comparison delete_features.py @ 7:f9a6e151b3b4 draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174

6:8f76685cdfc8

#!/usr/bin/env python
import argparse
from webapollo import WebApolloInstance
from webapollo import WAAuth, OrgOrGuess, GuessOrg, AssertUser
import logging
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Sample script to delete all features from 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)

        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']]))

7:f9a6e151b3b4

#!/usr/bin/env python
from __future__ import print_function
import argparse
import random
from webapollo import WebApolloInstance
from webapollo import WAAuth, OrgOrGuess, GuessOrg, AssertUser, retry
import logging
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Sample script to delete all features from an organism')
    WAAuth(parser)
    parser.add_argument('email', help='User Email')
    parser.add_argument('--type', help='Feature type filter')
    OrgOrGuess(parser)

    args = parser.parse_args()

    wa = WebApolloInstance(args.apollo, args.username, args.password)

        org_cn = org_cn[0]

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

    sequences = wa.organisms.getSequencesForOrganism(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.setSequence(sequence['name'], org['id'])
        # Then get a list of features.
        features = wa.annotations.getFeatures()
        # 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.deleteFeatures([feature['uniquename']])
                print('Deleted %s [type=%s]' % (feature['uniquename'], feature['type']['name']))

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