gentoo-overlay/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch

--- 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)
-)