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.iteritems():
if familySize not in familySize2BeagleFileHandler:
tmpOutputFnamePrefix = '%s_familySize%s' % (outputFnamePrefix,
familySize)
writer = MatrixFile(inputFname='%s.bgl' %
(tmpOutputFnamePrefix),
openMode='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(inputFname='%s.markers' % (outputFnamePrefix),
openMode='w',
delimiter=' ')
counter += 1
sys.stderr.write("%s files outputted.\n" % (counter))
return PassingData(
familySize2BeagleFileHandler=familySize2BeagleFileHandler,
markersFile=markersFile)
def run(self):
"""
"""
if self.debug:
import pdb
pdb.set_trace()
reader = MatrixFile(inputFname=self.inputFname)
reader.constructColName2IndexFromHeader()
meanMendelErrorIndex = reader.getColIndexGivenColHeader(
"meanMendelError")
noOfLociIndex = reader.getColIndexGivenColHeader("sampled_base_count")
sumOfMendelErrorIndex = reader.getColIndexGivenColHeader(
"sumOfMendelError")
plinkPedigreeFile = PlinkPedigreeFile(inputFname=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, openMode='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()
