-------- Forwarded Message --------
Subject: Re: [Numpy-discussion] Problem with np.savetxt
Date: Thu, 10 Oct 2019 10:10:58 -0400
From: Stephen P. Molnar <s.mol...@sbcglobal.net>
To: numpy-discussion@python.org
I am slowly and not quickly stumbling forward, but at this point my
degree of mental entropy (confusion) is monumental.
This works:
import numpy as np
print('${d}')
data = np.genfromtxt("14-7.log", usecols=(1), skip_header=27,
skip_footer=1, encoding=None)
print(data)
np.savetxt('14-7.dG', data, fmt='%12.9f', header='14-7')
print(data)
which produces:
runfile('/home/comp/Apps/Python/PsoVina/DeltaGTable_V_s.py',
wdir='/home/comp/Apps/Python/PsoVina', current_namespace=True)
${d}
[-9.96090267 -8.97950478 -8.94261136 -8.91552301 -8.73650883 -8.66338714
-8.41073971 -8.38914635 -8.29679891 -8.16845411 -8.12799082 -8.12710377
-7.97909074 -7.94187268 -7.90076621 -7.88148523 -7.83782648 -7.8159095
-7.72254029 -7.72034674]
[-9.96090267 -8.97950478 -8.94261136 -8.91552301 -8.73650883 -8.66338714
-8.41073971 -8.38914635 -8.29679891 -8.16845411 -8.12799082 -8.12710377
-7.97909074 -7.94187268 -7.90076621 -7.88148523 -7.83782648 -7.8159095
-7.72254029 -7.72034674]
Note; the print statements are for a quick check o the output, which is:
# 14-7
-9.960902669
-8.979504781
-8.942611364
-8.915523010
-8.736508831
-8.663387139
-8.410739711
-8.389146347
-8.296798909
-8.168454106
-8.127990818
-8.127103774
-7.979090739
-7.941872682
-7.900766215
-7.881485228
-7.837826485
-7.815909505
-7.722540286
-7.720346742
Also, this bash script works:
#!/bin/bash
# Run.dG.list_1
while IFS= read -r d
do
echo "${d}.log"
done <ligand.list
which returns the three log file names:
14-7.log
15-7.log
18-7.log
C-VX3.log
But, if I run this bash script:
#!/bin/bash
# Run.dG.list_1
while IFS= read -r d
do
echo "${d}.log"
python3 DeltaGTable_V_sl.py
done <ligand.list
where DeltaGTable_V_sl.py is:
import numpy as np
print('${d}')
data = np.genfromtxt('${d}.log', usecols=(1), skip_header=27,
skip_footer=1, encoding=None)
print(data)
np.savetxt('${d}.dG', data, fmt='%12.9f', header='${d}')
print(data.dG)
I get:
(base) comp@AbNormal:~/Apps/Python/PsoVina$ sh ./Run.dG.list_1.sh
14-7.log
python3: can't open file 'DeltaGTable_V_sl.py': [Errno 2] No such file
or directory
15-7.log
python3: can't open file 'DeltaGTable_V_sl.py': [Errno 2] No such file
or directory
18-7.log
python3: can't open file 'DeltaGTable_V_sl.py': [Errno 2] No such file
or directory
C-VX3.log
python3: can't open file 'DeltaGTable_V_sl.py': [Errno 2] No such file
or directory
So, it would appear that the log file labels are in the workspace, but
'${d}.log' is not being recognized as fname by genfromtxt. Although i
have googled every combination of terms I can think of I am obviously
missing something.
As I have potentially hundreds of files to process, I would appreciate
pointers towards a solution to the problem.
Thanks in advance.
On 10/08/2019 10:49 AM, Stephen P. Molnar wrote:
Many thanks or your kind replies.
I really appreciate your suggestions.
On 10/08/2019 09:44 AM, Andras Deak wrote:
PS. if you just want to specify the width of the fields you wouldn't
have to convert anything, because you can specify the size and
justification of a %s format. But arguably having float data as floats
is more natural anyway.
On Tue, Oct 8, 2019 at 3:42 PM Andras Deak <deak.and...@gmail.com>
wrote:
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,
Andr??s
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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https://mail.python.org/mailman/listinfo/numpy-discussion
_______________________________________________
NumPy-Discussion mailing list
NumPy-Discussion@python.org
https://mail.python.org/mailman/listinfo/numpy-discussion
--
Stephen P. Molnar, Ph.D.
www.molecular-modeling.net
614.312.7528 (c)
Skype: smolnar1
_______________________________________________
NumPy-Discussion mailing list
NumPy-Discussion@python.org
https://mail.python.org/mailman/listinfo/numpy-discussion
