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Modified solid to fastq converter tool to specify path to perl script that does conversion

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This commit is contained in:
Kelly Vincent
2009-09-24 14:09:17 -04:00
parent 52b8b0b667
commit 1b0c05e257
1 changed files with 2 additions and 2 deletions
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tools/next_gen_conversion/solid_to_fastq.py
+2 -2
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@@ -30,7 +30,7 @@ def __main__():
tmpf = tempfile.NamedTemporaryFile() #forward reads
if options.input3 != "None" and options.input4 != "None":
tmpr = tempfile.NamedTemporaryFile() #reverse reads
cmd1 = "bwa_solid2fastq_modified.pl 'yes' %s %s %s %s %s %s %s 2>&1" %(tmpf.name,tmpr.name,None,options.input1,options.input2,options.input3,options.input4)
cmd1 = "%s/bwa_solid2fastq_modified.pl 'yes' %s %s %s %s %s %s %s 2>&1" %(os.path.split(sys.argv[0])[0], tmpf.name,tmpr.name,None,options.input1,options.input2,options.input3,options.input4)
try:
os.system(cmd1)
os.system('gunzip -c %s >> %s' %(tmpf.name,options.output1))
@@ -40,7 +40,7 @@ def __main__():
tmpr.close()
# if single-end data
else:
cmd1 = "bwa_solid2fastq_modified.pl 'no' %s %s %s %s %s %s %s 2>&1" % (tmpf.name, None, None, options.input1, options.input2, None, None)
cmd1 = "%s/bwa_solid2fastq_modified.pl 'no' %s %s %s %s %s %s %s 2>&1" % (os.path.split(sys.argv[0])[0], tmpf.name, None, None, options.input1, options.input2, None, None)
try:
os.system(cmd1)
os.system('gunzip -c %s >> %s' % (tmpf.name, options.output1))