annotate get_feature_info.py @ 5:234d7babf34b draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae

# A simple tool to connect to the Ensembl server and retrieve feature
# information using the Ensembl REST API.
from __future__ import print_function

import json
import optparse
from itertools import islice

import requests
from six.moves.urllib.parse import urljoin

parser = optparse.OptionParser()
parser.add_option('-i', '--input', help='List of Ensembl IDs')
parser.add_option('-e', '--expand', type='choice', choices=['0', '1'],
                  default='0',
                  help='Expands the search to include any connected features. e.g. If the object is a gene, its transcripts, translations and exons will be returned as well.')

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('-f', '--format', type='choice',
                  choices=['full', 'condensed'], default='full',
                  help='Specify the formats to emit from this endpoint')
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 = 'lookup/id'

headers = {'Content-Type': 'application/json', 'Accept': 'application/json'}
params = dict((k, getattr(options, k)) for k in ['format', 'expand'])

first = True

print('{')

with open(options.input) as f:
    while True:
        ids = [line.strip() for line in islice(f, 50)]
        if not ids:
            break
        if not first:
            print(",")
        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[1:-1])

        first = False

print('}')