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

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

i examining code here.

when running code get:

[root@mycomp]$ python needleman-wunsch.py traceback (most recent phone 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) (conv, val) in zip(converters, vals)] valueerror: not convert string float: r n d c q e g h l k m f p s t w y v

a minimal illustration reproduces is:

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

with data.txt being:

r n d c q 5 -2 -1 -2 -1 -1 r -2 7 -1 -2 -4 1 n -1 -1 7 2 -2 0

you can have the original blosum50.txt file , total code the link above.

erasing first line of blosum50.txt gave same error.

you can replace loadtxt with

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

this skips header, converts column names nan , chops them off.

python numpy alignment sequence