IndexError: index 261861 is out of bounds for axis 0 with size 169567

Question

我是编程初学者，遇到以下问题：我想写一个定义，在其中我使用 vcf 文件（使用 pyvcf）中所选染色体的数据创建一个空矩阵。空矩阵已正确创建。

IndexError：索引 261861 超出轴 0 的范围，大小为 169567

但是如果我尝试将第二条染色体作为输入，则会出现上述错误。第一条染色体在索引 262860 处结束，这就是为什么我想以某种方式将行的数据放在矩阵的这一行中，但我不明白为什么！

这是我的代码：

def creatematrix(newfile):

'''Based on the choice of a chromosome, this function fetches the positions and the DP values out of the vcf and saves it in a matrix.'''

    vcf_reader = vcf.Reader(open(newfile), 'r')
    numpos=0
    Chr=input("Chromosome: ")
    with open(newfile,'r') as newerfile: 
        for line in newerfile: 
            if line.startswith(Chr):
                numpos=numpos+1

    matrix = np.zeros(shape=(numpos,6)) -> here i am creating the matrix with so much lines as lines are in the vcf for the chosen chromosome (numpos)

    z=0
    for rec in vcf_reader:
        if rec.CHROM==Chr:
            matrix[z,0]=rec.CHROM
            matrix[z,1]=rec.POS 
            for samples in rec.samples:
                matrix[z,2]=samples['GT']
                matrix[z,3]=samples['DP']
        z=z+1

我真的希望有人能帮我解决这个问题！

您好，米莲娜

Answer 1

您正在为 vcf_reader 中的每一行添加 z，而您只希望在您想要的染色体被识别时才这样做。

只需将 z=z+1 放在 if 语句中就可以达到这样的效果：

z=0
for rec in vcf_reader:
    if rec.CHROM==Chr:
        matrix[z,0]=rec.CHROM
        matrix[z,1]=rec.POS 
        for samples in rec.samples:   # You might want to check this for loop as well. Now you are overwriting matrix[z, 2] and matrix[z, 3] everytime so you only save the last samples?
            matrix[z,2]=samples['GT']
            matrix[z,3]=samples['DP']
        z=z+1 # z now only increases when the matched chromosome is found.

IndexError: index 261861 is out of bounds for axis 0 with size 169567

IndexError: index 261861 is out of bounds for axis 0 with size 169567

python

indexing

error-handling

vcf-vcard

matrix