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