snpmatch.py 文件源码

def parseGT(snpGT):
    first = snpGT[0]
    snpBinary = np.zeros(len(snpGT), dtype = "int8")
    if first.find('|') != -1:
        ## GT is phased
        separator = "|"
    elif first.find('/') != -1:
        ## GT is not phased
        separator = "/"
    elif np.char.isdigit(first):
        return np.array(np.copy(snpGT), dtype = "int8")
    else:
        die("unable to parse the format of GT in vcf!")
    hetGT = "0" + separator + "1"
    refGT = "0" + separator + "0"
    altGT = "1" + separator + "1"
    nocall = "." + separator + "."
    snpBinary[np.where(snpGT == altGT)[0]] = 1
    snpBinary[np.where(snpGT == hetGT)[0]] = 2
    snpBinary[np.where(snpGT == nocall)[0]] = -1
    return snpBinary