This is part of the bug and is the same reason you saw an error in the GUI. If you look at the file user_functions/spectrum.py in the relax trunk source code and go to line 236 (for the current revision r19893), you should be able to see the issue.
Regards, Edward On 6 June 2013 16:44, Troels Emtekær Linnet <tlin...@gmail.com> wrote: > In the relax prompt, this can produce the error: > > --------------------- > 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 > ----------------------------------------- > > > > > > 2013/6/6 Edward d'Auvergne <edw...@nmr-relax.com>: >> On a different note, if you notice anywhere in relax's execution where >> the messages are not informative enough, are misleading, or where >> additional messages would be useful, these can all be reported as >> bugs. Anything in relax that causes confusion should be considered a >> bug which should be fixed. >> >> Regards, >> >> Edward >> >> >> >> On 6 June 2013 15:26, Edward d'Auvergne <edw...@nmr-relax.com> wrote: >>> Oh, right, I see the problem. This user function currently only has >>> partial support for simultaneously loading all spectral data at once. >>> The current way to do this is to change the spectrum ID and intensity >>> column one-by-one while clicking on 'Apply' as you go. But I have >>> partly designed this user function to handle this situation, according >>> to the user function documentation: >>> >>> "Generic intensity file: This is a generic format which can be >>> created by scripting to support non-supported peak lists. It should >>> contain in the first few columns enough information to identify the >>> spin. This can include columns for the molecule name, residue number, >>> residue name, spin number, and spin name. Alternatively a spin ID >>> string column can be used. The peak intensities can be placed in >>> another column specified by the integration column number. >>> Intensities from multiple spectra can be placed into different >>> columns, and these can then be specified simultaneously by setting the >>> integration column value to a list of columns. This list must be >>> matched by setting the spectrum ID to a list of the same length..." >>> >>> Could you submit a bug report for this, attaching any files required >>> to replicate the bug? It would be useful to give a link to the Gmane >>> archive as well (going to >>> http://dir.gmane.org/gmane.science.nmr.relax.user -> clicking on >>> "using frames and threads" -> finding message -> clicking on "<<< >>> [thread] >>>" down the botton -> and copying the link). I could then >>> turn the instructions into a relax script, and incorporate both the >>> script and data files into the test suite directories and create a >>> system test to catch the bug. Or, if you wish, as a learning exercise >>> for becoming a relax developer you could give this a go yourself after >>> creating the report. This would all go into the relax trunk, and then >>> be ported to the relax_disp branch using svnmerge.py. >>> >>> Cheers, >>> >>> Edward >>> >>> >>> >>> On 6 June 2013 15:04, Troels Emtekær Linnet <tlin...@gmail.com> wrote: >>>> I think it is because that: >>>> spectrum_id='(2,6)' >>>> >>>> is translated to a string. >>>> >>>> Could it be corrected, so it does similar as: >>>> int_col=(6, 7) >>>> >>>> Best >>>> Troels Emtekær Linnet >>>> >>>> >>>> 2013/6/6 Troels Emtekær Linnet <tlin...@gmail.com>: >>>>> Hi, >>>>> >>>>> No, not any luck. >>>>> And, this time I am not renaming. >>>>> >>>>> Where can I find the longer error message? >>>>> --------- >>>>> Add spectra >>>>> Click "Add" >>>>> >>>>> The file name = test.seq >>>>> The Spectrum ID string: 2,0 >>>>> The Intensity column: 6,7 >>>>> ---------------- >>>>> protein 10 L 10 N 3.377659e+05 6.362446e+05 >>>>> protein 6 V 6 N 1.697771e+06 3.015788e+06 >>>>> protein 63 Y 63 N 8.673898e+05 1.726064e+06 >>>>> protein 4 Y 4 N 2.339480e+06 4.039142e+06 >>>>> protein 67 M 67 N 2.574062e+06 4.313824e+06 >>>>> protein 5 E 5 N 1.609356e+06 2.927111e+06 >>>>> protein 65 V 65 N 2.179341e+06 4.067343e+06 >>>>> protein 38 E 38 N 1.563795e+06 2.921316e+06 >>>>> protein 7 N 7 N 1.535896e+06 3.005234e+06 >>>>> protein 75 L 75 N 3.578841e+06 6.352595e+06 >>>>> ------------------------ >>>>> >>>>> ---------- >>>>> relax> relax_disp.exp_type(exp_type='cpmg fixed') >>>>> The fixed relaxation time period CPMG-type experiments. >>>>> >>>>> relax> >>>>> sequence.read(file='/sbinlab2/tlinnet/Desktop/ikn_20130510_S6wt_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/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) >>>>> Opening the file >>>>> '/sbinlab2/tlinnet/Desktop/ikn_20130510_S6wt_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq' >>>>> for reading. >>>>> # mol_name res_num res_name spin_num spin_name >>>>> protein 10 L 10 N >>>>> protein 6 V 6 N >>>>> protein 63 Y 63 N >>>>> protein 4 Y 4 N >>>>> protein 67 M 67 N >>>>> protein 5 E 5 N >>>>> protein 65 V 65 N >>>>> protein 38 E 38 N >>>>> protein 7 N 7 N >>>>> protein 75 L 75 N >>>>> >>>>> relax> >>>>> spectrum.read_intensities(file='/sbinlab2/tlinnet/Desktop/ikn_20130510_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/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/ikn_20130510_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq' >>>>> for reading. >>>>> Generic formatted data file. >>>>> >>>>> RelaxWarning: The sequence data in the line ['protein', '10', 'L', >>>>> '10', 'N', '3.377659e+05', '6.362446e+05'] is invalid, the data is >>>>> missing. >>>>> RelaxWarning: The sequence data in the line ['protein', '6', 'V', '6', >>>>> 'N', '1.697771e+06', '3.015788e+06'] is invalid, the data is missing. >>>>> RelaxWarning: The sequence data in the line ['protein', '63', 'Y', >>>>> '63', 'N', '8.673898e+05', '1.726064e+06'] is invalid, the data is >>>>> missing. >>>>> RelaxWarning: The sequence data in the line ['protein', '4', 'Y', '4', >>>>> 'N', '2.339480e+06', '4.039142e+06'] is invalid, the data is missing. >>>>> RelaxWarning: The sequence data in the line ['protein', '67', 'M', >>>>> '67', 'N', '2.574062e+06', '4.313824e+06'] is invalid, the data is >>>>> missing. >>>>> RelaxWarning: The sequence data in the line ['protein', '5', 'E', '5', >>>>> 'N', '1.609356e+06', '2.927111e+06'] is invalid, the data is missing. >>>>> RelaxWarning: The sequence data in the line ['protein', '65', 'V', >>>>> '65', 'N', '2.179341e+06', '4.067343e+06'] is invalid, the data is >>>>> missing. >>>>> RelaxWarning: The sequence data in the line ['protein', '38', 'E', >>>>> '38', 'N', '1.563795e+06', '2.921316e+06'] is invalid, the data is >>>>> missing. >>>>> RelaxWarning: The sequence data in the line ['protein', '7', 'N', '7', >>>>> 'N', '1.535896e+06', '3.005234e+06'] is invalid, the data is missing. >>>>> 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. >>>>> >>>>> ------------------------------- >>>>> >>>>> Troels Emtekær Linnet >>>>> >>>>> >>>>> 2013/6/6 Edward d'Auvergne <edw...@nmr-relax.com>: >>>>>> Hi, >>>>>> >>>>>> Have you had any luck finding the problem? I would guess that this >>>>>> doesn't work as the protein was renamed to something different to that >>>>>> of the data file, hence you would see messages such as: >>>>>> >>>>>> relax> spectrum.read_intensities(file='test.seq', dir=None, >>>>>> spectrum_id=None, heteronuc='N', proton='HN', int_method='height', >>>>>> int_col=6, spin_id_col=None, mol_name_col=1, res_num_col=2, >>>>>> res_name_col=3, spin_num_col=4, spin_name_col=5, int_col=6, sep=None, >>>>>> spin_id=None, ncproc=None) >>>>>> Opening the file '/data/edau/relax/branches/relax_disp/test.seq' for >>>>>> reading. >>>>>> Generic formatted data file. >>>>>> >>>>>> RelaxWarning: Cannot find the spin #protein:10@N within the sequence. >>>>>> RelaxWarning: Cannot find the spin #protein:6@N within the sequence. >>>>>> RelaxWarning: Cannot find the spin #protein:63@N within the sequence. >>>>>> RelaxWarning: Cannot find the spin #protein:4@N within the sequence. >>>>>> RelaxWarning: Cannot find the spin #protein:67@N within the sequence. >>>>>> RelaxWarning: Cannot find the spin #protein:5@N within the sequence. >>>>>> RelaxWarning: Cannot find the spin #protein:65@N within the sequence. >>>>>> RelaxWarning: Cannot find the spin #protein:38@N within the sequence. >>>>>> RelaxWarning: Cannot find the spin #protein:7@N within the sequence. >>>>>> RelaxWarning: Cannot find the spin #protein:75@N within the sequence. >>>>>> RelaxError: No data could be loaded from the peak list >>>>>> >>>>>> I tried this by copying the data in your post to a file and following >>>>>> the instructions. This is normal as the molecule with the name >>>>>> 'protein' no longer exists in the relax data store. Or did you see >>>>>> something different? The RelaxError text you wrote about is slightly >>>>>> different. >>>>>> >>>>>> Regards, >>>>>> >>>>>> Edward >>>>>> >>>>>> >>>>>> On 4 June 2013 15:10, Edward d'Auvergne <edward.dauver...@gmail.com> >>>>>> wrote: >>>>>>> I have to admit, the error message should be made more informative! >>>>>>> However that error statement (line 668 of lib/io.py) cannot be reached >>>>>>> without relax giving many warnings. The only possibility of reaching >>>>>>> the error without warnings is if the file is empty. Do you see >>>>>>> warnings which could indicate the problem? If not, I would suggest >>>>>>> creating a bug report for the problem and attaching a minimal set of >>>>>>> files to be able to reproduce the issue. It would be best if the >>>>>>> files are truncated to 1-2 spins (and maybe randomised if the data is >>>>>>> to be kept secret). If it really is a bug, then these files could be >>>>>>> be added to the test suite and turned into a system or GUI test to >>>>>>> catch the problem. >>>>>>> >>>>>>> Cheers, >>>>>>> >>>>>>> Edward >>>>>>> >>>>>>> >>>>>>> On 4 June 2013 14:37, Troels Emtekær Linnet <tlin...@gmail.com> wrote: >>>>>>>> Hi. >>>>>>>> >>>>>>>> I have made a custom intensity peak/model file, for easy import in >>>>>>>> relax. >>>>>>>> The form is: >>>>>>>> >>>>>>>> protein 10 L 10 N 3.377659e+05 6.362446e+05 >>>>>>>> protein 6 V 6 N 1.697771e+06 3.015788e+06 >>>>>>>> protein 63 Y 63 N 8.673898e+05 1.726064e+06 >>>>>>>> protein 4 Y 4 N 2.339480e+06 4.039142e+06 >>>>>>>> protein 67 M 67 N 2.574062e+06 4.313824e+06 >>>>>>>> protein 5 E 5 N 1.609356e+06 2.927111e+06 >>>>>>>> protein 65 V 65 N 2.179341e+06 4.067343e+06 >>>>>>>> protein 38 E 38 N 1.563795e+06 2.921316e+06 >>>>>>>> protein 7 N 7 N 1.535896e+06 3.005234e+06 >>>>>>>> protein 75 L 75 N 3.578841e+06 6.352595e+06 >>>>>>>> >>>>>>>> This goes fine for model import, with standard settings. >>>>>>>> >>>>>>>> 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 (Mon Jun >>>>>>>> 3 17:08:30 2013) >>>>>>>> The data pipe bundle = relax_disp (Mon Jun 3 17:08:30 2013) >>>>>>>> >>>>>>>> Click: Spin editor >>>>>>>> Click: Load spins >>>>>>>> Make a test file: test.seq >>>>>>>> >>>>>>>> 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 >>>>>>>> You can then rename molecule by, right click "Molecule: protein", >>>>>>>> "Name the molecule", Set "The new molecule name" to for example >>>>>>>> "Test". Apply, then OK. >>>>>>>> >>>>>>>> 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. >>>>>>>> >>>>>>>> I can import single wise. >>>>>>>> >>>>>>>> best >>>>>>>> Troels >>>>>>>> >>>>>>>> >>>>>>>> Troels Emtekær Linnet >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> relax (http://www.nmr-relax.com) >>>>>>>> >>>>>>>> This is the relax-users mailing list >>>>>>>> relax-users@gna.org >>>>>>>> >>>>>>>> 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-users _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org 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-users
