comparison get_sequences.py @ 7:d6bb417dc831 draft default tip

"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 17c65045b726d0695814bfe761e534f6521786f1"

6:70e4134eb0ed

                  help='Expand the sequence upstream of the sequence by this many basepairs. Only available when using genomic sequence type')
options, args = parser.parse_args()
if options.input is None:
    raise Exception('-i option must be specified')

server = 'http://rest.ensembl.org'
ext = 'sequence/id'

headers = {'Content-Type': 'text/x-fasta', 'Accept': 'text/x-fasta'}
params = dict((k, getattr(options, k)) for k in ['type', 'expand_3prime', 'expand_5prime'])
with open(options.input) as f:

        ids = [line.strip() for line in islice(f, 50)]
        if not ids:
            break
        data = {'ids': ids}
        r = requests.post(urljoin(server, ext), params=params, headers=headers,
                          data=json.dumps(data))

        if not r.ok:
            r.raise_for_status()

        print(r.text)

7:d6bb417dc831

                  help='Expand the sequence upstream of the sequence by this many basepairs. Only available when using genomic sequence type')
options, args = parser.parse_args()
if options.input is None:
    raise Exception('-i option must be specified')

server = 'https://rest.ensembl.org'
ext = 'sequence/id'

headers = {'Content-Type': 'text/x-fasta', 'Accept': 'text/x-fasta'}
params = dict((k, getattr(options, k)) for k in ['type', 'expand_3prime', 'expand_5prime'])
with open(options.input) as f:

        ids = [line.strip() for line in islice(f, 50)]
        if not ids:
            break
        data = {'ids': ids}
        r = requests.post(urljoin(server, ext), params=params, headers=headers,
                          data=json.dumps(data), allow_redirects=False)

        if not r.ok:
            r.raise_for_status()

        print(r.text)