def main():
scaffoldData, homHetRatios = readScaffoldData(sys.argv[1], delimiter=',')
homHetRatios = processMutationData(sys.argv[2], scaffoldData, homHetRatios)
# for each bin: output chromosome, bin, hom, het, ratio
for chrBin in sorted(homHetRatios):
print '\t'.join(map(str, list(chrBin) + homHetRatios[chrBin]))
pass
def main():
scaffoldData, homHetRatios = readScaffoldData(sys.argv[1], delimiter=",")
homHetRatios = processMutationData(sys.argv[2], scaffoldData, homHetRatios)
# for each bin: output chromosome, bin, hom, het, ratio
for chrBin in sorted(homHetRatios):
print "\t".join(map(str, list(chrBin) + homHetRatios[chrBin]))
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 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, _ = readScaffoldData(sys.argv[1], delimiter=',')
reader = csv.reader(open(sys.argv[2]), delimiter='\t', quotechar='"')
for row in reader:
contig, pos, sus_AO, sus_DP, sus_AF, res_AO, res_DP, res_AF = row
# scaffoldData: scaffold_id: (chromosome, bin)
chromosome_bin = scaffoldData.get(contig, None)
if chromosome_bin is None:
continue
chromosome, bin = chromosome_bin
out_row = map(str, [chromosome, bin, sus_AF, res_AF])
sys.stdout.write('\t'.join(out_row) + '\n')
pass
def main():
scaffoldData, _ = readScaffoldData(sys.argv[1], delimiter=',')
reader = csv.reader(open(sys.argv[2]), delimiter='\t', quotechar='"')
for row in reader:
contig, pos, sus_AO, sus_DP, sus_AF, res_AO, res_DP, res_AF = row
# scaffoldData: scaffold_id: (chromosome, bin)
chromosome_bin = scaffoldData.get(contig, None)
if chromosome_bin is None:
continue
chromosome, bin = chromosome_bin
out_row = map(str, [chromosome, bin, sus_AF, res_AF])
sys.stdout.write('\t'.join(out_row) + '\n')
pass
