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 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(self.fileNames).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
class Constants(object):
TOOL_ID = "pbalign.tasks.pbalign"
INPUT_FILE_TYPE = FileTypes.DS_SUBREADS
OUTPUT_FILE_TYPE = FileTypes.DS_ALIGN
OUTPUT_FILE_NAME = "mapped"
ALGORITHM_OPTIONS_ID = "pbalign.task_options.algorithm_options"
ALGORITHM_OPTIONS_DEFAULT = "--minMatch 12 --bestn 10 --minPctSimilarity 70.0"
MIN_ACCURACY_ID = "pbalign.task_options.min_accuracy"
MIN_LENGTH_ID = "pbalign.task_options.min_length"
NO_SPLIT_ID = "pbalign.task_options.no_split_subreads"
CONCORDANT_ID = "pbalign.task_options.concordant"
HIT_POLICY_ID = "pbalign.task_options.hit_policy"
DRIVER_EXE = "pbalign --resolved-tool-contract "
VERSION = get_version()
PARSER_DESC = """\
def getVersion(self):
"""Return version."""
return get_version()
def getVersion(self):
"""Return version."""
return get_version()
def run(self):
"""
The main function, it is called by PBToolRunner.start().
"""
startTime = time.time()
logging.info("pbalign version: {version}".format(version=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.
try:
self._alnService.run()
except RuntimeError:
return 1
# Create a temporary filtered SAM file as output for FilterService.
self.fileNames.filteredSam = self._tempFileManager.\
RegisterNewTmpFile(suffix=".sam")
# Call filter service.
self._filterService = FilterService(self.fileNames.alignerSamOut,
self.fileNames.targetFileName,
self.fileNames.filteredSam,
self._alnService.name,
self._alnService.scoreSign,
self.args,
self.fileNames.adapterGffFileName)
try:
self._filterService.run()
except RuntimeError:
return 1
# Output all hits either in SAM or CMP.H5.
try:
useSmrtTitle = False
if (self.args.algorithm != "blasr" or
self.fileNames.inputFileFormat == FILE_FORMATS.FASTA):
useSmrtTitle = True
self._output(
self.fileNames.filteredSam,
self.fileNames.targetFileName,
self.fileNames.outputFileName,
self.args.readType,
useSmrtTitle)
except RuntimeError:
return 1
# Call post service for quiver.
if self.args.forQuiver or self.args.loadQVs:
postService = ForQuiverService(self.fileNames,
self.args)
try:
postService.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
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