468346fde26973306a94cce63abdd4c4321a89a7,clairvoyante/utils_v2.py,,GetTrainingArray,#Any#Any#Any#Any#,59

Before Change

        Y[key] = baseVec
    f.stdout.close()
    f.wait()

    X = {}
    f = subprocess.Popen(shlex.split("gzip -fdc %s" % (tensor_fn) ), stdout=subprocess.PIPE, bufsize=8388608)
    total = 0

After Change

        f.wait()

    Y = {}
    if var_fn != None:
        f = subprocess.Popen(shlex.split("gzip -fdc %s" % (var_fn) ), stdout=subprocess.PIPE, bufsize=8388608)
        for row in f.stdout:
            row = row.split()
            ctgName = row[0]
            pos = int(row[1])
            if bed_fn != None:
                if len(tree[ctgName].search(pos)) == 0:
                    continue
            key = ctgName + ":" + str(pos)

            baseVec = [0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]
            //          --------------  ------  ------------    ------------------
            //          Base chng       Zygo.   Var type        Var length
            //          A   C   G   T   HET HOM REF SNP INS DEL 0   1   2   3   4   >=4
            //          0   1   2   3   4   5   6   7   8   9   10  11  12  13  14  15

            if row[4] == "0" and row[5] == "1":
                if len(row[2]) == 1 and len(row[3]) == 1:
                    baseVec[base2num[row[2][0]]] = 0.5
                    baseVec[base2num[row[3][0]]] = 0.5
                elif len(row[2]) > 1 or len(row[3]) > 1:
                    baseVec[base2num[row[2][0]]] = 0.5
                baseVec[4] = 1.

            elif row[4] == "1" and row[5] == "1":
                if len(row[2]) == 1 and len(row[3]) == 1:
                    baseVec[base2num[row[3][0]]] = 1
                elif len(row[2]) > 1 or len(row[3]) > 1:
                    pass
                baseVec[5] = 1.

            if len(row[2]) > 1 and len(row[3]) == 1: baseVec[9] = 1. // deletion
            elif len(row[3]) > 1 and len(row[2]) == 1: baseVec[8] = 1.  // insertion
            else: baseVec[7] = 1.  // SNP

            varLen = abs(len(row[2])-len(row[3]))
            if varLen > 4: baseVec[15] = 1.
            else: baseVec[10+varLen] = 1.

            Y[key] = baseVec
        f.stdout.close()
        f.wait()

    X = {}
    f = subprocess.Popen(shlex.split("gzip -fdc %s" % (tensor_fn) ), stdout=subprocess.PIPE, bufsize=8388608)
    total = 0
    mat = np.empty(((2*param.flankingBaseNum+1)*4*param.matrixNum), dtype=np.float32)

Instances