def run(self):
"""
"""
if self.debug:
import pdb
pdb.set_trace()
if not os.path.isfile(self.inputFname):
sys.stderr.write("Error: file, %s, is not a file.\n" %
(self.inputFname))
sys.exit(3)
inputFile = utils.openGzipFile(self.inputFname, 'r')
outputPolymorphismFile = PolymorphismTableFile(self.outputFname, openMode='w', isPhased=1, \
ploidy=self.ploidy)
outputChromosomeSequenceFile = open(self.outputChromosomeSequenceFname,
"w")
commandline = inputFile.next().strip()
outputPolymorphismFile.addAttribute('commandline',
value=commandline,
overwrite=True,
tableName='polymorphism')
for line in inputFile:
if self.iterationPattern.search(
line): #one iteration is regarded as one species
self.outputOneIteration(inputFile=inputFile, iterationLine=line, outputPolymorphismFile=outputPolymorphismFile,\
outputChromosomeSequenceFile=outputChromosomeSequenceFile, ploidy=self.ploidy)
inputFile.close()
outputPolymorphismFile.close()
outputChromosomeSequenceFile.close()
def run(self):
"""
input looks like (inputFileFormat=1)
msHOT-lite 2 1 -t 4781.50413187402 -r 790.4466018 ...
//
segsites: 40567
positions: 0.0002 0.0003
001001101011011001...
101001010100101111...
...
./msHOT-lite 2 1 -t 84989.8346003745 -r 34490.1412746802 30000000 -l -en 0.0013 1 0.0670 -en 0.0022 1 0.3866 -en 0.0032 1 0.3446 -en 0.0044 1 0.21
79 -en 0.0059 1 0.1513 -en 0.0076 1 0.1144 -en 0.0096 1 0.0910 -en 0.0121 1 0.0757 -en 0.0150 1 0.0662 -en 0.0184 1 0.0609 -en 0.0226 1 0.0583 -en
0.0275 1 0.0572 -en 0.0333 1 0.0571 -en 0.0402 1 0.0577 -en 0.0485 1 0.0589 -en 0.0583 1 0.0603 -en 0.0700 1 0.0615 -en 0.0839 1 0.0624 -en 0.100
5 1 0.0632 -en 0.1202 1 0.0641 -en 0.1437 1 0.0651 -en 0.1716 1 0.0663 -en 0.2048 1 0.0678 -en 0.2444 1 0.0696 -en 0.2914 1 0.0719 -en 0.3475 1 0.
0752 -en 0.4935 1 0.0794
//
@begin 6422
30000000
1100 01
6074 10
29966899 10
29971027 01
29973740 01
29982767 01
29985696 10
@end
"""
if self.debug:
import pdb
pdb.set_trace()
if not os.path.isfile(self.inputFname):
sys.stderr.write("Error: file, %s, is not a file.\n" %
(self.inputFname))
sys.exit(3)
inputFile = utils.openGzipFile(self.inputFname, 'r')
outputPolymorphismFile = PolymorphismTableFile(self.outputFname, openMode='w', isPhased=1, \
ploidy=self.ploidy)
commandline = inputFile.next().strip()
outputPolymorphismFile.addAttribute('commandline',
value=commandline,
overwrite=True,
tableName='polymorphism')
self._convert(inputFile=inputFile,
outputPolymorphismFile=outputPolymorphismFile,
ploidy=self.ploidy)
inputFile.close()
outputPolymorphismFile.close()
class SimulatePedigreeHaplotype(ComparePedigreeFromMultipleInput):
__doc__ = __doc__
option_default_dict = ComparePedigreeFromMultipleInput.option_default_dict.copy()
#option_default_dict.pop(('inputFname', 0, ))
option_default_dict.update({
('recombinationRate', 1, float):[1.5e-8, '', 1, 'recombination rate per meiosis'],\
('enableIntraLocusRecombination', 0, int):[0, '', 1, 'toggle to enable intra-locus recombination, \n\
only applicable to non-single-nucleotide loci'],\
('inputPedigreeFname', 1, ):['', '', 1, "pedigree file, LINKAGE format, Column 1: pedigree identifier.\n\
Column 2: individual's ID\n\
Column 3: the ID of the individual's father\n\
Column 4: the ID of the individual's mother\n\
Column 5: sex (1=male, 2=female)\n\
Column 6-N: affection status (optional)"],\
('mutationRate', 0, float):[0, '', 1, 'mutation rate per nucleotide per generation'],\
('ploidy', 0, int):[2, '', 1, 'how many sets of chromosomes one individual carries (for output). ploidy=2 means diploid.'],\
('speciesName', 0, ):['doggie', '', 1, 'a phantom species name (for output).'],\
})
def __init__(self, inputFnameLs=None, **keywords):
AbstractMapper.__init__(self, inputFnameLs=inputFnameLs, **keywords)
def sampleRecombinantHaplotype(self, parentalHaplotypeList=None, locusPositionList=None, recombinationRate=1.5e-8, enableIntraLocusRecombination=False,\
chromosomeLength=None):
"""
2013.3.6
argument enableIntraLocusRecombination is not used at this moment.
#. figure out how many recombinations (=n) for this chromosome, from binomial distribution
#. uniformly choose n positions from the chromosome
#. there are N-1 possible locations for recombination. N=chromosome length
"""
noOfRecombinationEvents = numpy.random.binomial(chromosomeLength, recombinationRate)
recombinationLocationList = None
ploidy = len(parentalHaplotypeList)
if noOfRecombinationEvents>0:
recombinationLocationList = numpy.random.randint(1, chromosomeLength+1, size=noOfRecombinationEvents)
#chromosomeLength+1 is excluded
recombinationLocationList.sort()
#reverse it so that the first recombination event is now the last, which first pops out upon pop().
recombinationLocationList.reverse()
nextRecombinationLocation = recombinationLocationList.pop()
locusIndexSpanAndHaplotypeIndexList = []
startLocusIndex =0
currentHaplotypeIndex = 0 #start from the first haplotype
noOfPolymorphicLoci = len(locusPositionList)
for i in xrange(noOfPolymorphicLoci):
locusPosition = locusPositionList[i]
if locusPosition>=nextRecombinationLocation:
locusIndexSpanAndHaplotypeIndexList.append((startLocusIndex, i+1, currentHaplotypeIndex))
#i is included in current haplotype block, next one starts from i+1
startLocusIndex = i+1
#a recombination, switches to a different haplotype for the next block
currentHaplotypeIndex = (currentHaplotypeIndex+1)%(ploidy) #alternate to the next parental haplotype index
if len(recombinationLocationList)>0:
nextRecombinationLocation = recombinationLocationList.pop()
else: #last recombination event has just been visited
#add the last block and exit
if startLocusIndex<noOfPolymorphicLoci: #make sure not beyond
locusIndexSpanAndHaplotypeIndexList.append((startLocusIndex, noOfPolymorphicLoci, currentHaplotypeIndex))
break
elif i==noOfPolymorphicLoci-1: #reach the last locus but there are still recombination to its right
#add the last block
locusIndexSpanAndHaplotypeIndexList.append((startLocusIndex, noOfPolymorphicLoci, currentHaplotypeIndex))
recombinantHaplotype = parentalHaplotypeList[0]
for locusIndexSpanAndHaplotypeIndex in locusIndexSpanAndHaplotypeIndexList:
startLocusIndex, stopLocusIndex, currentHaplotypeIndex = locusIndexSpanAndHaplotypeIndex
currentHaplotype = parentalHaplotypeList[currentHaplotypeIndex]
recombinantHaplotype[startLocusIndex:stopLocusIndex] = currentHaplotype[startLocusIndex:stopLocusIndex]
else: #no recombination, just pick one haplotype
i = numpy.random.randint(0, len(parentalHaplotypeList))
recombinantHaplotype = parentalHaplotypeList[i]
return PassingData(recombinantHaplotype=recombinantHaplotype, recombinationLocationList=recombinationLocationList)
def run(self):
if self.debug:
import pdb
pdb.set_trace()
#read in the pedigree graph
graphData = self.constructPedigreeGraphFromOneFile(inputFname=self.inputPedigreeFname)
# read in the haplotype pool for founders
self.inputPolymorphismTableFile = PolymorphismTableFile(self.inputFname, openMode='r', constructSNPData=False)
if not self.inputPolymorphismTableFile.isPhased:
sys.stderr.write("Error input file %s has unphased polymorphism data, can't sample haplotypes.\n"%(self.inputFname))
sys.exit(4)
# set up output
self.outputPolymorphismFile = PolymorphismTableFile(self.outputFname, openMode='w', isPhased=1, ploidy=self.ploidy)
self.outputPolymorphismFile.writePedigreeDiGraph2IndividualTable(diGraph=graphData.DG, \
populationName="", speciesName=self.speciesName, \
ploidy=self.ploidy)
self.outputPolymorphismFile.writeChrStartStopTupleList2LocusTable(chr_start_stop_list=\
self.inputPolymorphismTableFile.locusChrStartStopList,\
speciesName=self.speciesName, ploidy=self.ploidy)
# order the pedigree members based on their distance to the founders
founderDistance2NodeList = graphData.DG.orderMembersByDistanceToFounders()
#2013.10.16 YH: bug needs to be fixed here. orderMembersByDistanceToFounders() does not return a data structure like founderDistance2NodeList.
individualName2polymorphismData = {}
chromosomeLength = self.inputPolymorphismTableFile.snpData.col_id_ls[-1][2] #stop of the last locus is chromosomeLength
#. sample haplotypes for founders / their descendents
for founderDistance, individualNameList in founderDistance2NodeList.iteritems():
for individualName in individualNameList:
polymorphismData = OneIndividualPolymorphismData(isPhased=True, ploidy=self.ploidy)
if founderDistance==0: #sample haplotypes for founders
if self.inputPolymorphismTableFile.ploidy==2 and self.inputPolymorphismTableFile.isPhased:
#input is diploid, phased haplotype data
polymorphismData = self.inputPolymorphismTableFile.sampleOneIndividualPolymorphismWithReplacement()
else:
# self.inputPolymorphismTableFile.ploidy==1 or self.inputPolymorphismTableFile.ploidy is None:
#input is haplotype or unknown ploidy
for i in xrange(self.ploidy):
haplotype = self.inputPolymorphismTableFile.sampleOneRandomHaplotypeWithReplacement()
polymorphismData.addHaplotype(haplotype)
else: #sample recombinant haplotype based on two parents' four haplotypes
polymorphismData = OneIndividualPolymorphismData()
parents = graphData.DG.predecessors(individualName)
for parentName in parents:
parentalHaplotypeList = individualName2polymorphismData.get(parentName).haplotypeList
returnData = self.sampleRecombinantHaplotype(parentalHaplotypeList=parentalHaplotypeList, \
locusPositionList=self.inputPolymorphismTableFile.locusStartPositionList,\
recombinationRate=self.recombinationRate, \
enableIntraLocusRecombination=self.enableIntraLocusRecombination, \
chromosomeLength=chromosomeLength)
#output recombination events
if returnData.recombinationLocationList:
self.outputPolymorphismFile.writeRecombinationEvents(parentName=parentName, childName=individualName, \
recombinationLocationList=returnData.recombinationLocationList)
polymorphismData.addHaplotype(returnData.haplotype)
individualName2polymorphismData[individualName] = polymorphismData
#. output
self.outputPolymorphismFile.writeIndividualName2PolymorphismData(\
individualName2polymorphismData=individualName2polymorphismData,\
speciesName=self.speciesName, ploidy=self.ploidy)
self.outputPolymorphismFile.close()
def run(self):
if self.debug:
import pdb
pdb.set_trace()
#read in the pedigree graph
graphData = self.constructPedigreeGraphFromOneFile(inputFname=self.inputPedigreeFname)
# read in the haplotype pool for founders
self.inputPolymorphismTableFile = PolymorphismTableFile(self.inputFname, openMode='r', constructSNPData=False)
if not self.inputPolymorphismTableFile.isPhased:
sys.stderr.write("Error input file %s has unphased polymorphism data, can't sample haplotypes.\n"%(self.inputFname))
sys.exit(4)
# set up output
self.outputPolymorphismFile = PolymorphismTableFile(self.outputFname, openMode='w', isPhased=1, ploidy=self.ploidy)
self.outputPolymorphismFile.writePedigreeDiGraph2IndividualTable(diGraph=graphData.DG, \
populationName="", speciesName=self.speciesName, \
ploidy=self.ploidy)
self.outputPolymorphismFile.writeChrStartStopTupleList2LocusTable(chr_start_stop_list=\
self.inputPolymorphismTableFile.locusChrStartStopList,\
speciesName=self.speciesName, ploidy=self.ploidy)
# order the pedigree members based on their distance to the founders
founderDistance2NodeList = graphData.DG.orderMembersByDistanceToFounders()
#2013.10.16 YH: bug needs to be fixed here. orderMembersByDistanceToFounders() does not return a data structure like founderDistance2NodeList.
individualName2polymorphismData = {}
chromosomeLength = self.inputPolymorphismTableFile.snpData.col_id_ls[-1][2] #stop of the last locus is chromosomeLength
#. sample haplotypes for founders / their descendents
for founderDistance, individualNameList in founderDistance2NodeList.iteritems():
for individualName in individualNameList:
polymorphismData = OneIndividualPolymorphismData(isPhased=True, ploidy=self.ploidy)
if founderDistance==0: #sample haplotypes for founders
if self.inputPolymorphismTableFile.ploidy==2 and self.inputPolymorphismTableFile.isPhased:
#input is diploid, phased haplotype data
polymorphismData = self.inputPolymorphismTableFile.sampleOneIndividualPolymorphismWithReplacement()
else:
# self.inputPolymorphismTableFile.ploidy==1 or self.inputPolymorphismTableFile.ploidy is None:
#input is haplotype or unknown ploidy
for i in xrange(self.ploidy):
haplotype = self.inputPolymorphismTableFile.sampleOneRandomHaplotypeWithReplacement()
polymorphismData.addHaplotype(haplotype)
else: #sample recombinant haplotype based on two parents' four haplotypes
polymorphismData = OneIndividualPolymorphismData()
parents = graphData.DG.predecessors(individualName)
for parentName in parents:
parentalHaplotypeList = individualName2polymorphismData.get(parentName).haplotypeList
returnData = self.sampleRecombinantHaplotype(parentalHaplotypeList=parentalHaplotypeList, \
locusPositionList=self.inputPolymorphismTableFile.locusStartPositionList,\
recombinationRate=self.recombinationRate, \
enableIntraLocusRecombination=self.enableIntraLocusRecombination, \
chromosomeLength=chromosomeLength)
#output recombination events
if returnData.recombinationLocationList:
self.outputPolymorphismFile.writeRecombinationEvents(parentName=parentName, childName=individualName, \
recombinationLocationList=returnData.recombinationLocationList)
polymorphismData.addHaplotype(returnData.haplotype)
individualName2polymorphismData[individualName] = polymorphismData
#. output
self.outputPolymorphismFile.writeIndividualName2PolymorphismData(\
individualName2polymorphismData=individualName2polymorphismData,\
speciesName=self.speciesName, ploidy=self.ploidy)
self.outputPolymorphismFile.close()