def test_checkInputFile(self):
"""Test checkInputFile()."""
fastaFN = "{0}/data/ecoli.fasta".format(self.rootDir)
plsFN = "/home/UNIXHOME/yli/yliWorkspace/private/yli/" + \
"data/testLoadPulses/m121215_065521_richard_" + \
"c100425710150000001823055001121371_s1_p0.pls.h5"
self.assertTrue(filecmp.cmp(fastaFN, checkInputFile(fastaFN)))
self.assertTrue(filecmp.cmp(plsFN, checkInputFile(plsFN)))
fofnFN = "{0}/data/ecoli_lp.fofn".format(self.rootDir)
self.assertTrue(filecmp.cmp(fofnFN, checkInputFile(fofnFN)))
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)
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)
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(self.inputFileName)
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(self.inputFileName)
def test_checkInputFile(self):
"""Test checkInputFile()."""
fastaFN = path.join(self.rootDir, "data/ecoli.fasta")
plsFN = self.dataDir + \
"m121215_065521_richard_c100425710150000001823055001121371_s1_p0.pls.h5"
self.assertTrue(filecmp.cmp(fastaFN, checkInputFile(fastaFN)))
self.assertTrue(filecmp.cmp(plsFN, checkInputFile(plsFN)))
fofnFN = path.join(self.rootDir, "data/ecoli_lp.fofn")
self.assertTrue(filecmp.cmp(fofnFN, checkInputFile(fofnFN)))
xmlFN = path.join(self.rootDir, "data/subreads_dataset1.xml")
ret = checkInputFile(xmlFN)
self.assertTrue(ret.endswith('.xml'))
fs = DataSet(ret).toExternalFiles()
self.assertTrue(fs[0].endswith("m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.subreads.bam"))
self.assertTrue(fs[1].endswith("m130406_011850_42141_c100513442550000001823074308221310_s1_p0.1.subreads.bam"))
def test_checkInputFile(self):
"""Test checkInputFile()."""
fastaFN = path.join(self.rootDir, "data/ecoli.fasta")
plsFN = self.dataDir + \
"m121215_065521_richard_c100425710150000001823055001121371_s1_p0.pls.h5"
self.assertTrue(filecmp.cmp(fastaFN, checkInputFile(fastaFN)))
self.assertTrue(filecmp.cmp(plsFN, checkInputFile(plsFN)))
fofnFN = path.join(self.rootDir, "data/ecoli_lp.fofn")
self.assertTrue(filecmp.cmp(fofnFN, checkInputFile(fofnFN)))
xmlFN = path.join(self.rootDir, "data/subreads_dataset1.xml")
ret = checkInputFile(xmlFN)
self.assertTrue(ret.endswith('.xml'))
fs = DataSet(ret).toExternalFiles()
self.assertTrue(fs[0].endswith(
"m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.subreads.bam"
))
self.assertTrue(fs[1].endswith(
"m130406_011850_42141_c100513442550000001823074308221310_s1_p0.1.subreads.bam"
))