def openWriteBeagleFiles(self,
pedigreeFamilyData=None,
outputFnamePrefix=None):
"""
2013.05.02
The non-likelihood (unphased, trios, pairs) Beagle format:
I id sample1 sample1 sample2 sample2
A diabetes 1 1 2 2
M rs12082861 C C C C
M rs4912233 T C C C
M rs12732823 G A A A
M rs17451521 C C C C
M rs12033358 C T T T
The likelihood version is
marker alleleA alleleB 1000_709_1996093_GA_vs_524 1000_709_1996093_GA_vs_524 1000_709_1996093_GA_vs_524 1001_710_1995025_GA_vs_524 1001_710_1995025_GA_vs_524 1001_710_1995025_GA_vs_524 1002_711_2001039_GA_vs_524
Contig791:1086 C A 0.9693 0.0307 0.0000 0.6660 0.3338 0.0003 0.0000
Contig791:1649 G C 0.9406 0.0594 0.0000 0.9693 0.0307 0.0000 0.0000
Contig791:4084 A C 0.9980 0.0020 0.0000 0.9844 0.0156 0.0000 0.0000
The markers file has this format (markerID, position, alleleA, alleleB)
Contig791:1086 1086 C A
"""
sys.stderr.write(
"Opening beagle files (outputFnamePrefix =%s) to write ..." %
(outputFnamePrefix))
familySize2BeagleFileHandler = {}
familySize2SampleIDList = pedigreeFamilyData.familySize2SampleIDList
counter = 0
for familySize, sampleIDList in familySize2SampleIDList.items():
if familySize not in familySize2BeagleFileHandler:
tmpOutputFnamePrefix = '%s_familySize%s' % (outputFnamePrefix,
familySize)
writer = MatrixFile(path='%s.bgl' % (tmpOutputFnamePrefix),
mode='w',
delimiter=' ')
familySize2BeagleFileHandler[familySize] = writer
if familySize == 1:
headerRow = ['marker', 'alleleA', 'alleleB']
else:
headerRow = ['I', 'id']
for sampleID in sampleIDList:
if familySize == 1:
#likelihood format has sample name replicated three times, rather than 2 times
headerRow.extend([sampleID] * 3)
else:
headerRow.extend([sampleID] * 2)
writer.writeHeader(headerRow)
counter += 1
markersFile = MatrixFile(path='%s.markers' % (outputFnamePrefix),
mode='w',
delimiter=' ')
counter += 1
sys.stderr.write("%s files outputted.\n" % (counter))
return PassingData(
familySize2BeagleFileHandler=familySize2BeagleFileHandler,
markersFile=markersFile)
def __init__(self, path=None, **keywords):
MatrixFile.__init__(self, path=path, **keywords)
self.familyID2MemberList= {}
self.familySize2SampleIDList = {}
self._pedigreeGraph = None
self._childNodeSet = None
def __init__(self, path=None, **keywords):
MatrixFile.__init__(self, path=path, **keywords)
self.header = None
self.col_name2index = None #key is sampleID, value is index of first haplotype
self.sampleIDList = []
self.sampleID2index = {} #same as col_name2index
self.locusIDList = []
self.haplotypeMatrix = []
self.snpData = None #to store everything above . SNPData type
def run(self):
if self.debug:
import pdb
pdb.set_trace()
outputDir = os.path.split(self.outputFname)[0]
if outputDir and not os.path.isdir(outputDir):
os.makedirs(outputDir)
reader = VCFFile(inputFname=self.inputFname)
alignmentFile = pysam.Samfile(self.alignmentFilename, "rb")
writer = VCFFile(outputFname=self.outputFname, mode='w')
writer.metaInfoLs = reader.metaInfoLs
writer.header = reader.header
writer.writeMetaAndHeader()
statWriter = MatrixFile(self.missingStatFname, mode='w', delimiter='\t')
header = ["sampleID", "locusID", 'chromosome', 'start', 'stop', 'occurrence', 'missingReason', \
'fractionOfGoodRead', 'medianMapQ', 'totalNoOfReads']
statWriter.writeHeader(header)
counter = 0
real_counter = 0
minDepth = self.alignmentMedianDepth/self.alignmentDepthFold
maxDepth = self.alignmentMedianDepth*self.alignmentDepthFold
for vcfRecord in reader:
locusID = "%s_%s"%(vcfRecord.chromosome, vcfRecord.position)
alignedReadLs = alignmentFile.fetch(vcfRecord.chromosome, vcfRecord.position-1, vcfRecord.position+1) #start and end in fetch() are 0-based.
locusLowMapQData = self.returnLocusLowMapQualityIndicator(alignedReadLs=alignedReadLs,\
minMapQGoodRead=self.minMapQGoodRead, minFractionOfGoodRead=self.minFractionOfGoodRead)
locusLowMapQIndicator = locusLowMapQData.locusLowMapQIndicator
depth = locusLowMapQData.totalNoOfReads
if depth>=minDepth and depth <=maxDepth:
locusOutOfDepthIndicator = 0 #good
else:
locusOutOfDepthIndicator = 1
locusLowQualityIndicator = locusOutOfDepthIndicator + locusLowMapQIndicator
data_row = [self.sampleID, locusID, vcfRecord.chromosome, vcfRecord.position, vcfRecord.position,\
1, locusLowQualityIndicator, locusLowMapQData.fractionOfGoodRead, \
locusLowMapQData.medianMapQ, locusLowMapQData.totalNoOfReads]
statWriter.writerow(data_row)
if locusLowQualityIndicator>0:
real_counter += 1
#modify the VCF record
#get sample ID column, then set its genotype missing
vcfRecord.setGenotypeCallForOneSample(sampleID=self.sampleID, genotype="./.", convertGLToPL=True)
#2014.1.4 output VCF record
writer.writeVCFRecord(vcfRecord)
counter += 1
reader.close()
statWriter.close()
writer.close()
sys.stderr.write("%s (out of %s, %s) genotypes marked missing.\n"%(real_counter, counter, \
real_counter/float(counter)))
def run(self):
if self.debug:
import pdb
pdb.set_trace()
outputDir = os.path.split(self.outputFname)[0]
if outputDir and not os.path.isdir(outputDir):
os.makedirs(outputDir)
snp_pos2genotypeVectorLs = self.readInSNPID2GenotypeVectorLs(
self.inputFname).snp_pos2returnData
writer = MatrixFile(self.outputFname, mode='w', delimiter='\t')
header = [
'chromosome', 'position', 'noOfMatches', 'noOfTotal', 'concordance'
]
writer.writeHeader(header)
counter = 0
real_counter = 0
no_of_pairs = 0
snp_pos_ls = sorted(snp_pos2genotypeVectorLs)
for i in range(len(snp_pos_ls)):
counter += 1
key = snp_pos_ls[i]
chromosome, position = snp_pos_ls[i][:2]
genotypeVectorLs = snp_pos2genotypeVectorLs.get(key)
if len(genotypeVectorLs) > 1:
real_counter += 1
for k in range(0, len(genotypeVectorLs) - 1):
for l in range(k + 1, len(genotypeVectorLs)):
no_of_pairs += 1
noOfMatches = 0
noOfTotal = 0
genotypeVector0 = genotypeVectorLs[k]
genotypeVector1 = genotypeVectorLs[l]
for j in range(len(genotypeVector0)):
call1 = genotypeVector0[j]['GT']
call2 = genotypeVector1[j]['GT']
if call1 != 'NA' and call2 != 'NA':
noOfTotal += 1
if SNP.nt2number[call1] == SNP.nt2number[
call2]:
noOfMatches += 1
if noOfTotal > 0:
concordance = float(noOfMatches) / float(noOfTotal)
else:
concordance = -1
data_row = [
chromosome, position, noOfMatches, noOfTotal,
concordance
]
writer.writerow(data_row)
writer.close()
sys.stderr.write("%s (out of %s, %s) snps have >1 same-position entries. %s pairs.\n"%(real_counter, counter, \
real_counter/float(counter), no_of_pairs))
def __init__(self, path=None, **keywords):
MatrixFile.__init__(self, path=path, **keywords)
#summary data
self.no_of_intervals = 0
self.interval_value_ls = []
self.interval_length_ls = []
self.chromosome_size = 0
self.min_interval_value = None
self.max_interval_value = None
self.median_interval_value = None
self.min_interval_length = None
self.max_interval_length = None
self.median_interval_length = None
self.interval_ls = []
def getLocusID2MissingFraction(self, inputFname=None):
"""
2014.01.08
"""
sys.stderr.write("Reading in the missing statistics from %s ... "%(inputFname))
locusID2Stat = {}
reader = MatrixFile(path=inputFname)
reader.constructColName2IndexFromHeader()
locusIDIndex = reader.getColIndexGivenColHeader("locusID")
statIndex = reader.getColIndexGivenColHeader("occurrence_byFixedValue")
counter = 0
for row in reader:
locusID = row[locusIDIndex]
chromosome, start = locusID.split('_')[:2]
start = int(start)
stat = float(row[statIndex])
key = (chromosome, start, start)
if key in locusID2Stat:
if stat < locusID2Stat[key]:
#take lowest value
locusID2Stat[key] = stat
else:
locusID2Stat[key] = stat
counter += 1
del reader
sys.stderr.write(" %s unique loci with missing fraction out of %s total loci.\n"%(len(locusID2Stat), counter))
return locusID2Stat
def readInSwitchDensity(self, inputFname=None):
"""
2013.07.11
"""
sys.stderr.write("Reading in switch density from %s ..." %
(inputFname))
reader = MatrixFile(path=inputFname)
reader.constructColName2IndexFromHeader()
noOfSwitchesPerLocusIndex = reader.getColIndexGivenColHeader(
"noOfSwitchesPerLocus")
counter = 0
real_counter = 0
switchDensity = 0
for row in reader:
switchDensity = float(row[noOfSwitchesPerLocusIndex])
counter += 1
break
del reader
return PassingData(switchDensity=switchDensity)
def openOneInputFile(self, inputFname=None):
"""
2013.09.05 split out of fileWalker() , added VCFFile
"""
if self.inputFileFormat==2:
reader = YHFile(inputFname, mode='r', tableName=self.h5TableName)
elif self.inputFileFormat==3:
reader = HDF5MatrixFile(inputFname, mode='r')
elif self.inputFileFormat==4:
reader = VCFFile(inputFname=inputFname)
else:
reader = MatrixFile(inputFname)
return reader
def outputFinalData(self,
outputFname,
key2dataLs=None,
delimiter=None,
header=None):
"""
header output is not dependent on key2dataLs anymore
"""
writer = MatrixFile(path=outputFname, delimiter=delimiter, mode='w')
if header and delimiter:
writer.writerow(header)
if key2dataLs and delimiter:
keyLs = sorted(key2dataLs)
for key in keyLs:
dataLs = key2dataLs.get(key)
writer.writerow(list(key) + dataLs)
writer.close()
def run(self):
if self.debug:
import pdb
pdb.set_trace()
outputDir = os.path.split(self.outputFname)[0]
if outputDir and not os.path.isdir(outputDir):
os.makedirs(outputDir)
switchPointData = self.readInStats(inputFname=self.inputFname)
sys.stderr.write("Processing data ...")
writer = MatrixFile(self.outputFname, mode='w')
header = [
"maxSwitchFrequency", "genomeCovered", 'genomeCoveredFraction',
"noOfLoci", 'noOfLociFraction'
]
writer.writeHeader(header)
data_matrix = switchPointData.data_matrix
totalSpan = switchPointData.totalSpan
totalNoOfLoci = switchPointData.totalNoOfLoci
#sort it based on switchFrequency
data_matrix.sort(reverse=True)
maxSwitchFrequencyLs = []
cumulativeRegionSpanLs = []
cumulativeNoOfLociLs = []
for i in range(len(data_matrix)):
switchFrequency, regionSpan, noOfLoci = data_matrix[i]
maxSwitchFrequencyLs.append(switchFrequency)
if i == 0:
cumulativeRegionSpan = totalSpan - regionSpan
cumulativeNoOfLoci = totalNoOfLoci - noOfLoci
else:
cumulativeRegionSpan = cumulativeRegionSpanLs[i -
1] - regionSpan
cumulativeNoOfLoci = cumulativeNoOfLociLs[i - 1] - noOfLoci
cumulativeRegionSpanLs.append(cumulativeRegionSpan)
cumulativeNoOfLociLs.append(cumulativeNoOfLoci)
writer.writerow([switchFrequency, cumulativeRegionSpan, cumulativeRegionSpan/float(totalSpan),\
cumulativeNoOfLoci, cumulativeNoOfLoci/float(totalNoOfLoci)])
writer.close()
sys.stderr.write(".\n")
def setup(self, **keywords):
"""
do not open the file if it's a png file.
run before anything is run.
"""
writer = None
if self.outputFileFormat in [1,4]:
suffix = os.path.splitext(self.outputFname)[1]
if self.outputFname and suffix!='.png':
writer = MatrixFile(self.outputFname, mode='w', delimiter='\t')
else:
#HDF5MatrixFile
#can't generate HDF5MatrixFile, because it needs dtypeList
pass
#pass it to the invariantPData
self.invariantPData.writer = writer
self.writer = writer
def getLocusNewID2mapPvalue(self, liftOverLocusMapPvalueFname=None):
"""
2014.01.04
oldChromosome, oldStart, oldStop, oldStrand, newChromosome, newStart, newStop, mapPvalue
"""
sys.stderr.write("Reading in the coordinate map from %s ..." %
(liftOverLocusMapPvalueFname))
locusNewID2mapPvalue = {}
reader = MatrixFile(path=liftOverLocusMapPvalueFname)
reader.constructColName2IndexFromHeader()
strandIndex = reader.getColIndexGivenColHeader("oldStrand")
newChromosomeIndex = reader.getColIndexGivenColHeader("newChromosome")
newStartIndex = reader.getColIndexGivenColHeader("newStart")
newStopIndex = reader.getColIndexGivenColHeader("newStop")
mapPvalueIndex = reader.getColIndexGivenColHeader("mapPvalue")
counter = 0
for row in reader:
strand = row[strandIndex]
newChromosome = row[newChromosomeIndex]
newStart = int(row[newStartIndex])
newStop = int(row[newStopIndex])
mapPvalue = float(row[mapPvalueIndex])
key = (newChromosome, newStart, newStop)
if key in locusNewID2mapPvalue:
if mapPvalue < locusNewID2mapPvalue[key]:
#take lowest value
locusNewID2mapPvalue[key] = mapPvalue
else:
locusNewID2mapPvalue[key] = mapPvalue
counter += 1
del reader
sys.stderr.write(
"%s unique loci with map p-value out of %s total loci.\n" %
(len(locusNewID2mapPvalue), counter))
return locusNewID2mapPvalue
def readInStats(self, inputFname=None):
"""
2013.07.15
"""
sys.stderr.write("Reading stats from %s ..." % (inputFname))
data_matrix = []
reader = MatrixFile(inputFname)
reader.constructColName2IndexFromHeader()
switchFrequencyIndex = reader.getColIndexGivenColHeader(
"noOfSwitchPoints_by_noOfLociWithUniqueHit")
regionSpanIndex = reader.getColIndexGivenColHeader("regionSpan")
noOfLociIndex = reader.getColIndexGivenColHeader("#sitesInInput2")
totalSpan = 0
totalNoOfLoci = 0
counter = 0
for row in reader:
counter += 1
switchFrequency = row[switchFrequencyIndex]
regionSpan = row[regionSpanIndex]
noOfLoci = row[noOfLociIndex]
if switchFrequency and regionSpan and noOfLoci: #non-empty
switchFrequency = float(switchFrequency)
regionSpan = int(float(regionSpan))
noOfLoci = int(float(noOfLoci))
data_matrix.append([switchFrequency, regionSpan, noOfLoci])
totalSpan += regionSpan
totalNoOfLoci += noOfLoci
reader.close()
sys.stderr.write(" %s valid entries (from %s rows) with totalSpan=%s, totalNoOfLoci=%s.\n"%\
(len(data_matrix), counter, totalSpan, totalNoOfLoci))
return PassingData(data_matrix=data_matrix,
totalSpan=totalSpan,
totalNoOfLoci=totalNoOfLoci)
def outputOverlapSites(self, overlapping_sites_set=None, outputFname=None):
"""
overlapping_sites_set is a set of (chromosome, pos) tuples.
output is tab-delimited, 3-column. Last column is always 0 to mimic output of CalculateSNPMismatchRateOfTwoVCF.py
chromosome position 0
"""
sys.stderr.write("Outputting overlap %s sites ..." %
(len(overlapping_sites_set)))
header = ['chromosome', 'position', 'random']
overlapping_sites_list = list(overlapping_sites_set)
writer = MatrixFile(outputFname, mode='w', delimiter='\t')
writer.writerow(header)
overlapping_sites_list.sort()
for chromosome, pos in overlapping_sites_list:
writer.writerow([chromosome, pos, 0])
sys.stderr.write("%s sites.\n" % (len(overlapping_sites_list)))
def calculatePerSampleMismatchFraction(self, vcfFile1=None, vcfFile2=None, outputFname=None, overlapping_sample_id_set=None,\
NA_call_encoding_set = set(['.', 'NA'])):
"""
2013.08.13 bugfix, derive overlapping_sites_set by itself, rather than use calculateOverlappingSites()
2013.07.17 vcf files are no longer pre-loaded.
2012.8.16
"""
sys.stderr.write(
"Finding matches for each sample at overlapping sites ...")
writer = MatrixFile(outputFname, mode='w', delimiter='\t')
header = [
'sample_id', 'no_of_matches', 'no_of_non_NA_pairs', 'matchFraction'
]
no_of_samples_to_compare = len(overlapping_sample_id_set)
vcfFile1._resetInput()
vcfFile1.parseFile()
vcfFile2._resetInput()
vcfFile2.parseFile()
overlapping_sites_set = set(vcfFile1.locus_id_ls) & set(
vcfFile2.locus_id_ls)
sys.stderr.write(" %s overlapping loci, " %
(len(overlapping_sites_set)))
header_ls_for_no_of_matches = []
header_ls_for_no_of_non_NA_pairs = []
header_ls_for_matchFraction = []
overlapping_sample_id_list = sorted(overlapping_sample_id_set)
"""
for sample_id in overlapping_sample_id_list:
header_ls_for_no_of_matches.append('no_of_matches_for_%s'%(sample_id))
header_ls_for_no_of_non_NA_pairs.append('no_of_non_NA_pairs_for_%s'%(sample_id))
header_ls_for_matchFraction.append('matchFraction_for_%s'%(sample_id))
#header = header + header_ls_for_no_of_matches + header_ls_for_no_of_non_NA_pairs + header_ls_for_matchFraction
"""
no_of_matches_per_sample_ls = [0] * no_of_samples_to_compare
no_of_non_NA_pairs_per_sample_ls = [0] * no_of_samples_to_compare
for locus_id in overlapping_sites_set:
row_index1 = vcfFile1.locus_id2row_index[locus_id]
row_index2 = vcfFile2.locus_id2row_index[locus_id]
for j in range(len(overlapping_sample_id_list)):
sample_id = overlapping_sample_id_list[j]
col_index1 = vcfFile1.sample_id2index.get(sample_id)
col_index2 = vcfFile2.sample_id2index.get(sample_id)
#2012.1.17 bugfix below. so that 'AG' and 'GA' are same.
call1 = vcfFile1.genotype_call_matrix[row_index1][col_index1]
call2 = vcfFile2.genotype_call_matrix[row_index2][col_index2]
if call1 not in NA_call_encoding_set and call2 not in NA_call_encoding_set:
no_of_non_NA_pairs_per_sample_ls[j] += 1
if nt2number[call1] == nt2number[
call2]: #2013.07.03 bugfix, 'AT' and 'TA' should be same. no phase
no_of_matches_per_sample_ls[j] += 1
else:
#do nothing
pass
matchFractionLs = [-1] * no_of_samples_to_compare
for j in range(no_of_samples_to_compare):
if no_of_non_NA_pairs_per_sample_ls[j] > 0:
matchFractionLs[j] = no_of_matches_per_sample_ls[j] / float(
no_of_non_NA_pairs_per_sample_ls[j])
writer.writerow(header)
for i in range(no_of_samples_to_compare):
data_row = [overlapping_sample_id_list[i], no_of_matches_per_sample_ls[i], no_of_non_NA_pairs_per_sample_ls[i],\
matchFractionLs[i]]
writer.writerow(data_row)
del writer
sys.stderr.write("%s samples.\n" % (no_of_samples_to_compare))
def traverse(self):
"""
"""
newHeader = []
key2dataLs = {}
#key is the keyColumn,
# dataLs corresponds to the sum of each column from valueColumnLs
noOfDataColumnsFromPriorFiles = 0
for inputFname in self.inputFnameLs:
if not os.path.isfile(inputFname):
if self.exitNonZeroIfAnyInputFileInexistent:
logging.error(f'{inputFname} does not exist.')
sys.exit(3)
else:
continue
reader = None
try:
inputFile = utils.openGzipFile(inputFname)
if self.inputDelimiter is None or self.inputDelimiter == '':
self.inputDelimiter = figureOutDelimiter(inputFile)
reader = MatrixFile(file_handle=inputFile,
delimiter=self.inputDelimiter)
except:
logging.error(f'Except type: {sys.exc_info()}')
import traceback
traceback.print_exc()
valueColumnLs = []
try:
header = next(reader)
self.handleNewHeader(header,
newHeader,
self.keyColumnLs,
valueColumnLs,
keyColumnSet=self.keyColumnSet)
if self.noHeader:
inputFile.seek(0)
reader = MatrixFile(file_handle=inputFile,
delimiter=self.inputDelimiter)
except:
#in case something wrong (i.e. file is empty)
logging.error(f'Except type: {sys.exc_info()}')
import traceback
traceback.print_exc()
if reader is not None and valueColumnLs:
visitedKeySet = set()
for row in reader:
try:
self.handleValueColumns(row,
key2dataLs=key2dataLs,
keyColumnLs=self.keyColumnLs,
valueColumnLs=valueColumnLs,
noOfDataColumnsFromPriorFiles=
noOfDataColumnsFromPriorFiles,
visitedKeySet=visitedKeySet)
except:
logging.error(f'Ignore this row: {row}.')
logging.error(f'Except type: {sys.exc_info()}')
import traceback
traceback.print_exc()
del reader
#append empty data to keys who are missing in the current file.
totalKeySet = set(key2dataLs.keys())
unvisitedKeySet = totalKeySet - visitedKeySet
for key in unvisitedKeySet:
for i in valueColumnLs:
key2dataLs[key].append('')
noOfDataColumnsFromPriorFiles += len(valueColumnLs)
if self.noHeader:
newHeader = None
returnData = PassingData(key2dataLs=key2dataLs,
delimiter=self.inputDelimiter,
header=newHeader)
return returnData
def run(self):
"""
"""
if self.debug:
import pdb
pdb.set_trace()
reader = MatrixFile(path=self.inputFname)
reader.constructColName2IndexFromHeader()
meanMendelErrorIndex = reader.getColIndexGivenColHeader(
"meanMendelError")
noOfLociIndex = reader.getColIndexGivenColHeader("sampled_base_count")
sumOfMendelErrorIndex = reader.getColIndexGivenColHeader(
"sumOfMendelError")
plinkPedigreeFile = PlinkPedigreeFile(path=self.pedigreeFname)
familyStructureData = plinkPedigreeFile.getFamilyStructurePlinkWay()
twoParentFamilyCountData = self.getNoOfFamiliesAndKidsGivenParentSetSize(noOfParents2FamilyData=familyStructureData.noOfParents2FamilyData, \
parentSetSize=2)
singleParentFamilyCountData = self.getNoOfFamiliesAndKidsGivenParentSetSize(noOfParents2FamilyData=familyStructureData.noOfParents2FamilyData, \
parentSetSize=1)
zeroParentFamilyCountData = self.getNoOfFamiliesAndKidsGivenParentSetSize(noOfParents2FamilyData=familyStructureData.noOfParents2FamilyData, \
parentSetSize=0)
writer = MatrixFile(self.outputFname, mode='w', delimiter='\t')
header = ["ID", "noOfTotalLoci", \
"noOfTwoParentFamilies", "noOfParentsInTwoParentFamilies", "noOfKidsInTwoParentFamilies", "noOfIndividualsInTwoParentFamilies", \
"noOfSingleParentFamilies", "noOfParentsInSingleParentFamilies", "noOfKidsInSingleParentFamilies", "noOfIndividualsInSingleParentFamilies", \
"noOfZeroParentFamilies", "noOfParentsInZeroParentFamilies", "noOfKidsInZeroParentFamilies", "noOfIndividualsInZeroParentFamilies", \
"noOfTotalMendelErrors", \
"noOfMendelErrorsPerLocusPerNuclearFamily", "noOfMendelErrorsPerNuclearFamily"]
writer.writeHeader(header)
for row in reader:
meanMendelError = float(row[meanMendelErrorIndex])
noOfLoci = int(row[noOfLociIndex])
sumOfMendelError = int(row[sumOfMendelErrorIndex])
noOfNuclearFamilies = twoParentFamilyCountData.noOfFamilies
if noOfNuclearFamilies > 0:
noOfMendelErrorsPerLocusPerNuclearFamily = meanMendelError / float(
noOfNuclearFamilies)
noOfMendelErrorsPerNuclearFamily = sumOfMendelError / float(
noOfNuclearFamilies)
else:
noOfMendelErrorsPerLocusPerNuclearFamily = -1
noOfMendelErrorsPerNuclearFamily = -1
data_row = [row[0], noOfLoci, \
noOfNuclearFamilies, twoParentFamilyCountData.noOfParents, twoParentFamilyCountData.noOfKids, \
twoParentFamilyCountData.noOfIndividuals,\
singleParentFamilyCountData.noOfFamilies, singleParentFamilyCountData.noOfParents, singleParentFamilyCountData.noOfKids,\
singleParentFamilyCountData.noOfIndividuals,\
zeroParentFamilyCountData.noOfFamilies, zeroParentFamilyCountData.noOfParents, zeroParentFamilyCountData.noOfKids,\
zeroParentFamilyCountData.noOfIndividuals,\
sumOfMendelError, \
noOfMendelErrorsPerLocusPerNuclearFamily,noOfMendelErrorsPerNuclearFamily ]
writer.writerow(data_row)
plinkPedigreeFile.close()
reader.close()
writer.close()
def calculateOverlappingSites(self, vcfFile1=None, vcfFile2=None, outputFname=None, overlappingSitesOutputFname=None,\
chromosome=None, chrLength=None):
"""
2013.07.17 vcf files are no longer pre-loaded. read in locus ids first.
"""
writer = MatrixFile(outputFname, mode='w', delimiter='\t')
header = ['#chromosome', 'length', '#sitesInInput1', '#sitesInInput2', '#overlapping', 'overlappingOverTotal', \
'overlappingOverInput1', 'overlappingOverInput2', '#segregatingSitesNormalized', ]
vcf1_locus_id_list = []
for row in vcfFile1.reader:
vcf1_locus_id_list.append((row[0], row[1]))
vcf2_locus_id_list = []
for row in vcfFile2.reader:
vcf2_locus_id_list.append((row[0], row[1]))
no_of_sites_of_input1 = len(vcf1_locus_id_list)
no_of_sites_of_input2 = len(vcf2_locus_id_list)
overlapping_sites_set = set(vcf1_locus_id_list) & set(
vcf2_locus_id_list)
if overlappingSitesOutputFname:
#outputFname = "%s_overlapSitePos.tsv"%(outputFnamePrefix)
self.outputOverlapSites(
overlapping_sites_set=overlapping_sites_set,
outputFname=overlappingSitesOutputFname)
no_of_overlapping_sites = len(overlapping_sites_set)
no_of_total_sites = no_of_sites_of_input1 + no_of_sites_of_input2 - no_of_overlapping_sites
if no_of_total_sites > 0:
overlapping_fraction = no_of_overlapping_sites / float(
no_of_total_sites)
else:
overlapping_fraction = -1
if no_of_sites_of_input1 > 0:
overlappingOverInput1 = no_of_overlapping_sites / float(
no_of_sites_of_input1)
else:
overlappingOverInput1 = -1
if no_of_sites_of_input2 > 0:
overlappingOverInput2 = no_of_overlapping_sites / float(
no_of_sites_of_input2)
else:
overlappingOverInput2 = -1
no_of_samples = len(vcfFile1.sample_id2index)
no_of_samples_in_vcf2 = len(vcfFile2.sample_id2index)
overlapping_sample_id_set = set(vcfFile1.sample_id2index.keys()) & set(
vcfFile2.sample_id2index.keys())
if no_of_samples != no_of_samples_in_vcf2:
sys.stderr.write("Warning: sample size in %s is %s, in %s is %s. not matching.\n"%\
(vcfFile1.inputFname, no_of_samples, vcfFile2.inputFname, no_of_samples_in_vcf2))
#exclude the ref sample in the 1st column
if no_of_samples > 1:
normalizingConstant = float(
utils.sumOfReciprocals(no_of_samples * 2 - 1))
else:
normalizingConstant = 1
noOfSegregatesSitesNormalized = no_of_overlapping_sites / (
normalizingConstant * chrLength)
writer.writerow(header)
"""
#reformat for output
no_of_matches_per_sample_ls = map(repr, no_of_matches_per_sample_ls)
no_of_non_NA_pairs_per_sample_ls = map(repr, no_of_non_NA_pairs_per_sample_ls)
matchFractionLs = map(repr, matchFractionLs)
"""
writer.writerow([chromosome, chrLength, no_of_sites_of_input1, no_of_sites_of_input2, no_of_overlapping_sites, \
overlapping_fraction, overlappingOverInput1, overlappingOverInput2, \
noOfSegregatesSitesNormalized])
del writer
return PassingData(overlapping_sample_id_set=overlapping_sample_id_set,
overlapping_sites_set=overlapping_sites_set)
def setup(self, **keywords):
"""
2012.10.15
run before anything is run
"""
AbstractMatrixFileWalker.setup(self, **keywords)
#self.writer = BeagleGenotypeFile(path=self.outputFname, mode='w')
#read in the IBD check result
self.ibdData = SNP.readAdjacencyListDataIntoMatrix(inputFname=self.pedigreeKinshipFilePath, \
rowIDHeader=None, colIDHeader=None, \
rowIDIndex=0, colIDIndex=1, \
dataHeader=None, dataIndex=2, hasHeader=False)
#. read in the alignment coverage data
alignmentCoverageFile = MatrixFile(
path=self.individualAlignmentCoverageFname)
alignmentCoverageFile.constructColName2IndexFromHeader()
alignmentReadGroup2coverageLs = alignmentCoverageFile.constructDictionary(
keyColumnIndexList=[0], valueColumnIndexList=[1])
alignmentCoverageFile.close()
sys.stderr.write(
"Reading in all samples from %s VCF input files ... \n" %
(len(self.inputFnameLs)))
# read all the Beagle files
individualID2HaplotypeData = {}
for inputFname in self.inputFnameLs:
vcfFile = VCFFile(inputFname=inputFname)
#vcfFile.readInAllHaplotypes()
for individualID in vcfFile.getSampleIDList():
individualID2HaplotypeData[individualID] = None
#haplotypeList = vcfFile.getHaplotypeListOfOneSample(individualID)
#individualID2HaplotypeData[individualID] = PassingData(haplotypeList=haplotypeList,
# locusIDList=vcfFile.locusIDList)
# get all haplotypes , etc.
# get all sample IDs
sys.stderr.write("%s individuals total.\n" %
(len(individualID2HaplotypeData)))
#. read in the pedigree or deduce it from Beagle Trio/Duo genotype file (columns)
#. construct individualID2pedigreeContext, context: familySize=1/2/3, familyPosition=1/2 (parent/child)
sys.stderr.write("Constructing individualID2pedigreeContext ...")
plinkPedigreeFile = PlinkPedigreeFile(path=self.pedigreeFname)
pGraph = plinkPedigreeFile.pedigreeGraph
#shrink the graph to only individuals with data
pGraph = nx.subgraph(pGraph, individualID2HaplotypeData.keys())
cc_subgraph_list = nx.connected_component_subgraphs(
pGraph.to_undirected())
individualID2familyContext = {}
outDegreeContainer = NumberContainer(minValue=0)
familySizeContainer = NumberContainer(minValue=0)
individualCoverageContainer = NumberContainer(minValue=0)
familyCoverageContainer = NumberContainer(minValue=0)
for cc_subgraph in cc_subgraph_list:
familySize = len(cc_subgraph)
familySizeContainer.addOneValue(familySize)
familyCoverage = 0
for n in cc_subgraph: #assuming each family is a two-generation trio/nuclear family
individualCoverage = self.getIndividualCoverage(
individualID=n,
alignmentReadGroup2coverageLs=alignmentReadGroup2coverageLs
)
individualCoverage = float(individualCoverage)
individualCoverageContainer.addOneValue(individualCoverage)
familyCoverage += individualCoverage
in_degree = pGraph.in_degree(n)
out_degree = pGraph.out_degree(n)
outDegreeContainer.addOneValue(out_degree)
familyContext = PassingData(familySize=familySize, in_degree=in_degree, out_degree=out_degree, \
individualCoverage=individualCoverage,\
familyCoverage=None)
if n not in individualID2familyContext:
individualID2familyContext[n] = familyContext
else:
sys.stderr.write(
"Node %s already in individualID2familyContext.\n" %
(n))
familyCoverageContainer.addOneValue(familyCoverage)
#set the family coverage for each member, used in weighing the individual. better covered family => better haplotype
for n in cc_subgraph:
individualID2familyContext[n].familyCoverage = familyCoverage
plinkPedigreeFile.close()
sys.stderr.write("%s individuals.\n" %
(len(individualID2familyContext)))
# weigh each unique individual based on its sequencing coverage + no of offspring => probability mass for each individual
sys.stderr.write(
"Weighing each individual , assigning probability mass ...")
individualID2probabilityMass = {}
for individualID, familyContext in individualID2familyContext.items():
outDegreeQuotient = outDegreeContainer.normalizeValue(
familyContext.familySize)
individualCoverageQuotient = individualCoverageContainer.normalizeValue(
familyContext.individualCoverage)
#familyCoverageQuotient = familyCoverageContainer.normalizeValue(familyContext.familyCoverage)
importanceScore = outDegreeQuotient + individualCoverageQuotient
representativeImportanceScore = importanceScore
individualID2probabilityMass[
individualID] = representativeImportanceScore
sys.stderr.write(" %s IDs with probability mass assigned.\n" %
(len(individualID2probabilityMass)))
self.individualID2probabilityMass = individualID2probabilityMass
self.individualID2HaplotypeData = individualID2HaplotypeData
def traverse(self):
"""
"""
newHeader = []
key2dataLs = {}
#key is the keyColumn,
# dataLs corresponds to the sum of each column from valueColumnLs
delimiter = None
for inputFname in self.inputFnameLs:
if not os.path.isfile(inputFname):
if self.exitNonZeroIfAnyInputFileInexistent:
sys.exit(3)
else:
continue
reader = None
try:
inputFile = utils.openGzipFile(inputFname)
delimiter = figureOutDelimiter(inputFile)
reader = MatrixFile(file_handle=inputFile, delimiter=delimiter)
except:
logging.error(f'Except type: {sys.exc_info()}')
import traceback
traceback.print_exc()
try:
header = next(reader)
self.handleNewHeader(header,
newHeader,
self.keyColumnLs,
self.valueColumnLs,
keyColumnSet=self.keyColumnSet)
if self.noHeader:
inputFile.seek(0)
reader = MatrixFile(file_handle=inputFile,
delimiter=delimiter)
except:
logging.error(f'Except type: {sys.exc_info()}')
import traceback
traceback.print_exc()
if reader is not None:
for row in reader:
try:
self.handleValueColumns(
row,
key2dataLs=key2dataLs,
keyColumnLs=self.keyColumnLs,
valueColumnLs=self.valueColumnLs)
except:
#in case something wrong (i.e. file is empty)
logging.error(f'Ignore this row: {row}.')
logging.error(f'Except type: {sys.exc_info()}')
import traceback
traceback.print_exc()
del reader
if self.noHeader:
newHeader = None
returnData = PassingData(key2dataLs=key2dataLs,
delimiter=delimiter,
header=newHeader)
return returnData
