From 1b0c05e257e8ad909f8bae4f7e3e01ca4fb7d84b Mon Sep 17 00:00:00 2001 From: Kelly Vincent Date: Thu, 24 Sep 2009 14:09:17 -0400 Subject: [PATCH] Modified solid to fastq converter tool to specify path to perl script that does conversion --- tools/next_gen_conversion/solid_to_fastq.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/next_gen_conversion/solid_to_fastq.py b/tools/next_gen_conversion/solid_to_fastq.py index c08c4d23c8b..90bc890b734 100644 --- a/tools/next_gen_conversion/solid_to_fastq.py +++ b/tools/next_gen_conversion/solid_to_fastq.py @@ -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))