Exception("You do not have write permission on this organism")

    wa.annotations.load_gff3(org_cn, args.gff3, args.source)