def main():
scaffoldData, homHetRatios = readScaffoldData(sys.argv[1], delimiter=",")
# print each row with data in scaffoldData
print "\t".join(["Marker", "Chr", "Start", "End", "Pheno", "Color"])
for chrBin, row in readMutationData(sys.argv[2], scaffoldData, delimiter=","):
out = [row[0], chrBin[0], chrBin[1], chrBin[1], row[7], 2 if row[7] == "het" else 1]
print "\t".join(map(str, out))
pass
def main():
scaffoldData, homHetRatios = readScaffoldData(sys.argv[1], delimiter=',')
# print each row with data in scaffoldData
print '\t'.join(['Marker', 'Chr', 'Start', 'End', 'Pheno', 'Color'])
for chrBin, row in readMutationData(sys.argv[2],
scaffoldData,
delimiter=','):
out = [
row[0], chrBin[0], chrBin[1], chrBin[1], row[7],
2 if row[7] == 'het' else 1
]
print '\t'.join(map(str, out))
pass
def processMutationData(fn, scaffoldData, homHetRatios, delimiter=" "):
"""
Counts the number of hom/het mutations per bin, and
calculates het/hom ratio. The hom/het counts are stored in another dictonary per bin
such that we can directly count the number of occurrences of "het" and "hom".
"""
for chrBin, row in readMutationData(fn, scaffoldData, delimiter=delimiter):
homHetRatios[chrBin][row[7]] += 1
# Finished reading data, now calculate ratios.
for chrBin in homHetRatios:
if homHetRatios[chrBin]["hom"] > 0:
homHetRatios[chrBin]["ratio"] = homHetRatios[chrBin]["het"] / homHetRatios[chrBin]["hom"]
else:
# if hom-count is zero, no ratio can be calculated
homHetRatios[chrBin]["ratio"] = "NA"
# convert dictionaries to lists [hom, het, ratio]
homHetRatios[chrBin] = [homHetRatios[chrBin]["hom"], homHetRatios[chrBin]["het"], homHetRatios[chrBin]["ratio"]]
return homHetRatios
def processMutationData(fn, scaffoldData, homHetRatios, delimiter=' '):
"""
Counts the number of hom/het mutations per bin, and
calculates het/hom ratio. The hom/het counts are stored in another dictonary per bin
such that we can directly count the number of occurrences of "het" and "hom".
"""
for chrBin, row in readMutationData(fn, scaffoldData, delimiter=delimiter):
homHetRatios[chrBin][row[7]] += 1
# Finished reading data, now calculate ratios.
for chrBin in homHetRatios:
if homHetRatios[chrBin]['hom'] > 0:
homHetRatios[chrBin]['ratio'] = homHetRatios[chrBin][
'het'] / homHetRatios[chrBin]['hom']
else:
# if hom-count is zero, no ratio can be calculated
homHetRatios[chrBin]['ratio'] = 'NA'
# convert dictionaries to lists [hom, het, ratio]
homHetRatios[chrBin] = [
homHetRatios[chrBin]['hom'], homHetRatios[chrBin]['het'],
homHetRatios[chrBin]['ratio']
]
return homHetRatios