From e27b8312cd43d84b086891183d71e9fe4cdd0b10 Mon Sep 17 00:00:00 2001 From: Ning-Yi SHAO Date: Sat, 30 Mar 2019 16:34:40 -0700 Subject: [PATCH] Update MapFastq.py To escape the tab in the bwa conversion. https://github.com/djhn75/RNAEditor/issues/21#issue-393698423 solved. --- MapFastq.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/MapFastq.py b/MapFastq.py index 25b9da8..cf9a012 100755 --- a/MapFastq.py +++ b/MapFastq.py @@ -92,7 +92,7 @@ def startAnalysis(self): #convert sai to sam samFile=self.rnaEdit.params.output+".sam" - cmd = [self.rnaEdit.params.sourceDir + "bwa", "sampe", "-r", "@RG\tID:bwa\tSM:A\tPL:ILLUMINA\tPU:HiSEQ2000", self.rnaEdit.params.refGenome, saiFile1, saiFile2, self.fastqFile1, self.fastqFile2] + cmd = [self.rnaEdit.params.sourceDir + "bwa", "sampe", "-r", "@RG\\tID:bwa\\tSM:A\\tPL:ILLUMINA\\tPU:HiSEQ2000", self.rnaEdit.params.refGenome, saiFile1, saiFile2, self.fastqFile1, self.fastqFile2] Helper.proceedCommand("convert sai to sam", cmd, saiFile1, samFile, self.rnaEdit) elif self.rnaEdit.params.paired == False: #For single end sequencing #Align Fastq Reads to the Genome @@ -103,7 +103,7 @@ def startAnalysis(self): #convert sai to sam samFile=self.rnaEdit.params.output+".sam" - cmd = [self.rnaEdit.params.sourceDir + "bwa", "samse", "-r", "@RG\tID:bwa\tSM:A\tPL:ILLUMINA\tPU:HiSEQ2000", self.rnaEdit.params.refGenome, saiFile, self.fastqFile] + cmd = [self.rnaEdit.params.sourceDir + "bwa", "samse", "-r", "@RG\\tID:bwa\\tSM:A\\tPL:ILLUMINA\\tPU:HiSEQ2000", self.rnaEdit.params.refGenome, saiFile, self.fastqFile] #cmd = [self.rnaEdit.params.sourceDir + "bwa", "samse", self.rnaEdit.params.refGenome, saiFile, self.fastqFile] Helper.proceedCommand("convert sai to sam", cmd, saiFile, samFile, self.rnaEdit) @@ -315,4 +315,4 @@ def checkDependencies(args): mapFastQ=MapFastq(args.input, args.RefGenome.name, args.dbsnp.name,args.output, args.sourceDir, args.threads, args.maxDiff, args.seedDiff, args.paired, args.keepTemp, args.overwrite) mapFastQ.startAnalysis() - del mapFastQ \ No newline at end of file + del mapFastQ