comparison create_features_from_gff3.py @ 13:6905bb3ce9db draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7bf18c69becc57152efdadedf7ebd0bcfa382a15"

12:30ea2be4a236

#!/usr/bin/env python
import argparse
import logging

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

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
    parser.add_argument('email', help='User Email')
    parser.add_argument('--source', help='URL where the input dataset can be found.')
    OrgOrGuess(parser)

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

    orgs = accessible_organisms(gx_user, [org_cn], 'WRITE')
    if not orgs:
        raise Exception("You do not have write permission on this organism")

    wa.annotations.load_gff3(org_cn, args.gff3, args.source)

13:6905bb3ce9db

#!/usr/bin/env python
import argparse
import json
import logging

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

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
    parser.add_argument('email', help='User Email')
    parser.add_argument('--source', help='URL where the input dataset can be found.')
    parser.add_argument('--use_name', action='store_true', help='Use the given name instead of generating one.')
    parser.add_argument('--disable_cds_recalculation', action='store_true', help='Disable CDS recalculation and instead use the one provided.')
    OrgOrGuess(parser)

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

    orgs = accessible_organisms(gx_user, [org_cn], 'WRITE')
    if not orgs:
        raise Exception("You do not have write permission on this organism")

    load_result = wa.annotations.load_gff3(org_cn, args.gff3, args.source, use_name=args.use_name, disable_cds_recalculation=args.disable_cds_recalculation)
    print(json.dumps(load_result, indent=2))