diff 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_genetree/get_genetree.py	Thu Aug 11 14:29:07 2016 -0400
@@ -0,0 +1,58 @@
+# 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