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 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) :
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 validateOptionExistence(self,options) :
assertOptionExists(options.normalBam,"normal sample BAM file")
assertOptionExists(options.alignerMode,"aligner mode")
assertOptionExists(options.referenceFasta,"reference fasta file")
MantaWorkflowOptionsBase.validateOptionExistence(self,options)
# check that the reference and the two bams are using the same set of chromosomes:
bamList=[]
bamLabels=[]
if options.normalBam is not None :
bamList.append(options.normalBam)
bamLabels.append("Normal")
if options.tumorBam is not None :
bamList.append(options.tumorBam)
bamLabels.append("Tumor")
checkChromSet(options.samtoolsBin,
options.referenceFasta,
bamList,
bamLabels,
isReferenceLocked=True)
def validateOptionExistence(self, options):
if (options.normalBamList is None) or (len(options.normalBamList)
== 0):
raise OptParseException("No normal sample BAM files specified")
assertOptionExists(options.alignerMode, "aligner mode")
assertOptionExists(options.referenceFasta, "reference fasta file")
MantaWorkflowOptionsBase.validateOptionExistence(self, options)
# check that the reference and all bams are using the same
# set of chromosomes:
bamList = []
bamLabels = []
def appendBams(inputBamList, inputLabel):
if inputBamList is None: return
for inputBamFile in inputBamList:
bamList.append(inputBamFile)
bamLabels.append(inputLabel)
appendBams(options.normalBamList, "Normal")
appendBams(options.tumorBamList, "Tumor")
checkChromSet(options.samtoolsBin,
options.referenceFasta,
bamList,
bamLabels,
isReferenceLocked=True)
# check for repeated bam entries:
#
bamSet = set()
for bamFile in bamList:
if bamFile in bamSet:
raise OptParseException("Repeated input BAM file: %s" %
(bamFile))
bamSet.add(bamFile)
def validateOptionExistence(self,options) :
if (options.normalBamList is None) or (len(options.normalBamList) == 0) :
raise OptParseException("No normal sample BAM files specified")
assertOptionExists(options.alignerMode,"aligner mode")
assertOptionExists(options.referenceFasta,"reference fasta file")
MantaWorkflowOptionsBase.validateOptionExistence(self,options)
# check that the reference and all bams are using the same
# set of chromosomes:
bamList=[]
bamLabels=[]
def appendBams(inputBamList,inputLabel) :
if inputBamList is None : return
for inputBamFile in inputBamList :
bamList.append(inputBamFile)
bamLabels.append(inputLabel)
appendBams(options.normalBamList,"Normal")
appendBams(options.tumorBamList,"Tumor")
checkChromSet(options.samtoolsBin,
options.referenceFasta,
bamList,
bamLabels,
isReferenceLocked=True)
# check for repeated bam entries:
#
bamSet=set()
for bamFile in bamList :
if bamFile in bamSet :
raise OptParseException("Repeated input BAM file: %s" % (bamFile))
bamSet.add(bamFile)
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 validateOptionExistence(self, options):
assertOptionExists(options.runDir, "run directory")
assertOptionExists(options.referenceFasta, "reference fasta file")
def validateOptionExistence(self,options) :
assertOptionExists(options.runDir,"run directory")
assertOptionExists(options.alignerMode,"aligner mode")
assertOptionExists(options.referenceFasta,"reference fasta file")
def validateOptionExistence(self, options):
assertOptionExists(options.runDir, "run directory")
def validateOptionExistence(self,options) :
assertOptionExists(options.runDir,"run directory")