def validateAndSanitizeExistingOptions(self,options) :
options.normalBam=validateFixExistingFileArg(options.normalBam,"normal sample BAM file")
options.tumorBam=validateFixExistingFileArg(options.tumorBam,"tumor sample BAM file")
# check for bam index files:
for bam in (options.tumorBam,options.normalBam) :
if bam is None : continue
baiFile=bam+".bai"
if not os.path.isfile(baiFile) :
raise OptParseException("Can't find expected BAM index file: '%s'" % (baiFile))
# check alignerMode:
if options.alignerMode is not None :
options.alignerMode = options.alignerMode.lower()
if options.alignerMode not in self.validAlignerModes :
raise OptParseException("Invalid aligner mode: '%s'" % options.alignerMode)
options.referenceFasta=validateFixExistingFileArg(options.referenceFasta,"reference")
# check for reference fasta index file:
if options.referenceFasta is not None :
faiFile=options.referenceFasta + ".fai"
if not os.path.isfile(faiFile) :
raise OptParseException("Can't find expected fasta index file: '%s'" % (faiFile))
MantaWorkflowOptionsBase.validateAndSanitizeExistingOptions(self,options)
def validateAndSanitizeOptions(self, options):
assertOptionExists(options.runDir, "run directory")
options.runDir = os.path.abspath(options.runDir)
assertOptionExists(options.referenceFasta, "reference fasta file")
options.referenceFasta = validateFixExistingFileArg(
options.referenceFasta, "reference fasta file")
# check for reference fasta index file:
referenceFastaIndex = options.referenceFasta + ".fai"
if not os.path.isfile(referenceFastaIndex):
raise OptParseException(
"Can't find expected fasta index file: '%s'" %
(referenceFastaIndex))
if options.isEstimateSequenceError:
# Determine if dynamic error estimation is feasible based on the reference size
# - Given reference contig set (S) with sequence length of at least 5 Mb
# - The total sequence length from S must be at least 50 Mb
class Constants:
Megabase = 1000000
minChromSize = options.errorEstimationMinChromMb * Megabase
minTotalSize = options.errorEstimationMinTotalMb * Megabase
# read fasta index
(_, chromSizes) = getFastaChromOrderSize(referenceFastaIndex)
totalEstimationSize = 0
for chromSize in chromSizes.values():
if chromSize < Constants.minChromSize: continue
totalEstimationSize += chromSize
if totalEstimationSize < Constants.minTotalSize:
sys.stderr.write(
"WARNING: Cannot estimate sequence errors from data due to small or overly fragmented reference sequence. Sequence error estimation disabled.\n"
)
options.isEstimateSequenceError = False
checkFixTabixListOption(options.indelCandidatesList,
"candidate indel vcf")
checkFixTabixListOption(options.forcedGTList, "forced genotype vcf")
options.callRegionsBed = checkFixTabixIndexedFileOption(
options.callRegionsBed, "call-regions bed")
if (options.regionStrList is None) or (len(options.regionStrList)
== 0):
options.genomeRegionList = None
else:
options.genomeRegionList = [
parseGenomeRegion(rr) for r in options.regionStrList
for rr in r.split("+")
]
options.snvScoringModelFile = validateFixExistingFileArg(
options.snvScoringModelFile, "SNV empirical scoring model file")
options.indelScoringModelFile = validateFixExistingFileArg(
options.indelScoringModelFile,
"Indel empirical scoring model file")
def validateAndSanitizeExistingOptions(self, options):
StrelkaSharedWorkflowOptionsBase.validateAndSanitizeExistingOptions(
self, options)
groomBamList(options.normalBamList, "normal sample")
groomBamList(options.tumorBamList, "tumor sample")
checkFixTabixListOption(options.noiseVcfList, "noise vcf")
options.somaticSnvScoringModelFile = validateFixExistingFileArg(
options.somaticSnvScoringModelFile,
"Somatic SNV empirical scoring file")
options.somaticIndelScoringModelFile = validateFixExistingFileArg(
options.somaticIndelScoringModelFile,
"Somatic indel empirical scoring file")
def validateAndSanitizeExistingOptions(self, options):
options.runDir = os.path.abspath(options.runDir)
options.referenceFasta = validateFixExistingFileArg(
options.referenceFasta, "reference")
# check for reference fasta index file:
if options.referenceFasta is not None:
faiFile = options.referenceFasta + ".fai"
if not os.path.isfile(faiFile):
raise OptParseException(
"Can't find expected fasta index file: '%s'" % (faiFile))
checkFixTabixListOption(options.indelCandidatesList,
"candidate indel vcf")
checkFixTabixListOption(options.forcedGTList, "forced genotype vcf")
if (options.regionStrList is None) or (len(options.regionStrList)
== 0):
options.genomeRegionList = None
else:
options.genomeRegionList = [
parseGenomeRegion(rr) for r in options.regionStrList
for rr in r.split("+")
]
def validateAndSanitizeExistingOptions(self, options):
options.runDir = os.path.abspath(options.runDir)
# check alignerMode:
if options.alignerMode is not None:
options.alignerMode = options.alignerMode.lower()
if options.alignerMode not in self.validAlignerModes:
raise OptParseException("Invalid aligner mode: '%s'" %
options.alignerMode)
options.referenceFasta = validateFixExistingFileArg(
options.referenceFasta, "reference")
# check for reference fasta index file:
if options.referenceFasta is not None:
faiFile = options.referenceFasta + ".fai"
if not os.path.isfile(faiFile):
raise OptParseException(
"Can't find expected fasta index file: '%s'" % (faiFile))
# check for bed file of call regions and its index file
if options.callRegionsBed is not None:
options.callRegionsBed = os.path.abspath(options.callRegionsBed)
checkTabixIndexedFile(options.callRegionsBed, "call-regions bed")
if (options.regionStrList is None) or (len(options.regionStrList)
== 0):
options.genomeRegionList = None
else:
options.genomeRegionList = [
parseGenomeRegion(r) for r in options.regionStrList
]
def validateAndSanitizeOptions(self, options):
assertOptionExists(options.runDir, "run directory")
options.runDir = os.path.abspath(options.runDir)
workflowScriptPath = os.path.join(options.runDir,
options.workflowScriptName)
if os.path.exists(workflowScriptPath):
raise OptParseException(
"Run directory already contains workflow script file '%s'. Each analysis must be configured in a separate directory."
% (workflowScriptPath))
# check reference fasta file exists
assertOptionExists(options.referenceFasta, "reference fasta file")
options.referenceFasta = validateFixExistingFileArg(
options.referenceFasta, "reference")
# check for reference fasta index file:
faiFile = options.referenceFasta + ".fai"
if not os.path.isfile(faiFile):
raise OptParseException(
"Can't find expected fasta index file: '%s'" % (faiFile))
# check for bed file of call regions and its index file
options.callRegionsBed = checkFixTabixIndexedFileOption(
options.callRegionsBed, "call-regions bed")
if (options.regionStrList is None) or (len(options.regionStrList)
== 0):
options.genomeRegionList = None
else:
options.genomeRegionList = [
parseGenomeRegion(r) for r in options.regionStrList
]
# validate chromosome names appearing in region tags and callRegions bed file
if (options.callRegionsBed is not None) or (options.genomeRegionList
is not None):
refChromInfo = getFastaInfo(options.referenceFasta)
if options.callRegionsBed is not None:
for chrom in getTabixChromSet(options.tabixBin,
options.callRegionsBed):
if chrom not in refChromInfo:
raise OptParseException(
"Chromosome label '%s', in call regions bed file '%s', not found in reference genome."
% (chrom, options.callRegionsBed))
if options.genomeRegionList is not None:
for (genomeRegionIndex,
genomeRegion) in enumerate(options.genomeRegionList):
chrom = genomeRegion["chrom"]
if chrom not in refChromInfo:
raise OptParseException(
"Chromosome label '%s', parsed from region argument '%s', not found in reference genome."
%
(chrom, options.regionStrList[genomeRegionIndex]))
def validateAndSanitizeOptions(self, options):
MantaWorkflowOptionsBase.validateAndSanitizeOptions(self, options)
def safeLen(x):
if x is None: return 0
return len(x)
if ((safeLen(options.normalBamList) == 0)
and (safeLen(options.tumorBamList) == 0)):
raise OptParseException(
"No normal or tumor sample alignment files specified")
if (safeLen(options.tumorBamList) > 1):
raise OptParseException("Can't accept more then one tumor sample")
if ((safeLen(options.tumorBamList) > 0)
and (safeLen(options.normalBamList) > 1)):
raise OptParseException(
"Can't accept multiple normal samples for tumor subtraction")
if options.isRNA:
if ((safeLen(options.normalBamList) != 1)
or (safeLen(options.tumorBamList) != 0)):
raise OptParseException(
"RNA mode currently requires exactly one normal sample")
else:
if options.isUnstrandedRNA:
raise OptParseException(
"Unstranded only applied for RNA inputs")
if options.existingAlignStatsFile is not None:
options.existingAlignStatsFile = validateFixExistingFileArg(
options.existingAlignStatsFile, "existing align stats")
groomBamList(options.normalBamList, "normal sample")
groomBamList(options.tumorBamList, "tumor sample")
bamSetChecker = BamSetChecker()
if safeLen(options.normalBamList) > 0:
bamSetChecker.appendBams(options.normalBamList, "Normal")
if safeLen(options.tumorBamList) > 0:
bamSetChecker.appendBams(options.tumorBamList, "Tumor")
bamSetChecker.check(options.htsfileBin, options.referenceFasta)
def validateAndSanitizeExistingOptions(self, options):
def checkForBamIndex(bamFile):
baiFile = bamFile + ".bai"
if not os.path.isfile(baiFile):
raise OptParseException(
"Can't find expected BAM index file: '%s'" % (baiFile))
def groomBamList(bamList, sampleLabel):
if bamList is None: return
for (index, bamFile) in enumerate(bamList):
bamList[index] = validateFixExistingFileArg(
bamFile, "%s BAM file" % (sampleLabel))
checkForBamIndex(bamList[index])
groomBamList(options.normalBamList, "normal sample")
groomBamList(options.tumorBamList, "tumor sample")
# check alignerMode:
if options.alignerMode is not None:
options.alignerMode = options.alignerMode.lower()
if options.alignerMode not in self.validAlignerModes:
raise OptParseException("Invalid aligner mode: '%s'" %
options.alignerMode)
options.referenceFasta = validateFixExistingFileArg(
options.referenceFasta, "reference")
# check for reference fasta index file:
if options.referenceFasta is not None:
faiFile = options.referenceFasta + ".fai"
if not os.path.isfile(faiFile):
raise OptParseException(
"Can't find expected fasta index file: '%s'" % (faiFile))
if (options.regionStrList is None) or (len(options.regionStrList)
== 0):
options.genomeRegionList = None
else:
options.genomeRegionList = [
parseGenomeRegion(r) for r in options.regionStrList
]
MantaWorkflowOptionsBase.validateAndSanitizeExistingOptions(
self, options)
def validateAndSanitizeOptions(self,options) :
assertOptionExists(options.runDir,"run directory")
options.runDir = os.path.abspath(options.runDir)
workflowScriptPath = os.path.join(options.runDir, options.workflowScriptName)
if os.path.exists(workflowScriptPath):
raise OptParseException("Run directory already contains workflow script file '%s'. Each analysis must be configured in a separate directory." % (workflowScriptPath))
# check reference fasta file exists
assertOptionExists(options.referenceFasta,"reference fasta file")
options.referenceFasta=validateFixExistingFileArg(options.referenceFasta,"reference")
# check for reference fasta index file:
faiFile=options.referenceFasta + ".fai"
if not os.path.isfile(faiFile) :
raise OptParseException("Can't find expected fasta index file: '%s'" % (faiFile))
# check for bed file of call regions and its index file
options.callRegionsBed = checkFixTabixIndexedFileOption(options.callRegionsBed, "call-regions bed")
if (options.regionStrList is None) or (len(options.regionStrList) == 0) :
options.genomeRegionList = None
else :
options.genomeRegionList = [parseGenomeRegion(r) for r in options.regionStrList]
# validate chromosome names appearing in region tags and callRegions bed file
if (options.callRegionsBed is not None) or (options.genomeRegionList is not None) :
refChromInfo = getFastaInfo(options.referenceFasta)
if options.callRegionsBed is not None :
for chrom in getTabixChromSet(options.tabixBin, options.callRegionsBed) :
if chrom not in refChromInfo :
raise OptParseException("Chromosome label '%s', in call regions bed file '%s', not found in reference genome." %
(chrom, options.callRegionsBed))
if options.genomeRegionList is not None :
for (genomeRegionIndex, genomeRegion) in enumerate(options.genomeRegionList) :
chrom = genomeRegion["chrom"]
if chrom not in refChromInfo :
raise OptParseException("Chromosome label '%s', parsed from region argument '%s', not found in reference genome." %
(chrom, options.regionStrList[genomeRegionIndex]))
def validateAndSanitizeExistingOptions(self,options) :
options.runDir=os.path.abspath(options.runDir)
# check alignerMode:
if options.alignerMode is not None :
options.alignerMode = options.alignerMode.lower()
if options.alignerMode not in self.validAlignerModes :
raise OptParseException("Invalid aligner mode: '%s'" % options.alignerMode)
options.referenceFasta=validateFixExistingFileArg(options.referenceFasta,"reference")
# check for reference fasta index file:
if options.referenceFasta is not None :
faiFile=options.referenceFasta + ".fai"
if not os.path.isfile(faiFile) :
raise OptParseException("Can't find expected fasta index file: '%s'" % (faiFile))
if (options.regionStrList is None) or (len(options.regionStrList) == 0) :
options.genomeRegionList = None
else :
options.genomeRegionList = [parseGenomeRegion(r) for r in options.regionStrList]
def validateAndSanitizeOptions(self,options) :
MantaWorkflowOptionsBase.validateAndSanitizeOptions(self,options)
def safeLen(x) :
if x is None : return 0
return len(x)
if ((safeLen(options.normalBamList) == 0) and
(safeLen(options.tumorBamList) == 0)) :
raise OptParseException("No normal or tumor sample alignment files specified")
if (safeLen(options.tumorBamList) > 1) :
raise OptParseException("Can't accept more then one tumor sample")
if ((safeLen(options.tumorBamList) > 0) and (safeLen(options.normalBamList) > 1)) :
raise OptParseException("Can't accept multiple normal samples for tumor subtraction")
if options.isRNA :
if ((safeLen(options.normalBamList) != 1) or
(safeLen(options.tumorBamList) != 0)) :
raise OptParseException("RNA mode currently requires exactly one normal sample")
else :
if options.isUnstrandedRNA :
raise OptParseException("Unstranded only applied for RNA inputs")
if options.existingAlignStatsFile is not None :
options.existingAlignStatsFile=validateFixExistingFileArg(options.existingAlignStatsFile,"existing align stats")
groomBamList(options.normalBamList,"normal sample")
groomBamList(options.tumorBamList, "tumor sample")
bamSetChecker = BamSetChecker()
if safeLen(options.normalBamList) > 0 :
bamSetChecker.appendBams(options.normalBamList,"Normal")
if safeLen(options.tumorBamList) > 0 :
bamSetChecker.appendBams(options.tumorBamList,"Tumor")
bamSetChecker.check(options.htsfileBin,
options.referenceFasta)
def validateAndSanitizeExistingOptions(self,options) :
def checkForBamIndex(bamFile):
baiFile=bamFile + ".bai"
if not os.path.isfile(baiFile) :
raise OptParseException("Can't find expected BAM index file: '%s'" % (baiFile))
def groomBamList(bamList, sampleLabel):
if bamList is None : return
for (index,bamFile) in enumerate(bamList) :
bamList[index]=validateFixExistingFileArg(bamFile,"%s BAM file" % (sampleLabel))
checkForBamIndex(bamList[index])
groomBamList(options.normalBamList,"normal sample")
groomBamList(options.tumorBamList, "tumor sample")
# check alignerMode:
if options.alignerMode is not None :
options.alignerMode = options.alignerMode.lower()
if options.alignerMode not in self.validAlignerModes :
raise OptParseException("Invalid aligner mode: '%s'" % options.alignerMode)
options.referenceFasta=validateFixExistingFileArg(options.referenceFasta,"reference")
# check for reference fasta index file:
if options.referenceFasta is not None :
faiFile=options.referenceFasta + ".fai"
if not os.path.isfile(faiFile) :
raise OptParseException("Can't find expected fasta index file: '%s'" % (faiFile))
if (options.regionStrList is None) or (len(options.regionStrList) == 0) :
options.genomeRegionList = None
else :
options.genomeRegionList = [parseGenomeRegion(r) for r in options.regionStrList]
MantaWorkflowOptionsBase.validateAndSanitizeExistingOptions(self,options)
def validateAndSanitizeOptions(self, options):
assertOptionExists(options.runDir, "run directory")
options.runDir = os.path.abspath(options.runDir)
workflowScriptPath = os.path.join(options.runDir,
options.workflowScriptName)
if os.path.exists(workflowScriptPath):
raise OptParseException(
"Run directory already contains workflow script file '%s'. Each analysis must be configured in a separate directory."
% (workflowScriptPath))
assertOptionExists(options.referenceFasta, "reference fasta file")
options.referenceFasta = validateFixExistingFileArg(
options.referenceFasta, "reference fasta file")
# check for reference fasta index file:
referenceFastaIndex = options.referenceFasta + ".fai"
if not os.path.isfile(referenceFastaIndex):
raise OptParseException(
"Can't find expected fasta index file: '%s'" %
(referenceFastaIndex))
if options.isEstimateSequenceError:
# Determine if dynamic error estimation is feasible based on the reference size
# - Given reference contig set (S) with sequence length of at least 5 Mb
# - The total sequence length from S must be at least 50 Mb
class Constants:
Megabase = 1000000
minChromSize = options.errorEstimationMinChromMb * Megabase
minTotalSize = options.errorEstimationMinTotalMb * Megabase
# read fasta index
(_, chromSizes) = getFastaChromOrderSize(referenceFastaIndex)
totalEstimationSize = 0
for chromSize in chromSizes.values():
if chromSize < Constants.minChromSize: continue
totalEstimationSize += chromSize
if totalEstimationSize < Constants.minTotalSize:
sys.stderr.write(
"WARNING: Cannot estimate sequence errors from data due to small or overly fragmented reference sequence. Sequence error estimation disabled.\n"
)
options.isEstimateSequenceError = False
checkFixTabixListOption(options.indelCandidatesList,
"candidate indel vcf")
checkFixTabixListOption(options.forcedGTList, "forced genotype vcf")
options.callRegionsBed = checkFixTabixIndexedFileOption(
options.callRegionsBed, "call-regions bed")
def extendedRegionStrList():
"""
A generator on the regionStrList which parses the (intentionally undocumented/possibly deprecated) '+' entry format
to specify multiple regions in a single argument.
"""
for r in options.regionStrList:
for rr in r.split("+"):
yield rr
if (options.regionStrList is None) or (len(options.regionStrList)
== 0):
options.genomeRegionList = None
else:
options.genomeRegionList = [
parseGenomeRegion(r) for r in extendedRegionStrList()
]
# validate chromosome names appearing in region tags and callRegions bed file
if (options.callRegionsBed is not None) or (options.genomeRegionList
is not None):
refChromInfo = getFastaInfo(options.referenceFasta)
if options.callRegionsBed is not None:
for chrom in getTabixChromSet(options.tabixBin,
options.callRegionsBed):
if chrom not in refChromInfo:
raise OptParseException(
"Chromosome label '%s', in call regions bed file '%s', not found in reference genome."
% (chrom, options.callRegionsBed))
if options.genomeRegionList is not None:
for (genomeRegionIndex,
genomeRegion) in enumerate(options.genomeRegionList):
chrom = genomeRegion["chrom"]
if chrom not in refChromInfo:
raise OptParseException(
"Chromosome label '%s', parsed from region argument '%s', not found in reference genome."
% (chrom, list(
extendedRegionStrList())[genomeRegionIndex]))
options.snvScoringModelFile = validateFixExistingFileArg(
options.snvScoringModelFile, "SNV empirical scoring model file")
options.indelScoringModelFile = validateFixExistingFileArg(
options.indelScoringModelFile,
"Indel empirical scoring model file")
def groomBamList(bamList, sampleLabel):
if bamList is None: return
for (index, bamFile) in enumerate(bamList):
bamList[index] = validateFixExistingFileArg(
bamFile, "%s BAM file" % (sampleLabel))
checkForBamIndex(bamList[index])
def groomBamList(bamList, sampleLabel):
if bamList is None : return
for (index,bamFile) in enumerate(bamList) :
bamList[index]=validateFixExistingFileArg(bamFile,"%s BAM file" % (sampleLabel))
checkForBamIndex(bamList[index])