[bug #21959] cpmg_analysis -- April 23, 2014 - 11:43

URL:
  <http://gna.org/bugs/?21959>

                 Summary: cpmg_analysis
                 Project: relax
            Submitted by: None
            Submitted on: Wed 23 Apr 2014 09:43:15 AM UTC
                Category: relax sample scripts
Specific analysis category: None
                Priority: 5 - Normal
                Severity: 3 - Normal
                  Status: None
             Assigned to: None
         Originator Name: 
        Originator Email: mengjun.xue@xxxxxxxxxxxxxxxxxxxx
             Open/Closed: Open
                 Release: 3.1.7
         Discussion Lock: Any
        Operating System: 32-bit MS Windows

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Details:

Dear Edward and Troels,

Thank you so much for your response. I have tried the script again as you
suggested, but it does not work on my computer, I have attached the log file.

log_cpmg_analysis_04222014: I set the DATA_PATH =
'..\..\test_suite\shared_data\dispersion\Hansen' in cpmg_analysis.py,  I copy
the cpmg_analysis.py to the base relax directory, and then run the
cpmg_analysis.py under cmd,C:\program files\relax-3.1.7\relax
cpmg_analysis.py

log_cpmg_analysis_04232014a: I set the DATA_PATH =
'..\\..\\test_suite\\shared_data\\dispersion\\Hansen' in cpmg_analysis.py,  I
copy the cpmg_analysis.py to the base relax directory, and then run the
cpmg_analysis.py under cmd, C:\program files\relax-3.1.7\relax
cpmg_analysis.py

log_cpmg_analysis_04232014b: I set the DATA_PATH =
'..\..\test_suite\shared_data\dispersion\Hansen' in cpmg_analysis.py, and run
the cpmg_analysis.py under cmd, C:\program files\relax-3.1.7\relax
sample_scripts\relax_disp\cpmg_analysis.py

Thank you.

Best regards,

Mengjun


Hi,

There's no need to separate them now.  I've fixed both in relax.  For
the error you see now, if I run:

$ ./relax sample_scripts/relax_disp/cpmg_analysis.py

from the base relax directory, then it will find the data in the test
suite directories and perform the test analysis.  Also in the Windows
PowerShell:
.\relax sample_scripts\relax_disp\cpmg_analysis.py
Both work for me.  But Troels' response
(http://thread.gmane.org/gmane.science.nmr.relax.devel/5296/focus=5326)
is exactly correct.  The '\t' is the Python tab character, so the
missing '\' will really cause problems.  Python gets around such
problems by using the os.sep and os.pardir variables, as I have used
in the updated scripts
(http://svn.gna.org/viewcvs/*checkout*/relax/trunk/sample_scripts/relax_disp/cpmg_analysis.py?content-type=text%2Fplain).

Regards,

Edward


Hi Mengjun.

There is missing a \
.\\..\test_suite

should be
.\\..\\test_suite

2014-04-23 10:23 GMT+02:00 <mengjun.xue@xxxxxxxxxxxxxxxxxxxx>:
Hi Edward,

Thank you very much for your suggestions. Should I separate the the questions
about test suite and cmpg_analysis.py and resubmit them ? For the
cpmy_analysis.py, I have change it to
'..\..\test_suite\shared_data\dispersion\Hansen' as your suggestion, and try
to run the script again, but there are following relaxerror,

relax> spectrum.read_intensities(file='500_MHz\\reference.in_sparky',
dir='..\\..\test_suite\\shared_data\\dispersion\\Hansen',
spectrum_id='500_reference.in', dim=1, int_method='height', int_col=None,
spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None,
spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, ncproc=None)
RelaxError: The sequence data does not exist.

Thank you.

Best regards,

Mengjun




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File Attachments:


-------------------------------------------------------
Date: Wed 23 Apr 2014 09:43:15 AM UTC  Name: log_cpmg_analyis_04232014  Size:
11kB   By: None

<http://gna.org/bugs/download.php?file_id=20565>
-------------------------------------------------------
Date: Wed 23 Apr 2014 09:43:15 AM UTC  Name: log_cpmg_analysis_04232014a 
Size: 11kB   By: None

<http://gna.org/bugs/download.php?file_id=20566>
-------------------------------------------------------
Date: Wed 23 Apr 2014 09:43:15 AM UTC  Name: log_cpmg_analysis_04232014b 
Size: 11kB   By: None

<http://gna.org/bugs/download.php?file_id=20567>

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