diff get_feature_info.py @ 1:98aba0efe77a draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_feature_info.py	Mon Dec 12 07:47:26 2016 -0500
@@ -0,0 +1,41 @@
+# A simple tool to connect to the Ensembl server and retrieve feature
+# information using the Ensembl REST API.
+import json
+import optparse
+from urlparse import urljoin
+
+import requests
+
+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'])
+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