Re: Data set formatRe: Data set format|
Hi all, Here is the script I used for jw_mapping to get the strange errors about data format... # Script for reduced spectral density mapping. # Create the run. name = 'jw_600' run.create(name, 'jw') # Nuclei type nuclei('N') # Load the sequence. sequence.read(name, 'ready_consistent_Ambler_no_W_600_NOE_duplicata_RMSD.dat-4') # Load the relaxation data. relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'ready_consistent_Ambler_no_W_600_R1_4.dat-4') relax_data.read(name, 'R2', '600', 600.0 * 1e6, 'ready_consistent_Ambler_no_W_600_R2_2.dat-4') relax_data.read(name, 'NOE', '600', 600.0 * 1e6, 'ready_consistent_Ambler_no_W_600_NOE_duplicata_RMSD.dat-4') # Set the bond length and CSA values. value.set(name, 1.02 * 1e-10, 'bond_length') value.set(name, -172 * 1e-6, 'csa') # Select the frequency. jw_mapping.set_frq(name, frq=600.0 * 1e6) # Reduced spectral density mapping. calc(name) # Monte Carlo simulations. monte_carlo.setup(name, number=500) monte_carlo.create_data(name) calc(name) monte_carlo.error_analysis(name) # Create grace files. grace.write(name, y_data_type='j0', file='j0_600.agr', force=1) grace.write(name, y_data_type='jwx', file='jwx_600.agr', force=1) grace.write(name, y_data_type='jwh', file='jwh_600.agr', force=1) # View the grace files. grace.view(file='j0_600.agr') grace.view(file='jwx_600.agr') grace.view(file='jwh_600.agr') # Finish. results.write(run=name, file='results_600', force=1) state.save('save_600', force=1) As Ed proposed, the MC simulations were done before the strange error messages. When the grace options were activated, it stopped at this place and when the grace options were commented out, it stopped at the result writing command... Important notice, I didn't specify the columns. For what Gary proposed (see below), I absolutely agree with everything. Cheers Sébastien :) Gary Thompson wrote: Hi, Sorry, would you be able to resend your message? It was only sent to me and not Seb or the mailing list. Cheers, Edward On 8/28/07, gary thompson <garyt.and.sarahb@xxxxxxxxx> wrote:Dear Seb The things (I think ;-)) that are generally needed are 1. we should fail quickly if something is wrong 2. the failure message should have a. a filename with a complete path b. a line number and a field number c. the line itself with the error indicated error failed to read data from wobble.txt, bad data format! file: /wibble/wobble.txt had an integer at line 56 column 6 when it should be a string 1 2 3 b a 6 ... 3. The things to check for are a. correct number of arguments b. the correct type for arguments allowing comments in these files is also a good idea that i looked at at one point specifically this allows a. the user (or program) to record meta information abou the file b. would allow files such as the monte carlo outputs to have meta information to allow the human reader to more easily distinguish the sections in the file any way there are some off the cuff thoughts regards gary On 8/27/07, Edward d'Auvergne < edward.dauvergne@xxxxxxxxx> wrote:Hi, For the reading in of data, such as the R1 relaxation rates, the only requirement for the format is that the data is in a column formatted text file. The different columns can be changed by the num_col=0, name_col=1, data_col=2, and error_col=3 arguments. The column separator changed by the 'sep' argument. In the future, even more diverse formats will be accepted as these arise and are reported on the mailing lists. With this in mind, coming up with a more descriptive error message would be worthwhile. Currently you will get something such as: RelaxError: "The relaxation data is invalid (num=" + file_data[i][num_col] + ", name=" + file_data[i][name_col] + ", data="", error=" + file_data[i][error_col] + ")." This could probably be broken into simpler messages for different types of error. The checks are currently for the residue number being an integer, and the data and error being floating point numbers. Would anyone have any suggestions or ideas for how this could be better reported to the user? What tests and what types of messages would you use? The system has to be flexible enough to handle absolutely all rubbish thrown at it by a user ;) Cheers, Edward On 8/21/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote: --
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|| Sebastien Morin ||
||| Etudiant au PhD en biochimie |||
|||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne |||||
|||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
||| 1-418-656-2131 #4530 |||
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