| --- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457 +0200 |
| +++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701 +0200 |
| @@ -1,7 +1,7 @@ |
| #pipeline script for assembly + Bambus 2 |
| #contributed by Todd J Treangen |
| |
| -import string, sys, os, subprocess#, spincursor |
| +import sys, os, subprocess#, spincursor |
| |
| RED = "\033[0;31m" |
| GREEN = "\033[0;32m" |
| @@ -360,7 +360,7 @@ |
| print "\t\t%s...failed%s"%(RED,NONE) |
| sys.exit(1) |
| |
| - p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) |
| + p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) |
| |
| if xopt_dict["verbose"] == 1: |
| print "10) running OutputResults" |
| @@ -388,4 +388,3 @@ |
| else: |
| print "\t\t%s...failed%s"%(RED,NONE) |
| sys.exit(1) |
| -) |
