def run(args):
kgp = kgpInterface(args.data, sys.path[0] + "/KGP_populations.txt")
outfile = open(args.outfile, 'wb')
freqOnly = args.frequencies_only.lower().startswith('t')
wroteHeader = False
for line in kgp.iterate():
if not wroteHeader:
outfile.write('CHROM\tPOS\tID')
if not freqOnly:
for p in kgp.populations[args.pop]:
outfile.write('\t%s_1\t%s_2' % (p, p))
outfile.write('\n')
wroteHeader = True
line.extractChrAndPos()
line.extractAlleles()
line.extractGenotypes()
outfile.write('\t'.join(
[line.chromosome, str(line.position), line.name]))
if freqOnly:
counts = countingDict()
total = 0.0
for p in kgp.populations[args.pop]:
i = kgp.individualIndices[p]
if line.genotypes[i][0] != None:
counts[line.genotypes[i][0]] += 1
total += 1.0
if line.genotypes[i][1] != None:
counts[line.genotypes[i][1]] += 1
total += 1.0
for i, c in counts.iteritems():
outfile.write('\t%s:\t%f' % (line.alleles[i], c / total))
else:
for p in kgp.populations[args.pop]:
i = kgp.individualIndices[p]
a1 = line.genotypes[i][0]
if a1 == None:
a1 = '.'
else:
a1 = line.alleles[a1]
a2 = line.genotypes[i][1]
if a2 == None:
a2 = '.'
else:
a2 = line.alleles[a2]
outfile.write('\t%s\t%s' % (a1, a2))
outfile.write('\n')
outfile.close()
def run(args):
kgp = kgpInterface(args.data,sys.path[0] + "/KGP_populations.txt")
outfile = open(args.outfile,'wb')
freqOnly = args.frequencies_only.lower().startswith('t')
wroteHeader = False
for line in kgp.iterate():
if not wroteHeader:
outfile.write('CHROM\tPOS\tID')
if not freqOnly:
for p in kgp.populations[args.pop]:
outfile.write('\t%s_1\t%s_2' % (p,p))
outfile.write('\n')
wroteHeader = True
line.extractChrAndPos()
line.extractAlleles()
line.extractGenotypes()
outfile.write('\t'.join([line.chromosome,str(line.position),line.name]))
if freqOnly:
counts = countingDict()
total = 0.0
for p in kgp.populations[args.pop]:
i = kgp.individualIndices[p]
if line.genotypes[i][0] != None:
counts[line.genotypes[i][0]] += 1
total += 1.0
if line.genotypes[i][1] != None:
counts[line.genotypes[i][1]] += 1
total += 1.0
for i,c in counts.iteritems():
outfile.write('\t%s:\t%f' % (line.alleles[i],c/total))
else:
for p in kgp.populations[args.pop]:
i = kgp.individualIndices[p]
a1 = line.genotypes[i][0]
if a1 == None:
a1 = '.'
else:
a1 = line.alleles[a1]
a2 = line.genotypes[i][1]
if a2 == None:
a2 = '.'
else:
a2 = line.alleles[a2]
outfile.write('\t%s\t%s' % (a1,a2))
outfile.write('\n')
outfile.close()
def run(args, tickFunction=tick, numTicks=100):
kgp = kgpInterface(args.data, sys.path[0] + "/KGP_populations.txt")
outfile, takenTags, headerline, myPopulations, myPopulationIndices = parseVcfHeader(
args.infile, args.outfile, args.popFile)
statsToCalculate = {
} # {INFO tag : (allStats.statistic,targetPop,backgroundPop,"ASC"/"DEC",REF/ALT hack: True/False,backTag))}
alleleOrders = {}
def storeCalcDetails(stat, calculation):
if not len(calculation) > 0:
raise Exception('Must specify a target population!')
target = calculation[0]
background = calculation[1] if len(calculation) > 1 else None
direction = calculation[2] if len(calculation) > 2 else 'ASC'
hack = len(calculation) > 3 and calculation[3].strip().lower(
).startswith('t')
tag = "%s_%s_" % (target, allStats.STAT_NAMES[stat])
if background == None:
backTag = "ALT"
tag += backTag
infoLine = "##INFO=<ID=%s,Number=A,Type=Float,Description=\"calcStats.py: %s for the %s population\">\n" % (
tag, allStats.STAT_NAMES[stat], target)
else:
backTag = "%s_%s_AO" % (direction, background)
temp = backTag
dupNumber = 2
while backTag in takenTags or backTag in myPopulations.iterkeys(
) or backTag in kgp.populations.iterkeys():
backTag = temp + str(dupNumber)
dupNumber += 1
alleleOrders[backTag] = (direction, background)
tag += backTag
if hack:
tag += "_rHack"
infoLine = "##INFO=<ID=%s,Number=.,Type=Float,Description=\"calcStats.py: %s for the %s population, with alleles ordered by %s AF in the %s population (%s).%s\">\n" % (
tag, allStats.STAT_NAMES[stat], target, "ascending"
if direction == 'ASC' else "descending", background, backTag,
" When %s has no data, the REF/ALT allele order is used." %
background if hack else "")
dupNumber = 2
temp = tag
while tag in takenTags:
tag = temp + str(dupNumber)
dupNumber += 1
statsToCalculate[tag] = (stat, target, background, direction, hack,
backTag)
return infoLine
if args.calculate_AF != None:
for calculation in args.calculate_AF:
outfile.write(storeCalcDetails(allStats.AF, calculation))
if args.calculate_Carriage != None:
for calculation in args.calculate_Carriage:
outfile.write(storeCalcDetails(allStats.Carriage, calculation))
if args.calculate_Samples_w_calls != None:
for calculation in args.calculate_Samples_w_calls:
assert len(calculation) == 1
outfile.write(
storeCalcDetails(allStats.Samples_w_calls, calculation))
for popTag, (direction, background) in alleleOrders.iteritems():
outfile.write(
"##INFO=<ID=%s,Number=.,Type=String,Description=\"calcStats.py: All observed alleles for each locus, ordered by %s AF in the %s population.\">\n"
% (popTag, "ascending" if direction == 'ASC' else "descending",
background))
outfile.write(headerline)
def getPopIndices(pop):
if myPopulationIndices.has_key(pop):
vcfIndices = []
kgpIndices = []
for i in myPopulationIndices[pop]:
if isinstance(i, str):
if not i in kgp.header[9:]:
raise Exception(
"Unknown sample (not in your .vcf or the KGP): %s"
% i)
i = kgp.header.index(i) - 9
kgpIndices.append(i)
else:
vcfIndices.append(i)
else:
vcfIndices = []
kgpIndices = kgp.populationIndices[pop]
return (vcfIndices, kgpIndices)
for vcfLine, kgpLine in kgp.iterateVcf(args.infile,
tickFunction=tickFunction,
numTicks=numTicks):
# first get the allele orders we need, add them as INFO fields
alleleLists = {} # popTag : []
vcfLine.extractAlleles()
vcfLine.extractInfo()
if kgpLine != None:
kgpLine.extractAlleles()
for popTag, (direction, background) in alleleOrders.iteritems():
vcfIndices, kgpIndices = getPopIndices(background)
tempAlleles = set(vcfLine.alleles)
if kgpLine != None:
tempAlleles.update(kgpLine.alleles)
tempAlleles = list(tempAlleles)
tempFreqs = allStats.calculate(allStats.AF, vcfLine, vcfIndices,
kgpLine, kgpIndices, tempAlleles)
if len(tempFreqs) < 1 or math.isinf(tempFreqs[0]):
vcfLine.info[popTag] = "."
alleleLists[popTag] = None
else:
if direction == 'ASC':
alleleLists[popTag] = sorted(
tempAlleles,
key=lambda i: tempFreqs[tempAlleles.index(i)])
else:
alleleLists[popTag] = sorted(
tempAlleles,
key=lambda i: tempFreqs[tempAlleles.index(i)],
reverse=True)
vcfLine.info[popTag] = ",".join(alleleLists[popTag])
# now calculate based on those allele orders
for tag, (stat, target, background, direction, hack,
backTag) in statsToCalculate.iteritems():
vcfIndices, kgpIndices = getPopIndices(target)
if backTag == 'ALT':
alleles = vcfLine.alleles
else:
alleles = alleleLists[backTag]
if alleles == None:
if hack:
alleles = vcfLine.alleles
else:
vcfLine.info[tag] = "."
continue
result = allStats.calculate(stat, vcfLine, vcfIndices, kgpLine,
kgpIndices, alleles)
if isinstance(result, list):
result = ",".join([str(r) for r in result])
else:
result = str(result)
vcfLine.info[tag] = result
outfile.write(str(vcfLine))
outfile.close()
def run(args, tickFunction=tick, numTicks=100):
kgp = kgpInterface(args.data,sys.path[0] + "/KGP_populations.txt")
outfile,takenTags,headerline,myPopulations,myPopulationIndices = parseVcfHeader(args.infile,args.outfile,args.popFile)
statsToCalculate = {} # {INFO tag : (allStats.statistic,targetPop,backgroundPop,"ASC"/"DEC",REF/ALT hack: True/False,backTag))}
alleleOrders = {}
def storeCalcDetails(stat,calculation):
if not len(calculation) > 0:
raise Exception('Must specify a target population!')
target = calculation[0]
background = calculation[1] if len(calculation) > 1 else None
direction = calculation[2] if len(calculation) > 2 else 'ASC'
hack = len(calculation) > 3 and calculation[3].strip().lower().startswith('t')
tag = "%s_%s_" % (target,allStats.STAT_NAMES[stat])
if background == None:
backTag = "ALT"
tag += backTag
infoLine = "##INFO=<ID=%s,Number=A,Type=Float,Description=\"calcStats.py: %s for the %s population\">\n" % (tag,allStats.STAT_NAMES[stat],target)
else:
backTag = "%s_%s_AO" % (direction,background)
temp = backTag
dupNumber = 2
while backTag in takenTags or backTag in myPopulations.iterkeys() or backTag in kgp.populations.iterkeys():
backTag = temp + str(dupNumber)
dupNumber += 1
alleleOrders[backTag] = (direction,background)
tag += backTag
if hack:
tag += "_rHack"
infoLine = "##INFO=<ID=%s,Number=.,Type=Float,Description=\"calcStats.py: %s for the %s population, with alleles ordered by %s AF in the %s population (%s).%s\">\n" % (tag,
allStats.STAT_NAMES[stat],
target,
"ascending" if direction == 'ASC' else "descending",
background,
backTag,
" When %s has no data, the REF/ALT allele order is used." % background if hack else "")
dupNumber = 2
temp = tag
while tag in takenTags:
tag = temp + str(dupNumber)
dupNumber += 1
statsToCalculate[tag] = (stat,target,background,direction,hack,backTag)
return infoLine
if args.calculate_AF != None:
for calculation in args.calculate_AF:
outfile.write(storeCalcDetails(allStats.AF,calculation))
if args.calculate_Carriage != None:
for calculation in args.calculate_Carriage:
outfile.write(storeCalcDetails(allStats.Carriage,calculation))
if args.calculate_Samples_w_calls != None:
for calculation in args.calculate_Samples_w_calls:
assert len(calculation) == 1
outfile.write(storeCalcDetails(allStats.Samples_w_calls,calculation))
for popTag,(direction,background) in alleleOrders.iteritems():
outfile.write("##INFO=<ID=%s,Number=.,Type=String,Description=\"calcStats.py: All observed alleles for each locus, ordered by %s AF in the %s population.\">\n" % (popTag,
"ascending" if direction == 'ASC' else "descending",
background))
outfile.write(headerline)
def getPopIndices(pop):
if myPopulationIndices.has_key(pop):
vcfIndices = []
kgpIndices = []
for i in myPopulationIndices[pop]:
if isinstance(i,str):
if not i in kgp.header[9:]:
raise Exception("Unknown sample (not in your .vcf or the KGP): %s" % i)
i = kgp.header.index(i)-9
kgpIndices.append(i)
else:
vcfIndices.append(i)
else:
vcfIndices = []
kgpIndices = kgp.populationIndices[pop]
return (vcfIndices,kgpIndices)
for vcfLine,kgpLine in kgp.iterateVcf(args.infile,tickFunction=tickFunction,numTicks=numTicks):
# first get the allele orders we need, add them as INFO fields
alleleLists = {} # popTag : []
vcfLine.extractAlleles()
vcfLine.extractInfo()
if kgpLine != None:
kgpLine.extractAlleles()
for popTag,(direction,background) in alleleOrders.iteritems():
vcfIndices,kgpIndices = getPopIndices(background)
tempAlleles = set(vcfLine.alleles)
if kgpLine != None:
tempAlleles.update(kgpLine.alleles)
tempAlleles = list(tempAlleles)
tempFreqs = allStats.calculate(allStats.AF,vcfLine,vcfIndices,kgpLine,kgpIndices,tempAlleles)
if len(tempFreqs) < 1 or math.isinf(tempFreqs[0]):
vcfLine.info[popTag] = "."
alleleLists[popTag] = None
else:
if direction == 'ASC':
alleleLists[popTag] = sorted(tempAlleles,key=lambda i:tempFreqs[tempAlleles.index(i)])
else:
alleleLists[popTag] = sorted(tempAlleles,key=lambda i:tempFreqs[tempAlleles.index(i)],reverse=True)
vcfLine.info[popTag] = ",".join(alleleLists[popTag])
# now calculate based on those allele orders
for tag,(stat,target,background,direction,hack,backTag) in statsToCalculate.iteritems():
vcfIndices,kgpIndices = getPopIndices(target)
if backTag == 'ALT':
alleles = vcfLine.alleles
else:
alleles = alleleLists[backTag]
if alleles == None:
if hack:
alleles = vcfLine.alleles
else:
vcfLine.info[tag] = "."
continue
result = allStats.calculate(stat,vcfLine,vcfIndices,kgpLine,kgpIndices,alleles)
if isinstance(result,list):
result = ",".join([str(r) for r in result])
else:
result = str(result)
vcfLine.info[tag] = result
outfile.write(str(vcfLine))
outfile.close()
