comparison export.py @ 5:f7e9c792047b draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2

4:40b26f8269a3

from BCBio import GFF

from Bio import SeqIO

from webapollo import CnOrGuess, GuessCn, WAAuth, WebApolloInstance

try:
    import StringIO as io
except ImportError:
    import io

    WAAuth(parser)
    CnOrGuess(parser)
    parser.add_argument('--gff', type=argparse.FileType('w'))
    parser.add_argument('--fasta', type=argparse.FileType('w'))
    parser.add_argument('--json', type=argparse.FileType('w'))

    args = parser.parse_args()

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

    org_cn_list, seqs = GuessCn(args, wa)

    org_data = []
    for org_cn in org_cn_list:
        indiv_org_data = export(org_cn, seqs)
        org_data.append(indiv_org_data)
    args.json.write(json.dumps(org_data, indent=2))

5:f7e9c792047b

from BCBio import GFF

from Bio import SeqIO

from webapollo import CnOrGuess, GuessCn, PermissionCheck, WAAuth, WebApolloInstance

try:
    import StringIO as io
except ImportError:
    import io

    WAAuth(parser)
    CnOrGuess(parser)
    parser.add_argument('--gff', type=argparse.FileType('w'))
    parser.add_argument('--fasta', type=argparse.FileType('w'))
    parser.add_argument('--json', type=argparse.FileType('w'))
    parser.add_argument('email', help='User Email')
    args = parser.parse_args()

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

    org_cn_list, seqs = GuessCn(args, wa)

    # User must have an apollo account, if not, create it
    gx_user = wa.users.assertOrCreateUser(args.email)

    org_data = []
    for org_cn in org_cn_list:
        # User must have read permission on organism
        if not PermissionCheck(gx_user, org_cn, "READ"):
            continue
        indiv_org_data = export(org_cn, seqs)
        org_data.append(indiv_org_data)
    args.json.write(json.dumps(org_data, indent=2))