annotate get_genetree/get_genetree.py @ 0:f0018341e9f6 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty

# A simple tool to connect to the Ensembl server and retrieve genetree using
# the Ensembl REST API.
import optparse
from urlparse import urljoin

import requests

parser = optparse.OptionParser()
parser.add_option('--id_type', type='choice', default='gene_id',
                  choices=['gene_id', 'gene_tree_id'], help='Input type')
parser.add_option('-i', '--input', help='Ensembl ID')
parser.add_option('--format', type='choice',
                  choices=['json', 'orthoxml', 'phyloxml', 'nh'],
                  default='json', help='Output format')
parser.add_option('-s', '--sequence', type='choice',
                  choices=['protein', 'cdna', 'none'], default='protein',
                  help='The type of sequence to bring back. Setting it to none results in no sequence being returned')

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

parser.add_option('-a', '--aligned', type='choice', choices=['0', '1'],
                  default='0', help='Return the aligned string if true. Otherwise, return the original sequence (no insertions)')
parser.add_option('-c', '--cigar_line', type='choice', choices=['0', '1'],
                  default='0',
                  help='Return the aligned sequence encoded in CIGAR format')
parser.add_option('--nh_format', type='choice',
                  choices=['full', 'display_label_composite', 'simple', 'species', 'species_short_name', 'ncbi_taxon', 'ncbi_name', 'njtree', 'phylip'],
                  default='simple',
                  help='The format of a NH (New Hampshire) request')
options, args = parser.parse_args()
if options.input is None:
    raise Exception('-i option must be specified')

server = 'http://rest.%s.org' % options.species

if options.id_type == 'gene_id':
    ext = 'genetree/member/id'
elif options.id_type == 'gene_tree_id':
    ext = 'genetree/id'

if options.format == 'json':
    content_type = 'application/json'
elif options.format == 'orthoxml':
    content_type = 'text/x-orthoxml+xml'
elif options.format == 'phyloxml':
    content_type = 'text/x-phyloxml+xml'
elif options.format == 'nh':
    content_type = 'text/x-nh'
headers = {'Content-Type': content_type}
params = dict((k, getattr(options, k)) for k in ['sequence', 'aligned', 'cigar_line', 'nh_format'])
r = requests.get(urljoin(server, '/'.join([ext, options.input])), params=params, headers=headers)

if not r.ok:
    r.raise_for_status()

print r.text