I've now added the test.seq file to the relax test suite data store (see http://article.gmane.org/gmane.science.nmr.relax.scm/17651). This is within the relax trunk in the directory test_suite/shared_data/peak_lists, as that seems the most appropriate. Again take note of how the commit message is constructed so that you can replicate it once you have commit access to the relax repository. If you like, you could try creating a new test in the file test_suite/system_tests/peak_lists.py on your system, using the commands you have given in the bug report (http://gna.org/bugs/?20873), and see if you can trigger the failure. It is probably not complicated enough to require an external script, so you could do it all within one test method. This could then be converted to a patch and attached to the bug report. After that, the debugging can begin.
Cheers, Edward On 6 June 2013 16:58, Troels E. Linnet <[email protected]> wrote: > URL: > <http://gna.org/bugs/?20873> > > Summary: Custom Peak intensity reading cannot read a list of > spectrum_id > Project: relax > Submitted by: tlinnet > Submitted on: Thu 06 Jun 2013 02:58:58 PM GMT > Category: relax's source code > Severity: 3 - Normal > Priority: 5 - Normal > Status: None > Privacy: Public > Assigned to: None > Originator Name: > Originator Email: > Open/Closed: Open > Discussion Lock: Any > Release: Repository: trunk > Operating System: GNU/Linux > > _______________________________________________________ > > Details: > > See: http://article.gmane.org/gmane.science.nmr.relax.user/1452 > ---------- > Using a Generic intensity file. > The input of the spectrum id is converted to a string, and not a list or > tuble. > > spectrum_id='(2,6)' > > is translated to a string. > This should be corrected, to do similar as the intensity columns: > int_col=(6, 7) > > > ---------------------------------- > To reproduce error > ---------------------------------- > Start new analysis > Relaxation dispersion analysis > Relaxation dispersion experiment type selection > CPMG, fixed time > Data pipe set up > The starting data pipe for the analysis = origin - relax_disp > The data pipe bundle = relax_disp > > Spin editor > Click: Spin editor > Click: Load spins > > Click: From a file containing sequence data > The file name = test.seq > The spin ID string = Leave empty > Free format > Molecule name column (mol_name_col) = 1 > Residue number column (res_num_col) = 2 > Residue name column (res_name_col) = 3 > Spin number column (spin_num_col) = 4 > Spin name column (spin_name_col) = 5 > > Add spectra > Click "Add" > > The file name = test.seq > The Spectrum ID string: 2,0 > The Intensity column: 6,7 > rest is default > > Error: > No corresponding data could be found within the file. > > ERROR: > relax> spectrum.read_intensities(file='/sbinlab2/tlinnet/Desktop/test.seq', > dir=None, spectrum_id='2,0', heteronuc='N', proton='HN', int_method='height', > int_col=(6, 7), spin_id_col=None, mol_name_col=1, res_num_col=2, > res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, > ncproc=None) > Opening the file '/sbinlab2/tlinnet/Desktop/test.seq' for reading. > Generic formatted data file. > ..... > RelaxWarning: The sequence data in the line ['protein', '75', 'L', '75', 'N', > '3.578841e+06', '6.352595e+06'] is invalid, the data is missing. > RelaxError: No corresponding data could be found within the file. > > > In prompt: > pipe.create(pipe_name='origin rx', pipe_type='relax_disp', bundle='rx') > relax_disp.exp_type(exp_type='cpmg fixed') > > sequence.read(file='/sbinlab2/tlinnet/Desktop/test.seq', > dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, > res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, > spin_id=None) > > spectrum.read_intensities(file='/sbinlab2/tlinnet/Desktop/test.seq', > dir=None, spectrum_id=(2,0), heteronuc='N', proton='HN', > int_method='height', int_col=(6, 7), spin_id_col=None, mol_name_col=1, > res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, > sep=None, spin_id=None, ncproc=None) > > File "<input>", line 3, in <module> > File "/sbinlab2/software/NMR-relax/relax_disp/prompt/uf_objects.py", > line 200, in __call__ > lib.arg_check.is_str(value, desc_short, can_be_none=can_be_none) > File "/sbinlab2/software/NMR-relax/relax_disp/lib/arg_check.py", > line 862, in is_str > raise RelaxStrError(name, arg) > RelaxStrError: [31mRelaxError: The spectrum ID string argument '(2,0)' must > be a string. [0m > > > > > > _______________________________________________________ > > File Attachments: > > > ------------------------------------------------------- > Date: Thu 06 Jun 2013 02:58:58 PM GMT Name: test.seq Size: 432B By: > tlinnet > > <http://gna.org/bugs/download.php?file_id=18054> > > _______________________________________________________ > > Reply to this item at: > > <http://gna.org/bugs/?20873> > > _______________________________________________ > Message sent via/by Gna! > http://gna.org/ > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-devel mailing list > [email protected] > > 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 _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] 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
