def run(self):
"""
The main function, it is called by PBToolRunner.start().
"""
startTime = time.time()
logging.info("pbalign version: %s", get_version())
#logging.debug("Original arguments: " + str(self._argumentList))
# Create an AlignService by algorithm name.
self._alnService = self._createAlignService(self.args.algorithm,
self.args, self.fileNames,
self._tempFileManager)
# Make sane.
self._makeSane(self.args, self.fileNames)
# Run align service.
self._alnService.run()
# Create a temporary filtered SAM/BAM file as output for FilterService.
outFormat = getFileFormat(self.fileNames.outputFileName)
suffix = ".bam" if outFormat in \
[FILE_FORMATS.BAM, FILE_FORMATS.XML] else ".sam"
self.fileNames.filteredSam = self._tempFileManager.\
RegisterNewTmpFile(suffix=suffix)
# Call filter service on SAM or BAM file.
self._filterService = FilterService(
self.fileNames.alignerSamOut,
self.fileNames.targetFileName,
self.fileNames.filteredSam,
self.args.algorithm,
#self._alnService.name,
self._alnService.scoreSign,
self.args,
self.fileNames.adapterGffFileName)
self._filterService.run()
# Sort bam before output
if outFormat in [FILE_FORMATS.BAM, FILE_FORMATS.XML]:
# Sort/make index for BAM output.
BamPostService(filenames=self.fileNames,
nproc=self.args.nproc).run()
# Output all hits in SAM, BAM.
self._output(inSam=self.fileNames.filteredSam,
refFile=self.fileNames.targetFileName,
outFile=self.fileNames.outputFileName,
readType=self.args.readType)
# Delete temporay files anyway to make
self._cleanUp(False if (hasattr(self.args, "keepTmpFiles")
and self.args.keepTmpFiles is True) else True)
endTime = time.time()
logging.info("Total time: {:.2f} s.".format(float(endTime -
startTime)))
return 0
def test_run(self):
"""Test FilterService.run()."""
options = Opt(30, 70, 50, 1, None, "random")
obj = FilterService(self.alignedSam, self.targetFileName,
self.filteredSam, "BlasrService", -1, options)
_output, errCode, _errMsg = obj.run()
self.assertEqual(errCode, 0)
def test_init(self):
"""Test FilterService.__init__()."""
options = Opt(30, 70, 50, 1, None, "random")
obj = FilterService(self.alignedSam, self.targetFileName,
self.filteredSam, "BlasrService", -1, options)
self.assertTrue(obj.availability) # samFilter should be available
self.assertIn("-minPctSimilarity 70", obj.cmd)
self.assertIn("-minAccuracy 70", obj.cmd)
self.assertIn("-scoreSign -1", obj.cmd)
def test_run_without_scoreCutoff(self):
"""Test FilterService.run() without score cutoff."""
options2 = Opt(40, 50, None, None, None, "allbest")
obj2 = FilterService(self.alignedSam, self.targetFileName,
self.filteredSam, "BowtieService", 1, options2)
self.assertNotIn("-seed", obj2.cmd)
self.assertNotIn("-scoreCutoff", obj2.cmd)
self.assertIn("-scoreSign 1", obj2.cmd)
_output, errCode, _errMsg = obj2.run()
self.assertEqual(errCode, 0)
def run(self):
"""
The main function, it is called by PBToolRunner.start().
"""
startTime = time.time()
logging.info(
"pbalign version: {version}".format(version=get_version()))
# FIXME
#logging.debug("Original arguments: " + str(self._argumentList))
# Create an AlignService by algorithm name.
self._alnService = self._createAlignService(self.args.algorithm,
self.args, self.fileNames,
self._tempFileManager)
# Make sane.
self._makeSane(self.args, self.fileNames)
# Run align service.
try:
self._alnService.run()
except RuntimeError:
return 1
# Create a temporary filtered SAM/BAM file as output for FilterService.
outFormat = getFileFormat(self.fileNames.outputFileName)
suffix = ".bam" if outFormat in \
[FILE_FORMATS.BAM, FILE_FORMATS.XML] else ".sam"
self.fileNames.filteredSam = self._tempFileManager.\
RegisterNewTmpFile(suffix=suffix)
# Call filter service on SAM or BAM file.
self._filterService = FilterService(
self.fileNames.alignerSamOut,
self.fileNames.targetFileName,
self.fileNames.filteredSam,
self.args.algorithm,
#self._alnService.name,
self._alnService.scoreSign,
self.args,
self.fileNames.adapterGffFileName)
try:
self._filterService.run()
except RuntimeError:
return 1
# Sort bam before output
if outFormat in [FILE_FORMATS.BAM, FILE_FORMATS.XML]:
# Sort/make index for BAM output.
try:
BamPostService(self.fileNames).run()
except RuntimeError:
return 1
# Output all hits in SAM, BAM or CMP.H5.
try:
useSmrtTitle = False
if (self.args.algorithm != "blasr"
or self.fileNames.inputFileFormat == FILE_FORMATS.FASTA):
useSmrtTitle = True
self._output(inSam=self.fileNames.filteredSam,
refFile=self.fileNames.targetFileName,
outFile=self.fileNames.outputFileName,
readType=self.args.readType,
smrtTitle=useSmrtTitle)
except RuntimeError:
return 1
# Load QVs to cmp.h5 for Quiver
if outFormat == FILE_FORMATS.CMP and \
self.args.forQuiver or self.args.loadQVs:
# Call post service for quiver.
try:
ForQuiverService(self.fileNames, self.args).run()
except RuntimeError:
return 1
# Delete temporay files anyway to make
self._cleanUp(False if (hasattr(self.args, "keepTmpFiles")
and self.args.keepTmpFiles is True) else True)
endTime = time.time()
logging.info("Total time: {:.2f} s.".format(float(endTime -
startTime)))
return 0
