[Tutor] NumPy Generates ValueError: Some errors were detected ! Line #9 (got 42 columns instead of 1)

[Mats Wichmann]

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...