class CallerCore: def __init__(self, readFile1, readFile2, contigFile, plotPath, readType, showPlot, regularPath, pathToBedTools): self.maxCovReg = [-1,-1,-1,-1] self.readFile_1 = readFile1; # Path to the first reads file. self.readFile_2 = readFile2; # Path to the second reads file. self.contigFile = contigFile; # Path to the contig file that resulted from the above two files. self.plotPath = plotPath; # Path for output plots. self.readType = int(readType); # readType='0' for single end, and '1' for paired end reads. self.showPlot = int(showPlot); # showPlot='0' if plots are not supposed to be displayed right away, otherwise showplot='1'. self.regularPath = regularPath; # regularPath is the path for output alignment files. self.pathToBedTools = pathToBedTools; # Path to BED tools. if os.path.isfile(self.readFile_1)!=True: print "[AN:] File "+str(self.readFile_1)+" doesn't exist. Exiting..." exit(-1) if os.path.isfile(self.readFile_2)!=True: print "[AN:] File "+str(self.readFile_2)+" doesn't exist. Exiting..." exit(-1) if os.path.isfile(self.contigFile)!=True: print "[AN:] File "+str(self.contigFile)+" doesn't exist. Exiting..." exit(-1) def doBWA(self): self.bwa = BWACaller(self.readType, self.contigFile, self.readFile_1, self.readFile_2, self.regularPath) self.bwa.calculateIndex() self.bwa.align() if self.readType == 1: self.bwa.doSamsa() else: self.bwa.doSampe() def doSAM(self): print "[AN:] Getting basic alignment stats..." self.samtools = SAMTools(self.regularPath) self.samtools.execute() def doBAM(self): self.bedtools = BEDTools(self.regularPath, self.pathToBedTools) #change this ! self.bedtools.compute() def doCoverageStats(self): print "[AN:] Getting basic coverage stats..." coverage_stats = Coverage() coverage_stats.getContigData(self.contigFile) coverage_stats.getAlignmentData(self.regularPath+"test.bam.cov") coverage_stats.getCoveragePerContig() potCollaps = coverage_stats.getPotColapseRegions(4) self.maxCovReg = potCollaps[:] print "[AN:] Potential colapse regions because of high coverage:" for contig in potCollaps: print "\tContig ID:",contig[0],"\tcoverage:",contig[1] print "[AN:] Plotting coverage per contig..." coverage_stats.plotAllContigCov(self.plotPath, self.showPlot) print "[AN:] Done..." def getAllStats(self): return self.maxCovReg
def doBWA(self): self.bwa = BWACaller(self.readType, self.contigFile, self.readFile_1, self.readFile_2, self.regularPath) self.bwa.calculateIndex() self.bwa.align() if self.readType == 1: self.bwa.doSamsa() else: self.bwa.doSampe()
