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providing a starting tree skips first tree building step #29

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merged 1 commit into from
May 29, 2012
Merged

providing a starting tree skips first tree building step #29

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17 changes: 14 additions & 3 deletions run_gubbins.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
from array import *
from Bio import SeqIO
from cStringIO import StringIO
import shutil


# config variables
Expand Down Expand Up @@ -106,7 +107,11 @@ def fasttree_tree_building_command(i, starting_tree, current_tree_name,starting_
def fasttree_gubbins_command(base_filename,starting_base_filename, i,alignment_filename,gubbins_exec,min_snps):
current_tree_name = fasttree_current_tree_name(base_filename, i)
return gubbins_exec+" -r -v "+starting_base_filename+".vcf -t "+str(current_tree_name)+" -p "+starting_base_filename+".phylip -m "+ str(min_snps)+" "+ alignment_filename


def starting_tree_gubbins_command(base_filename,starting_base_filename, i,alignment_filename,gubbins_exec,min_snps,starting_tree):
return gubbins_exec+" -r -v "+starting_base_filename+".vcf -t "+str(starting_tree)+" -p "+starting_base_filename+".phylip -m "+ str(min_snps)+" "+ alignment_filename


def number_of_sequences_in_alignment(filename):
return len(get_sequence_names_from_alignment(filename))

Expand Down Expand Up @@ -197,7 +202,7 @@ def is_exe(fpath):
current_tree_name = ""

for i in range(1, args.iterations+1):

if args.tree_builder == "hybrid" :
if i == 1:
previous_tree_name = fasttree_previous_tree_name(base_filename, i)
Expand Down Expand Up @@ -233,7 +238,13 @@ def is_exe(fpath):

if args.verbose > 0:
print tree_building_command
subprocess.call(tree_building_command, shell=True)


if args.starting_tree is not None and i == 1:
copyfile(args.starting_tree, current_tree_name)
else:
subprocess.call(tree_building_command, shell=True)

if args.verbose > 0:
print int(time.time())

Expand Down