Mercurial > repos > gga > apollo_list_organism
view delete_features.py @ 17:8dc690130172 draft default tip
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b
author | gga |
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date | Wed, 11 Jan 2023 11:48:41 +0000 |
parents | bc2b80fc7e30 |
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#!/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'])