python - numpy.loadtxt "could not convert string to float"

Question

重现此内容的最小示例是:

import numpy
numpy.loadtxt("data.txt", delimiter='\t')

data.txt 为:

    A   R   N   D   C   Q
A   5   -2  -1  -2  -1  -1
R   -2  7   -1  -2  -4  1
N   -1  -1  7   2   -2  0

运行代码时出现 ValueError:

[root@mycomp]$ python Needleman-Wunsch.py 
Traceback (most recent call last):
    File "Needleman-Wunsch.py", line 92, in <module>
        (alignedSeq1, alignedSeq2) = computeFMatrix(seq1, seq2, -6)
    File "Needleman-Wunsch.py", line 34, in computeFMatrix
        similarityMatrixMap = readBLOSUM50("BLOSUM50.txt")
    File "Needleman-Wunsch.py", line 16, in readBLOSUM50
        similarityMatrix = np.loadtxt(fileName, delimiter='\t')
    File "/usr/local/lib/python2.7/site-packages/numpy/lib/npyio.py", line 827, in loadtxt
        items = [conv(val) for (conv, val) in zip(converters, vals)]    
    ValueError: could not convert string to float: A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V

你也可以有 the original BLOSUM50.txt file完整代码来自the link above .

删除 BLOSUM50.txt 的第一行给出了同样的错误。

Answer 1

您可以将 loadtxt 替换为

numpy.genfromtxt("data.txt", delimiter='\t', skip_header=True)[:, 1:]

这会跳过标题，将列名转换为 nan，然后将它们切掉。