Mercurial > repos > gga > apollo_fetch_jbrowse
view create_features_from_gff3.py @ 14:b7c44671f012 draft
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7f274d9deece87f6837ffb0a22d9231671be4542"
author | gga |
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date | Wed, 19 Aug 2020 06:58:13 -0400 |
parents | 6905bb3ce9db |
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#!/usr/bin/env python import argparse import json import logging from apollo import accessible_organisms from apollo.util import GuessOrg, OrgOrGuess 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='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() 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") 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))