comparison get_sequences.py @ 5:675fd774314e draft

"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit ed32f2e6d8174873cefcbe141084f857f84b0586"

4:0602dcf02768

from six.moves.urllib.parse import urljoin

parser = optparse.OptionParser()
parser.add_option('-i', '--input', help='List of Ensembl IDs')

parser.add_option('-s', '--species', type='choice',
                  choices=['ensembl', 'ensemblgenomes'], default='ensembl',
                  help='Specify the genome databases for vertebrates and other eukaryotic species')

parser.add_option('-t', '--type', type='choice',
                  choices=['genomic', 'cds', 'cdna', 'protein'],
                  default='genomic', help='Type of sequence')
parser.add_option('--expand_3prime', type='int', default=0,
                  help='Expand the sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type')

                  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.%s.org' % options.species
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:

5:675fd774314e

from six.moves.urllib.parse import urljoin

parser = optparse.OptionParser()
parser.add_option('-i', '--input', help='List of Ensembl IDs')

parser.add_option('-t', '--type', type='choice',
                  choices=['genomic', 'cds', 'cdna', 'protein'],
                  default='genomic', help='Type of sequence')
parser.add_option('--expand_3prime', type='int', default=0,
                  help='Expand the sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type')

                  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: