def processHeader(self, reader=None, extendHeader=None, chrLengthHeader="chrLength"):
"""
2012.8.7
"""
header = AddChromosomeLengthToTSVFile.processHeader(
self, reader=reader, extendHeader=extendHeader, chrLengthHeader=chrLengthHeader
)
header.append(self.hetFractionHeader)
return header
def processRow(self, row=None):
"""
2012.8.7
OBS(HOM1/HET/HOM2) (i.e. 13/3/0 )
"""
new_data_row = AddChromosomeLengthToTSVFile.processRow(self, row=row)
col_index = self.col_name2index.get(self.homoHetVectorHeader, None)
yValue = new_data_row[col_index]
vector = yValue.split("/")
vector = map(int, vector)
noOfHomo1, noOfHet, noOfHomo2 = vector
noOfTotal = sum(vector)
if noOfTotal > 0:
yValue = float(noOfHet / float(noOfTotal))
else:
yValue = -1
new_data_row.append(yValue)
return new_data_row
def __init__(self, inputFnameLs=None, **keywords):
"""
2011-7-12
"""
AddChromosomeLengthToTSVFile.__init__(self, inputFnameLs=inputFnameLs, **keywords)
