On 09/27/2019 09:28 AM, Mats Wichmann wrote:
On 9/27/19 5:47 AM, Stephen P. Molnar wrote:
0
I am writing code to combine text files and I have encountered an
error that I am having trouble solving. Google is no help.
The code is:
|#!/usr/bin/env python3# -*- coding: utf-8 -*-""" Created on Thu Sep
26 09:51:55 2019 @author: comp """importnumpy asnp NAME
=input("Enter Molecule ID: ")NAME_IN =NAME+'_apo-1acl.RMSD'DATA
=[]DATA =np.genfromtxt(NAME_IN,skip_header=8,dtype=None)|
The text file is:
|RMSD TABLE __________
_____________________________________________________________________ ||||||Rank|Sub-|Run|Binding|Cluster|Reference|Grep|Rank||Energy|RMSD
|RMSD
|Pattern_____|______|______|___________|_________|_________________|___________
118-7.230.0093.07RANKING 129-6.791.3992.64RANKING
2116-7.180.0093.19RANKING 312-6.930.0093.38RANKING
3217-6.840.2393.45RANKING 4115-6.550.0091.83RANKING
427-6.340.3391.77RANKING 515-6.410.0093.05RANKING
613-6.360.0092.84RANKING 6210-6.280.4792.92RANKING
636-6.270.4392.82RANKING 6418-6.250.3292.88RANKING
6513-6.240.9692.75RANKING 661-6.240.8792.60RANKING
6714-6.210.5192.90RANKING 6811-6.140.9892.78RANKING
6920-6.110.7192.67RANKING 61019-6.011.3693.00RANKING
7112-6.300.0093.28RANKING 814-5.850.0092.97RANKING
_______________________________________________________________________|
and the error is:
|runfile('/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/CombineRMSDFiles.py')
Enter Molecule ID: 13-7 13-7_apo-1acl.RMSD Traceback (most recent
call last): File
"/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/CombineRMSDFiles.py",
line 15, in <module> DATA = np.genfromtxt(NAME_IN, dtype=None,
skip_header=8) File
"/home/comp/Apps/Miniconda3/lib/python3.7/site-packages/numpy/lib/npyio.py",
line 2075, in genfromtxt raise ValueError(errmsg) ValueError: Some
errors were detected ! Line #29 (got 1 columns instead of 7)|
At this point, I'm not even sure how to ask the question.
Thanks in advance.
your posting has come across mangled, seemingly spaces have been
stripped. But trying to disentangle it:
"...pyio.py", line 2075, in genfromtxt
raise ValueError(errmsg)
ValueError: Some errors were detected ! Line #29 (got 1 columns
instead of 7)|
and in your data you have lines which are clearly not seven columns.
You've done skip_header=8 and it doesn't look here that's eight lines
in the data pasted, but maybe that's due to whatever happened to the
pasted data between the source and the email. It looks at the very
least like you should use a skip_footer keyword as well since you
show a footer line. Beyond that it's really hard to tell as the data
portion of the table looks like it has no separators...
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Sorry about the mangled files.
I put both the python script and the data file in my Dropbox account.
Here are the URL's:
https://www.dropbox.com/s/aattr8qnjwd8b8e/13-7a_apo-1acl.RMSD?dl=0
https://www.dropbox.com/s/aattr8qnjwd8b8e/13-7a_apo-1acl.RMSD?dl=0