Merge pull request #15 from andrewjpage/master

provide alignment filename not full path for fastree
nickjcroucher · May 8, 2012 · 91ca0c6 · 91ca0c6
2 parents 22698ec + 58e7a2d
commit 91ca0c6
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/run_gubbins.py b/run_gubbins.py
@@ -166,7 +166,7 @@ def create_pairwise_newick_tree(sequence_names, output_filename):
  if i == 1:
  previous_tree_name = fasttree_previous_tree_name(base_filename, i)
  current_tree_name = fasttree_current_tree_name(base_filename, i)
- tree_building_command = fasttree_tree_building_command(i, args.starting_tree,current_tree_name,args.alignment_filename,previous_tree_name,FASTTREE_EXEC,FASTTREE_PARAMS )
+ tree_building_command = fasttree_tree_building_command(i, args.starting_tree,current_tree_name,base_filename,previous_tree_name,FASTTREE_EXEC,FASTTREE_PARAMS )
  gubbins_command = fasttree_gubbins_command(base_filename,starting_base_filename, i,args.alignment_filename,GUBBINS_EXEC)
 
  elif i == 2:
@@ -194,7 +194,7 @@ def create_pairwise_newick_tree(sequence_names, output_filename):
  os.rename(base_filename+".vcf", previous_tree_name+".vcf")
  os.rename(base_filename+".phylip", previous_tree_name+".phylip")
  os.rename(base_filename+".snp_sites.aln", previous_tree_name+".snp_sites.aln")
- tree_building_command = fasttree_tree_building_command(i, args.starting_tree,current_tree_name,args.alignment_filename,previous_tree_name,FASTTREE_EXEC,FASTTREE_PARAMS )
+ tree_building_command = fasttree_tree_building_command(i, args.starting_tree,current_tree_name,base_filename,previous_tree_name,FASTTREE_EXEC,FASTTREE_PARAMS )
  gubbins_command = fasttree_gubbins_command(base_filename,starting_base_filename, i,args.alignment_filename,GUBBINS_EXEC)
 
  if args.verbose > 0: