On Tue, Oct 8, 2019 at 3:17 PM Stephen P. Molnar <s.mol...@sbcglobal.net> wrote:
>
> 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.
Hi,
One problem is the format: the error is telling you that you have
strings in your array (compare the `'<U12'` dtype and the output of
your `print(data)` call with strings inside), whereas %16.9f can only
be used to format floats (f for float). You would first have to
convert your array of strings to an array numbers. I don't usually use
genfromtxt so I'm not sure how you can make it return floats for you
in the first place, but I suspect `dtype=None` in the call to
genfromtxt might be responsible. In any case making it return numbers
should be the easier case.
The second problem is that you should make sure you mean `[data]` in
the call to savetxt. As it is now this would give you a 2d array of
shape (1, 20), and the output would correspondingly contain a single
row of 20 values (hence the 20 instances of '%16.9f' in the error
message). In case you meant to print one value per row in a single
column, you should drop the brackets around `data`:
np.savetxt('13-7', data, fmt='%16.9f', header='13-7')
And just a personal note, but I'd find an output file named '13-7' to
be a bit surprising. Perhaps some extension or prefix would help
organize these files?
Regards,
András
>
> Help will be much appreciated.
>
> Thanks in advance.
>
> --
> Stephen P. Molnar, Ph.D.
> www.molecular-modeling.net
> 614.312.7528 (c)
> Skype: smolnar1
>
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