def SetInputFile(self, inputFileName): """Verify and assign input file name and input file format.""" # Validate the user-specified input PacBio read file and get # the absolute and expanded path. Validate file format. if inputFileName is not None and inputFileName != "": self.inputFileName = checkInputFile(inputFileName) self.inputFileFormat = getRealFileFormat(inputFileName)
def SetPulseFileName(self, inputFileName, pulseFileName): """Verify and assign the pulse file from which pulses can be extracted. When inputFileName is a Base/Pulse/CCS.H5 file or a fofn of Base/Pulse/CCS.H5, pulse file is inputFileName. Otherwise, pulse file is pulseFileName.""" self.pulseFileName = None if inputFileName is not None and inputFileName != "": inputFormat = getRealFileFormat(inputFileName) if inputFormat in [FILE_FORMATS.BAS, FILE_FORMATS.BAX, FILE_FORMATS.PLS, FILE_FORMATS.PLX, FILE_FORMATS.CCS]: self.pulseFileName = checkInputFile(inputFileName) if self.pulseFileName is None: if pulseFileName is not None and pulseFileName != "": self.pulseFileName = checkInputFile(pulseFileName)