Hi Ed, What about making the code recognize automatically which columns are what ?
We could, for example, have the code determine the number of fields and then search the header for strings as 'res_num' or 'res_name', etc, and when all searched fields recognized, assume that the remaining fields are intensities to extract... The absent fields could be given a default value such as 'None'. For this, we would need to have the header sent to the intensity_generic() function (from the autodetect_format() function). I think this would be great because it could allow users not to input column numbers and have their files automatically parsed, in whatever fields the data is... What do you think of this approach ? Do you see any problem with it ? Let me know what you think. Regards, Séb :) Edward d'Auvergne wrote: > Sorry, this task of the generic formatted file is far more complicated > than I thought. It's structure should be modelled after the > generic_fns.value.read() function, as this takes a similarly formatted > file. Flexibility here is key - any int arguments for the > mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col > should be acceptable. I.e. you can put this information at the end of > the file if you are crazy enough. But most of the code in > generic_fns.value.read() can be used. It just needs to be shifted > into functions of generic_fns.spectrum such as > number_of_header_lines() and intensity_generic(). > > In the future I might write some functions in generic_fns.mol_res_spin > to parse any spin specific but generically formatted file. But for > now, the generic_fns.value.read() function needs to be mimicked. This > is an insanely complex task, considering the additional flexibility I > talked about in > https://mail.gna.org/public/relax-devel/2008-12/msg00016.html > especially the automatic reading with the spin specific columns being > allowed to be anywhere. So if you think this is too much, I can take > over at any point. > > Regards, > > Edward > > > > On Thu, Dec 4, 2008 at 7:30 PM, <[EMAIL PROTECTED]> wrote: > >> Author: semor >> Date: Thu Dec 4 19:30:11 2008 >> New Revision: 8138 >> >> URL: http://svn.gna.org/viewcvs/relax?rev=8138&view=rev >> Log: >> Modified the autodetection code for the generic format. >> >> This now recognizes the most generic format as in >> 'test_suite/shared_data/peak_lists/generic_intensity2.txt'. >> >> >> Modified: >> 1.3/generic_fns/spectrum.py >> >> Modified: 1.3/generic_fns/spectrum.py >> URL: >> http://svn.gna.org/viewcvs/relax/1.3/generic_fns/spectrum.py?rev=8138&r1=8137&r2=8138&view=diff >> ============================================================================== >> --- 1.3/generic_fns/spectrum.py (original) >> +++ 1.3/generic_fns/spectrum.py Thu Dec 4 19:30:11 2008 >> @@ -254,7 +254,7 @@ >> break >> >> # Generic format. >> - if line[0] in ['mol_name', 'res_num', 'res_name', 'spin_num', >> 'spin_name']: >> + if line[0] in ['mol_name', 'res_num', 'res_name', 'spin_num', >> 'spin_name'] or line[0] in ['Num', 'Name']: >> return 'generic' >> >> # Sparky format. >> >> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-commits 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-commits >> >> > > _______________________________________________ > relax (http://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://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
