Merge pull request #16 from andrewjpage/master

speedup phylip file writing

run_gubbins.py

@@ -133,7 +133,7 @@ def create_pairwise_newick_tree(sequence_names, output_filename):
 parser.add_argument('--outgroup', '-o', help='Outgroup name for rerooting')
 parser.add_argument('--starting_tree', '-s', help='Starting tree')
 parser.add_argument('--verbose', '-v', action='count', help='Turn on debugging')
-parser.add_argument('--tree_builder', '-t', help='Application to use for tree building (raxml, fasttree), default is to use FastTree for 1st iteration and RAxML for rest', default = "hybrid")
+parser.add_argument('--tree_builder', '-t', help='Application to use for tree building (raxml, fasttree, hybrid), default RAxML', default = "raxml")
 parser.add_argument('--iterations', '-i', help='Maximum No. of iterations, default is 5', type=int, default = 5)
 args = parser.parse_args()
 
@@ -202,7 +202,11 @@ def create_pairwise_newick_tree(sequence_names, output_filename):
  subprocess.call(tree_building_command, shell=True)
 
  reroot_tree(str(current_tree_name), args.outgroup)
-
+
+ if(os.path.exists("latest.tre")):
+ remove("latest.tre")
+ os.symlink(str(current_tree_name), "latest.tre")
+
  if args.verbose > 0:
  print gubbins_command
  subprocess.call(gubbins_command, shell=True)