comparison get_feature_info.py @ 5:234d7babf34b draft

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

4:10dc420f725a

# information using the Ensembl REST API.
from __future__ import print_function

import json
import optparse

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

parser = optparse.OptionParser()

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'])
with open(options.input) as f:
    ids = [line.strip() for line in f]
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)

5:234d7babf34b

# 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()

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('}')