Update MapFastq.py

To escape the tab in the bwa conversion. djhn75#21 (comment) solved.
ny-shao · Mar 30, 2019 · e27b831 · e27b831
1 parent e79f9c3
commit e27b831
Showing 1 changed file with 3 additions and 3 deletions.
diff --git 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
+    del mapFastQ