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 __init__(self,params) :
cleanPyEnv()
self.params=params
# normalize boolean option input:
safeSetBool(self.params,"enableRemoteReadRetrievalForInsertionsInGermlineCallingModes")
safeSetBool(self.params,"enableRemoteReadRetrievalForInsertionsInCancerCallingModes")
safeSetBool(self.params,"useOverlapPairEvidence")
# Use RNA option for minCandidate size
if self.params.isRNA:
self.params.minCandidateVariantSize = self.params.rnaMinCandidateVariantSize
# format bam lists:
if self.params.normalBamList is None : self.params.normalBamList = []
if self.params.tumorBamList is None : self.params.tumorBamList = []
# make sure run directory is setup:
self.params.runDir=os.path.abspath(self.params.runDir)
ensureDir(self.params.runDir)
# everything that's not intended to be a final result should dump directories/files in workDir
self.params.workDir=os.path.join(self.params.runDir,"workspace")
ensureDir(self.params.workDir)
# all finalized pretty results get transfered to resultsDir
self.params.resultsDir=os.path.join(self.params.runDir,"results")
ensureDir(self.params.resultsDir)
self.params.statsDir=os.path.join(self.params.resultsDir,"stats")
ensureDir(self.params.statsDir)
self.params.variantsDir=os.path.join(self.params.resultsDir,"variants")
ensureDir(self.params.variantsDir)
self.params.evidenceDir=os.path.join(self.params.resultsDir,"evidence")
ensureDir(self.params.evidenceDir)
# self.params.reportsDir=os.path.join(self.params.resultsDir,"reports")
# ensureDir(self.params.reportsDir)
indexRefFasta=self.params.referenceFasta+".fai"
if self.params.referenceFasta is None:
raise Exception("No reference fasta defined.")
else:
checkFile(self.params.referenceFasta,"reference fasta")
checkFile(indexRefFasta,"reference fasta index")
# read fasta index
(self.params.chromOrder,self.params.chromSizes) = getFastaChromOrderSize(indexRefFasta)
# determine subset of chroms where we can skip calling entirely
(self.params.callRegionList, self.params.chromIsSkipped) = getCallRegions(self.params)
self.paths = PathInfo(self.params)
self.params.isHighDepthFilter = (not (self.params.isExome or self.params.isRNA))
self.params.isIgnoreAnomProperPair = (self.params.isRNA)
# always use overlapping pairs for RNA calling
if (self.params.isRNA) :
self.params.useOverlapPairEvidence = True
def __init__(self, params, iniSections):
cleanPyEnv()
self.params = params
self.iniSections = iniSections
# Use RNA option for minCandidate size
if self.params.isRNA:
self.params.minCandidateVariantSize = self.params.rnaMinCandidateVariantSize
# format bam lists:
if self.params.normalBamList is None: self.params.normalBamList = []
if self.params.tumorBamList is None: self.params.tumorBamList = []
# make sure run directory is setup:
self.params.runDir = os.path.abspath(self.params.runDir)
ensureDir(self.params.runDir)
# everything that's not intended to be a final result should dump directories/files in workDir
self.params.workDir = os.path.join(self.params.runDir, "workspace")
ensureDir(self.params.workDir)
# all finalized pretty results get transfered to resultsDir
self.params.resultsDir = os.path.join(self.params.runDir, "results")
ensureDir(self.params.resultsDir)
self.params.statsDir = os.path.join(self.params.resultsDir, "stats")
ensureDir(self.params.statsDir)
self.params.variantsDir = os.path.join(self.params.resultsDir,
"variants")
ensureDir(self.params.variantsDir)
self.params.evidenceDir = os.path.join(self.params.resultsDir,
"evidence")
ensureDir(self.params.evidenceDir)
# self.params.reportsDir=os.path.join(self.params.resultsDir,"reports")
# ensureDir(self.params.reportsDir)
indexRefFasta = self.params.referenceFasta + ".fai"
if self.params.referenceFasta is None:
raise Exception("No reference fasta defined.")
else:
checkFile(self.params.referenceFasta, "reference fasta")
checkFile(indexRefFasta, "reference fasta index")
# read fasta index
(self.params.chromOrder,
self.params.chromSizes) = getFastaChromOrderSize(indexRefFasta)
# determine subset of chroms where we can skip calling entirely
(self.params.callRegionList,
self.params.chromIsSkipped) = getCallRegions(self.params)
self.paths = PathInfo(self.params)
self.params.isHighDepthFilter = (not (self.params.isExome
or self.params.isRNA))
self.params.isIgnoreAnomProperPair = (self.params.isRNA)
def __init__(self,params,iniSections) :
# clear out some potentially destabilizing env variables:
clearList = [ "PYTHONPATH", "PYTHONHOME"]
for key in clearList :
if key in os.environ :
del os.environ[key]
self.params=params
self.iniSections=iniSections
# make sure run directory is setup:
self.params.runDir=os.path.abspath(self.params.runDir)
ensureDir(self.params.runDir)
# everything that's not intended to be a final result should dump directories/files in workDir
self.params.workDir=os.path.join(self.params.runDir,"workspace")
ensureDir(self.params.workDir)
# all finalized pretty results get transfered to resultsDir
self.params.resultsDir=os.path.join(self.params.runDir,"results")
ensureDir(self.params.resultsDir)
self.params.statsDir=os.path.join(self.params.resultsDir,"stats")
ensureDir(self.params.statsDir)
self.params.variantsDir=os.path.join(self.params.resultsDir,"variants")
ensureDir(self.params.variantsDir)
# self.params.reportsDir=os.path.join(self.params.resultsDir,"reports")
# ensureDir(self.params.reportsDir)
indexRefFasta=self.params.referenceFasta+".fai"
if self.params.referenceFasta is None:
raise Exception("No reference fasta defined.")
else:
checkFile(self.params.referenceFasta,"reference fasta")
checkFile(indexRefFasta,"reference fasta index")
self.params.normalBamList = []
for bam in (self.params.normalBam,) :
if bam is None : continue
self.params.normalBamList.append(bam)
self.params.tumorBamList = []
for bam in (self.params.tumorBam,) :
if bam is None : continue
self.params.tumorBamList.append(bam)
# read fasta index
(self.params.chromOrder,self.params.chromSizes) = getFastaChromOrderSize(indexRefFasta)
# sanity check some parameter typing:
self.params.binSize = int(self.params.binSize)
self.params.nonlocalWorkBins = int(self.params.nonlocalWorkBins)
self.paths = PathInfo(self.params)
def __init__(self,params,iniSections) :
# clear out some potentially destabilizing env variables:
clearList = [ "PYTHONPATH", "PYTHONHOME"]
for key in clearList :
if key in os.environ :
del os.environ[key]
self.params=params
self.iniSections=iniSections
# format bam lists:
if self.params.normalBamList is None : self.params.normalBamList = []
if self.params.tumorBamList is None : self.params.tumorBamList = []
# make sure run directory is setup:
self.params.runDir=os.path.abspath(self.params.runDir)
ensureDir(self.params.runDir)
# everything that's not intended to be a final result should dump directories/files in workDir
self.params.workDir=os.path.join(self.params.runDir,"workspace")
ensureDir(self.params.workDir)
# all finalized pretty results get transfered to resultsDir
self.params.resultsDir=os.path.join(self.params.runDir,"results")
ensureDir(self.params.resultsDir)
self.params.statsDir=os.path.join(self.params.resultsDir,"stats")
ensureDir(self.params.statsDir)
self.params.variantsDir=os.path.join(self.params.resultsDir,"variants")
ensureDir(self.params.variantsDir)
# self.params.reportsDir=os.path.join(self.params.resultsDir,"reports")
# ensureDir(self.params.reportsDir)
indexRefFasta=self.params.referenceFasta+".fai"
if self.params.referenceFasta is None:
raise Exception("No reference fasta defined.")
else:
checkFile(self.params.referenceFasta,"reference fasta")
checkFile(indexRefFasta,"reference fasta index")
# read fasta index
(self.params.chromOrder,self.params.chromSizes) = getFastaChromOrderSize(indexRefFasta)
# sanity check some parameter typing:
MEGABASE = 1000000
self.params.scanSize = int(self.params.scanSizeMb) * MEGABASE
self.params.nonlocalWorkBins = int(self.params.nonlocalWorkBins)
self.paths = PathInfo(self.params)
self.params.isHighDepthFilter = (not (self.params.isExome or self.params.isRNA))
self.params.isIgnoreAnomProperPair = (self.params.isRNA)
def __init__(self,params,iniSections) :
cleanPyEnv()
self.params=params
self.iniSections=iniSections
# format bam lists:
if self.params.normalBamList is None : self.params.normalBamList = []
if self.params.tumorBamList is None : self.params.tumorBamList = []
# make sure run directory is setup:
self.params.runDir=os.path.abspath(self.params.runDir)
ensureDir(self.params.runDir)
# everything that's not intended to be a final result should dump directories/files in workDir
self.params.workDir=os.path.join(self.params.runDir,"workspace")
ensureDir(self.params.workDir)
# all finalized pretty results get transfered to resultsDir
self.params.resultsDir=os.path.join(self.params.runDir,"results")
ensureDir(self.params.resultsDir)
self.params.statsDir=os.path.join(self.params.resultsDir,"stats")
ensureDir(self.params.statsDir)
self.params.variantsDir=os.path.join(self.params.resultsDir,"variants")
ensureDir(self.params.variantsDir)
# self.params.reportsDir=os.path.join(self.params.resultsDir,"reports")
# ensureDir(self.params.reportsDir)
indexRefFasta=self.params.referenceFasta+".fai"
if self.params.referenceFasta is None:
raise Exception("No reference fasta defined.")
else:
checkFile(self.params.referenceFasta,"reference fasta")
checkFile(indexRefFasta,"reference fasta index")
# read fasta index
(self.params.chromOrder,self.params.chromSizes) = getFastaChromOrderSize(indexRefFasta)
self.paths = PathInfo(self.params)
self.params.isHighDepthFilter = (not (self.params.isExome or self.params.isRNA))
self.params.isIgnoreAnomProperPair = (self.params.isRNA)
def __init__(self, params, PathInfoType):
cleanPyEnv()
self.params = params
# make sure run directory is setup:
self.params.runDir = os.path.abspath(self.params.runDir)
ensureDir(self.params.runDir)
# everything that's not intended to be a final result should dump directories/files in workDir
self.params.workDir = os.path.join(self.params.runDir, "workspace")
ensureDir(self.params.workDir)
# all finalized pretty results get transferred to resultsDir
self.params.resultsDir = os.path.join(self.params.runDir, "results")
ensureDir(self.params.resultsDir)
self.params.variantsDir = os.path.join(self.params.resultsDir,
"variants")
ensureDir(self.params.variantsDir)
# timings and other stats go into statsDir
self.params.statsDir = os.path.join(self.params.resultsDir, "stats")
ensureDir(self.params.statsDir)
self.paths = PathInfoType(self.params)
referenceFastaIndex = self.params.referenceFasta + ".fai"
if self.params.referenceFasta is None:
raise Exception("No reference fasta defined.")
else:
checkFile(self.params.referenceFasta, "reference fasta")
checkFile(referenceFastaIndex, "reference fasta index")
# read fasta index
(self.params.chromOrder,
self.params.chromSizes) = getFastaChromOrderSize(referenceFastaIndex)
# determine subset of chroms where we can skip calling entirely
self.params.chromIsSkipped = getChromIsSkipped(self)
self.params.isHighDepthFilter = (not (self.params.isExome
or self.params.isRNA))
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")
