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)
