def setup(self, **keywords):
"""
"""
AbstractMatrixFileWalker.setup(self, **keywords)
#construct a individualCode2readGroup from readGroupFname
self.invariantPData.individualCode2readGroup = {}
reader = MatrixFile(inputFname=self.readGroupFname)
reader.constructColName2IndexFromHeader()
if self.readGroupHeader:
readGroupIndex = reader.getColIndexGivenColHeader(self.readGroupHeader)
else:
readGroupIndex = 0
for row in reader:
readGroup = row[readGroupIndex]
individualAlignment = self.db_vervet.parseAlignmentReadGroup(readGroup).individualAlignment
if individualAlignment:
individual_code = individualAlignment.individual_sequence.individual.code
self.invariantPData.individualCode2readGroup[individual_code] = readGroup
del reader
return 1
