annotate delete_organism.py @ 3:92a06569b9af draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 079b759c21c00200544a6d8d5521617dce8ca70d

#!/usr/bin/env python
from __future__ import print_function

import argparse
import logging

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


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Sample script to completely delete an organism')
    WAAuth(parser)
    parser.add_argument('email', help='User Email')
    OrgOrGuess(parser)

    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)

    # Call setSequence to tell apollo which organism we're working with
    wa.annotations.setSequence(org['commonName'], org['id'])
    # Then get a list of features.
    features = wa.annotations.getFeatures()
    # For each feature in the features
    for feature in features['features']:
        # We see that deleteFeatures wants a uniqueName, and so we pass
        # is the uniquename field in the feature.
        print(wa.annotations.deleteFeatures([feature['uniquename']]))