Re: [Tutor] NumPy Generates ValueError: Some errors were detected ! Line #9 (got 42 columns instead of 1)
On Sat, 28 Sep 2019 at 03:49, Stephen P. Molnar 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 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 , but
posted your followup message to
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.
Re: [Tutor] NumPy Generates ValueError: Some errors were detected ! Line #9 (got 42 columns instead of 1)
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:
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 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...
___
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
--
Stephen P. Molnar, Ph.D.Life is a fuzzy set
http://www.Molecular-Modeling.net Multivariate and stochastic
614.312.7528 (c)
Skype: smolnar1
Re: [Tutor] NumPy Generates ValueError: Some errors were detected ! Line #9 (got 42 columns instead of 1)
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 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...
___
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
--
Stephen P. Molnar, Ph.D.Life is a fuzzy set
http://www.Molecular-Modeling.net Multivariate and stochastic
614.312.7528 (c)
Skype: smolnar1
