[Numpy-discussion] Problem with np.savetxt

[Stephen P. Molnar]

I am embarrassed to be asking this question, but I have exhausted Google 
at this point .

I have a number of identically formatted text files from which I want to 
extract data, as an example (hopefully, putting these in as quotes will 
persevere the format):

> =======================================================================
> PSOVina version 2.0
> Giotto H. K. Tai & Shirley W. I. Siu
>
> Computational Biology and Bioinformatics Lab
> University of Macau
>
> Visit http://cbbio.cis.umac.mo for more information.
>
> PSOVina was developed based on the framework of AutoDock Vina.
>
> For more information about Vina, please visit http://vina.scripps.edu.
>
> =======================================================================
>
> Output will be 13-7_out.pdbqt
> Reading input ... done.
> Setting up the scoring function ... done.
> Analyzing the binding site ... done.
> Using random seed: 1828390527
> Performing search ... done.
>
> Refining results ... done.
>
> mode |   affinity | dist from best mode
>      | (kcal/mol) | rmsd l.b.| rmsd u.b.
> -----+------------+----------+----------
>    1    -8.862004149      0.000      0.000
>    2    -8.403522829      2.992      6.553
>    3    -8.401384636      2.707      5.220
>    4    -7.886402037      4.907      6.862
>    5    -7.845519031      3.233      5.915
>    6    -7.837434227      3.954      5.641
>    7    -7.834584887      3.188      7.294
>    8    -7.694395765      3.746      7.553
>    9    -7.691211177      3.536      5.745
>   10    -7.670759445      3.698      7.587
>   11    -7.661882758      4.882      7.044
>   12    -7.636280303      2.347      3.284
>   13    -7.635788052      3.511      6.250
>   14    -7.611175249      2.427      3.449
>   15    -7.586368357      2.142      2.864
>   16    -7.531307666      2.976      4.980
>   17    -7.520501084      3.085      5.775
>   18    -7.512906514      4.220      7.672
>   19    -7.307403528      3.240      4.354
>   20    -7.256063348      3.694      7.252
> Writing output ... done.
  At this point, my python script consists of only the following:

> #!/usr/bin/env python3
> # -*- coding: utf-8 -*-
> """
>
> Created on Tue Sep 24 07:51:11 2019
>
> """
> import numpy as np
>
> data = []
>
> data = np.genfromtxt("13-7.log", usecols=(1), dtype=None, 
> skip_header=27, skip_footer=1, encoding=None)
>
> print(data)
>
> np.savetxt('13-7', [data], fmt='%15.9f', header='13-7')

The problem lies in tfe np.savetxt line, on execution I get:

> runfile('/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/VINA20/SmallSet/DeltaGTable_V_s.py', 
> wdir='/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/VINA20/SmallSet', 
> current_namespace=True)
> ['-8.839713733' '-8.743377250' '-8.151051167' '-8.090452911'
>  '-7.967494477' '-7.854890056' '-7.757417879' '-7.741557490'
>  '-7.643885488' '-7.611595767' '-7.507605524' '-7.413920814'
>  '-7.389408331' '-7.384446364' '-7.374206276' '-7.368808179'
>  '-7.346641418' '-7.325037898' '-7.309614787' '-7.113209147']
> Traceback (most recent call last):
>
>   File 
> "/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/VINA20/SmallSet/DeltaGTable_V_s.py", 
> line 16, in <module>
>     np.savetxt('13-7', [data], fmt='%16.9f', header='13-7')
>
>   File "<__array_function__ internals>", line 6, in savetxt
>
>   File 
> "/home/comp/Apps/Miniconda3/lib/python3.7/site-packages/numpy/lib/npyio.py", 
> line 1438, in savetxt
>     % (str(X.dtype), format))
>
> TypeError: Mismatch between array dtype ('<U12') and format specifier 
> ('%16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f 
> %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f %16.9f 
> %16.9f')

The data is in the data file, but the only entry in '13-7', the saved 
file, is the label. Obviously, the error is in the format argument.

Help will be much appreciated.

Thanks in advance.

-- 
Stephen P. Molnar, Ph.D.
www.molecular-modeling.net
614.312.7528 (c)
Skype:  smolnar1