def __init__(self, bowtieOutputFile, alignedReadsFile): self.numberRegularExpression = re.compile("\d+") self.bowtieOutputFile = safeOpenFile( bowtieOutputFile, "r", "Error: no bowtie output file for translation found. Terminated.") self.alignedReadsFile = safeOpenFile( alignedReadsFile, "w", "Error: file can not be created. Terminated.")
def __init__(self, originalReadsFile, alignedReadsFile, correctedReadsFile, failedToAlignReadsFile, reportFile): # #overall reads counts (might be slow) # self.alignedReadsCount = fileLinesCount(alignedReadsFile) / 4 # self.failedToAlignReadsCount = fileLinesCount(failedToAlignReadsFile) / 4 # self.originalReadsCount = fileLinesCount(originalReadsFile) / 4 # file handlers self.originalReadsFile = safeOpenFile( originalReadsFile, "Comparator error: no file with original reads found. Terminated." ) self.alignedReadsFile = safeOpenFile( alignedReadsFile, "Comparator error: no file with aligned reads found. Terminated." ) self.correctedReadsFile = safeOpenFile( correctedReadsFile, "Comparator error: no file with corrected reads found. Terminated." ) self.failedToAlignReadsFile = safeOpenFile( failedToAlignReadsFile, "Comparator error: no file with reads failed to align found. Terminated." ) self.reportFile = open(reportFile, "w") # constants self.readLength = self.defineReadLength() # temporary self.alignedReadsCache = {} self.failedToAlignReadsCache = {} # report self.notAlignedReadsCount = 0 self.notFoundInAlignedReadsCount = 0 self.notFoundInOriginalReadsCount = 0 self.processedReadsCount = 0 self.correctedAndTrimmedReadsCount = 0 # corrected and trimmed self.correctedOnlyReadsCount = 0 self.trimmedOnlyReadsCount = 0 self.wronglyCorrectedNucleotidesQualities = numpy.zeros((127,), dtype=numpy.int32) self.wronglyUncorrectedNucleotidesQualities = numpy.zeros((127,), dtype=numpy.int32) self.finelyCorrectedNucleotidesQualities = numpy.zeros((127,), dtype=numpy.int32) self.shouldNotHaveBeenCorrectedNucleotidesQualities = numpy.zeros((127,), dtype=numpy.int32) self.wronglyTrimmedNucleotidesQualities = numpy.zeros((127,), dtype=numpy.int32) self.finelyTrimmedNucleotidesQualities = numpy.zeros((127,), dtype=numpy.int32)
def __init__(self, originalReadsFile, alignedReadsFile, correctedReadsFile, failedToAlignReadsFile, reportDir, reportTotal, noSmartGraphics): if reportDir[-1] == "/": self.reportDir = reportDir else: self.reportDir = reportDir + "/" if reportTotal: #overall reads counts (might be slow) self.alignedReadsCount = fileLinesCount(alignedReadsFile) / 4 self.failedToAlignReadsCount = fileLinesCount( failedToAlignReadsFile) / 4 self.originalReadsCount = fileLinesCount(originalReadsFile) / 4 self.noSmartGraphics = noSmartGraphics #file handlers self.originalReadsFile = safeOpenFile( originalReadsFile, "r", "Comparator error: no file with original reads found. Terminated.") self.alignedReadsFile = safeOpenFile( alignedReadsFile, "r", "Comparator error: no file with aligned reads found. Terminated.") self.correctedReadsFile = safeOpenFile( correctedReadsFile, "r", "Comparator error: no file with corrected reads found. Terminated." ) self.failedToAlignReadsFile = safeOpenFile( failedToAlignReadsFile, "r", "Comparator error: no file with reads failed to align found. Terminated." ) self.reportFile = safeOpenFile( self.reportDir + "report", "w", "Error: file can not be created. Terminated.") #constants self.readLength = self.defineReadLength() #temporary self.alignedReadsCache = {} self.failedToAlignReadsCache = {} #report self.notAlignedReadsCount = 0 self.notFoundInAlignedReadsCount = 0 self.notFoundInOriginalReadsCount = 0 self.processedReadsCount = 0 self.correctedAndTrimmedReadsCount = 0 #corrected and trimmed self.correctedOnlyReadsCount = 0 self.trimmedOnlyReadsCount = 0 self.wronglyCorrectedNucleotidesQualities = numpy.zeros( (127, ), dtype=numpy.int32) self.wronglyUncorrectedNucleotidesQualities = numpy.zeros( (127, ), dtype=numpy.int32) self.finelyCorrectedNucleotidesQualities = numpy.zeros( (127, ), dtype=numpy.int32) self.shouldNotHaveBeenCorrectedNucleotidesQualities = numpy.zeros( (127, ), dtype=numpy.int32) self.wronglyTrimmedNucleotidesQualities = numpy.zeros( (127, ), dtype=numpy.int32) self.finelyTrimmedNucleotidesQualities = numpy.zeros((127, ), dtype=numpy.int32)
def __init__(self, rawAlignedReadsFile, alignedReadsFile): self.numberRegularExpression = re.compile("\d+") self.inputFile = safeOpenFile( rawAlignedReadsFile, "Translator error: no input file for translation found. Terminated." ) self.outputFile = open(alignedReadsFile, "w")