comparison create_features_from_gff3.py @ 5:f7e9c792047b draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2

4:40b26f8269a3

from BCBio import GFF

from six.moves.builtins import str

from webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance, featuresToFeatureSchema, retry
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)


if __name__ == '__main__':

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

    wa = WebApolloInstance(args.apollo, args.username, args.password)
    # User must have an account
    gx_user = AssertUser(wa.users.loadUsers(email=args.email))

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

    # TODO: Check user perms on org.
    org = wa.organisms.findOrganismByCn(org_cn)

    bad_quals = ['date_creation', 'source', 'owner', 'date_last_modified', 'Name', 'ID']

    sys.stdout.write('# ')

5:f7e9c792047b

from BCBio import GFF

from six.moves.builtins import str

from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance, featuresToFeatureSchema, retry
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)


if __name__ == '__main__':

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

    wa = WebApolloInstance(args.apollo, args.username, args.password)
    # User must have an account
    gx_user = wa.users.assertOrCreateUser(args.email)

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

    if not PermissionCheck(gx_user, org_cn, "WRITE"):
        raise Exception("Action not permitted")
    org = wa.organisms.findOrganismByCn(org_cn)

    bad_quals = ['date_creation', 'source', 'owner', 'date_last_modified', 'Name', 'ID']

    sys.stdout.write('# ')