diff ete_species_tree_generator.py @ 1:a4ba317fc713 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ete_species_tree_generator.py	Fri Mar 17 16:23:39 2017 -0400
@@ -0,0 +1,56 @@
+import optparse
+
+from ete3 import NCBITaxa
+
+ncbi = NCBITaxa()
+
+parser = optparse.OptionParser()
+parser.add_option('-s', '--species', dest="input_species_filename",
+                  help='Species list in text format one species in each line')
+
+parser.add_option('-f', '--format', type='choice', choices=['0', '1', '2', '3', '4', '5', '6', '7', '8', '9', '100'], dest="format",
+                  default='8', help='outpur format for tree')
+
+parser.add_option('-t', '--treebest', type='choice', choices=['yes', 'no'], dest="treebest",
+                  default='no', help='To be used in TreeBest')
+
+parser.add_option('-d', '--database', type='choice', choices=['yes', 'no'], dest="database",
+                  default='no', help='Update database')
+
+options, args = parser.parse_args()
+
+if options.database == "yes":
+    try:
+        ncbi.update_taxonomy_database()
+    except:
+        pass
+
+if options.input_species_filename is None:
+    raise Exception('-s option must be specified, Species list in text format one species in each line')
+
+with open(options.input_species_filename) as f:
+    species_name = [_.strip().replace('_', ' ') for _ in f.readlines()]
+
+name2taxid = ncbi.get_name_translator(species_name)
+
+taxid = [name2taxid[_][0] for _ in species_name]
+
+tree = ncbi.get_topology(taxid)
+
+if options.treebest == "yes":
+    inv_map = {str(v[0]): k.replace(" ", "") + "*" for k, v in name2taxid.items()}
+else:
+    inv_map = {str(v[0]): k for k, v in name2taxid.items()}
+
+
+for leaf in tree:
+    leaf.name = inv_map[leaf.name]
+
+newickTree = tree.write(format=int(options.format))
+
+if options.treebest == "yes":
+    newickTree = newickTree.rstrip(';')
+    newickTree = newickTree + "root;"
+
+with open('newickTree.nhx', 'w') as newickFile:
+    newickFile.write(newickTree)