On Sat, 28 Sep 2019 at 03:49, Stephen P. Molnar <s.mol...@sbcglobal.net> wrote:
> On 09/27/2019 09:55 AM, Stephen P. Molnar wrote:
> > On 09/27/2019 09:28 AM, Mats Wichmann wrote:
> >> On 9/27/19 5:47 AM, Stephen P. Molnar wrote:
> >>> 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.
> >>>
> >>
> >> 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...
> >> _______________________________________________
> >> Tutor maillist - tu...@python.org
> >> To unsubscribe or change subscription options:
> >> https://mail.python.org/mailman/listinfo/tutor
> >
> > 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
> >
> Oh, dear. Just noticed my mistake.
>
> Here are the correct URL's:
>
> Data\ File:
> https://www.dropbox.com/s/aattr8qnjwd8b8e/13-7a_apo-1acl.RMSD?dl=0
> Python Script:
> https://www.dropbox.com/s/ni3pk0342q7o0qz/CombineRMSDFiles.py?dl=0
I get the feeling that you don't put much effort into asking questions
on the mailing lists that I see you on.
Here you have:
1) somehow posted your question to Python Tutor <tu...@python.org>, but
posted your followup message to <debian-u...@lists.debian.net>
2) somehow ignored the error message from python:
ValueError: Some errors were detected ! Line #29 (got 1 columns instead of 7)|
3) somehow ignored the advice you were given on Python Tutor:
> >> It looks at the very
> >> least like you should use a skip_footer keyword as well since you
> >> show a footer line
I checked your dropbox data file at your corrected URL.
Line 29 is a sequence of 71 underscore characters.
Like Mats Wichmann replied, I think that would explain the error message
"got 1 columns instead of 7", although I haven't bothered to test it.
