def SetOutputFileName(self, outputFileName):
"""Validate the user-specified output file and get the absolute and
expanded path. If output file format is XML or BAM, set output BAM
filename, BAM index bai file and PacBio BAM index pbi file.
"""
if outputFileName is not None and outputFileName != "":
self.outputFileName = checkOutputFile(outputFileName)
if getFileFormat(self.outputFileName) in [FILE_FORMATS.BAM,
FILE_FORMATS.XML]:
prefix = str(self.outputFileName[0:-3])
self.outBamFileName = prefix + "bam"
self.outBaiFileName = self.outBamFileName + ".bai"
self.outPbiFileName = self.outBamFileName + ".pbi"
def SetOutputFileName(self, outputFileName):
"""Validate the user-specified output file and get the absolute and
expanded path. If output file format is XML or BAM, set output BAM
filename, BAM index bai file and PacBio BAM index pbi file.
"""
if outputFileName is not None and outputFileName != "":
self.outputFileName = checkOutputFile(outputFileName)
if getFileFormat(self.outputFileName) in [FILE_FORMATS.BAM,
FILE_FORMATS.XML]:
prefix = str(self.outputFileName[0:-3])
self.outBamFileName = prefix + "bam"
self.outBaiFileName = self.outBamFileName + ".bai"
self.outPbiFileName = self.outBamFileName + ".pbi"
def test_checkOutputFile(self):
"""Test checkOutputFile()."""
samFN = "{0}/out/lambda_out.sam".format(self.rootDir)
cmpFN = "{0}/out/lambda_out.cmp.h5".format(self.rootDir)
self.assertTrue(filecmp.cmp(samFN, checkOutputFile(samFN)))
self.assertTrue(filecmp.cmp(cmpFN, checkOutputFile(cmpFN)))
def test_checkOutputFile(self):
"""Test checkOutputFile()."""
samFN = path.join(self.outDir, "lambda_out.sam")
cmpFN = path.join(self.outDir, "lambda_out.cmp.h5")
self.assertTrue(filecmp.cmp(samFN, checkOutputFile(samFN)))
self.assertTrue(filecmp.cmp(cmpFN, checkOutputFile(cmpFN)))
def test_checkOutputFile(self):
"""Test checkOutputFile()."""
samFN = path.join(self.outDir, "lambda_out.sam")
cmpFN = path.join(self.outDir, "lambda_out.cmp.h5")
self.assertTrue(filecmp.cmp(samFN, checkOutputFile(samFN)))
self.assertTrue(filecmp.cmp(cmpFN, checkOutputFile(cmpFN)))
def SetOutputFileName(self, outputFileName):
"""Validate the user-specified output file and get the absolute and
expanded path.
"""
if outputFileName is not None and outputFileName != "":
self.outputFileName = checkOutputFile(outputFileName)