--- a/get_genetree.py	Tue Oct 20 15:07:23 2020 +0000
+++ b/get_genetree.py	Mon Feb 17 14:49:24 2025 +0000
@@ -1,54 +1,93 @@
 # A simple tool to connect to the Ensembl server and retrieve genetree using
 # the Ensembl REST API.
-from __future__ import print_function
-
 import optparse
+from urllib.parse import urljoin
 
 import requests
-from six.moves.urllib.parse import urljoin
 
 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(
+    "--id_type",
+    type="choice",
+    default="gene_id",
+    choices=["gene_id", "gene_tree_id"],
+    help="Input type",
+)
+parser.add_option("--species", help="Species name/alias")
+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('-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')
+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')
+    raise Exception("-i option must be specified")
 
-server = 'https://rest.ensembl.org'
+server = "https://rest.ensembl.org"
 
-if options.id_type == 'gene_id':
-    ext = 'genetree/member/id'
-elif options.id_type == 'gene_tree_id':
-    ext = 'genetree/id'
+if options.id_type == "gene_id":
+    ext = f"genetree/member/id/{options.species}/{options.input}"
+elif options.id_type == "gene_tree_id":
+    ext = f"genetree/id/{options.input}"
 
-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 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 = {
+    k: getattr(options, k) for k in ("sequence", "aligned", "cigar_line", "nh_format")
+}
+r = requests.get(urljoin(server, ext), params=params, headers=headers)
 
 if not r.ok:
     r.raise_for_status()