annotate delete_features.py @ 17:3d693b93991f draft default tip

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b

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

import argparse
import logging
import random

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

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='Script to delete all features from an organism')
    parser.add_argument('email', help='User Email')
    parser.add_argument('--type', help='Feature type filter')
    OrgOrGuess(parser)

    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")
    org = wa.organisms.show_organism(org_cn)

    sequences = wa.organisms.get_sequences(org['id'])
    for sequence in sequences['sequences']:
        log.info("Processing %s %s", org['commonName'], sequence['name'])
        # Call setSequence to tell apollo which organism we're working with
        wa.annotations.set_sequence(org['id'], sequence['name'])
        # Then get a list of features.
        features = wa.annotations.get_features()
        # For each feature in the features
        for feature in sorted(features['features'], key=lambda x: random.random()):
            if args.type:
                if args.type == 'tRNA':
                    if feature['type']['name'] != 'tRNA':
                        continue

                elif args.type == 'terminator':
                    if feature['type']['name'] != 'terminator':
                        continue

                elif args.type == 'mRNA':
                    if feature['type']['name'] != 'mRNA':
                        continue

                else:
                    raise Exception("Unknown type")

            # We see that deleteFeatures wants a uniqueName, and so we pass
            # is the uniquename field in the feature.
            def fn():
                wa.annotations.delete_feature(feature['uniquename'])
                print('Deleted %s [type=%s]' % (feature['uniquename'], feature['type']['name']))

            if not retry(fn, limit=3):
                print('Error %s' % feature['uniquename'])