Hi Mengjun, This is a simple case of handling file system paths and directories correctly and understanding what the current directory is. When you run a relax script, the current working directory (CWD) will be set to the directory that contains the script. As you copied the script into the base relax directory, the base directory will be the CWD. If you have a look at the DATA_PATH variable, that is what is called a relative path. There is no root directory at the start ('C:\' in Windows, "/" in Linux and Macs) so it is not an absolute path. A relative path will then be relative to the CWD. That means that DATA_PATH is added to CWD. So if CWD is "C:\Program files\relax" and DATA_PATH is "..\..\test_suite\shared_data\dispersion\Hansen", then the absolute path used to find the file will be "C:\Program files\relax\..\..\test_suite\shared_data\dispersion\Hansen". Now, the '..' directory has a special meaning - it is the parent directory. This is the same on Windows, Linux and Mac. It is present in the absolute path twice. So the absolute path says to first walk into the "Program files" directory ("C:\Program files"), then into the "relax" directory ("C:\Program files\relax"), then back up into the parent directory (which is "C:\Program files"), and once more back up into the parent directory. So you will now be at "C:\". Therefore the absolute path collapses to "C:\test_suite\shared_data\dispersion\Hansen", which is a directory that most like does not exist on your system. So to get the script to run, you need to take all of this into account and change DATA_PATH to be relative to the directory the script is in, or change DATA_PATH to be the absolute path. I hope this explains the issue. Regards, Edward On 23 April 2014 11:43, anonymous <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
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 _______________________________________________________ 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 _______________________________________________________ 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> _______________________________________________________ Reply to this item at: <http://gna.org/bugs/?21959> _______________________________________________ Message sent via/by Gna! http://gna.org/ _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@xxxxxxx To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel