|
-
+
diff --git a/tools/metag_tools/split_paired_reads.py b/tools/metag_tools/split_paired_reads.py
index f2e4039e5a6..f2b01bc7b35 100644
--- a/tools/metag_tools/split_paired_reads.py
+++ b/tools/metag_tools/split_paired_reads.py
@@ -1,7 +1,7 @@
#! /usr/bin/python
"""
-Split Solexa paired end reads
+Split fixed length paired end reads
"""
import os, sys
@@ -12,9 +12,13 @@ if __name__ == '__main__':
outfile_end1 = open(sys.argv[2], 'w')
outfile_end2 = open(sys.argv[3], 'w')
- for i, line in enumerate(file(infile)):
+ i = 0
+
+ for line in file( infile ):
line = line.rstrip()
- if not line or line.startswith('#'): continue
+
+ if not line:
+ continue
end1 = ''
end2 = ''
@@ -42,5 +46,9 @@ if __name__ == '__main__':
outfile_end1.write('%s\n' %(end1))
outfile_end2.write('%s\n' %(end2))
+ i += 1
+
+ if i % 4 != 0 :
+ sys.stderr.write("WARNING: Number of lines in the input file was not divisible by 4.\nCheck consistency of the input fastq file.\n")
outfile_end1.close()
outfile_end2.close()
\ No newline at end of file
diff --git a/tools/solid_tools/maq_cs_wrapper.py b/tools/solid_tools/maq_cs_wrapper.py
index 82f29270975..e0c305dd9eb 100644
--- a/tools/solid_tools/maq_cs_wrapper.py
+++ b/tools/solid_tools/maq_cs_wrapper.py
@@ -48,9 +48,9 @@ def __main__():
cmd1 = "solid2fastq_modified.pl 'yes' %s %s %s %s %s %s %s 2>&1" %(tmpf.name,tmpr.name,tmps.name,f3_read_fname,f3_qual_fname,r3_read_fname,r3_qual_fname)
try:
os.system(cmd1)
- os.system('zcat -f %s >> %s' %(tmpf.name,tmpffastq.name))
- os.system('zcat -f %s >> %s' %(tmpr.name,tmprfastq.name))
- os.system('zcat -f %s >> %s' %(tmps.name,tmpsfastq.name))
+ os.system('gunzip -c %s >> %s' %(tmpf.name,tmpffastq.name))
+ os.system('gunzip -c %s >> %s' %(tmpr.name,tmprfastq.name))
+ os.system('gunzip -c %s >> %s' %(tmps.name,tmpsfastq.name))
except Exception, eq:
stop_err("Error converting data to fastq format." + str(eq))
@@ -135,7 +135,7 @@ def __main__():
cmd1 = "solid2fastq_modified.pl 'no' %s %s %s %s %s %s %s 2>&1" %(tmpf.name,None,None,f3_read_fname,f3_qual_fname,None,None)
try:
os.system(cmd1)
- os.system('zcat -f %s >> %s' %(tmpf.name,tmpfastq.name))
+ os.system('gunzip -c %s >> %s' %(tmpf.name,tmpfastq.name))
tmpf.close()
except:
stop_err("Error converting data to fastq format.")
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