Re: List Index out of Range -- December 14, 2010 - 11:22

Hi Leanne,

I've added your randomised, truncated data to the relax test suite,
but the test passes!  The peak lists attached to the bug report
(https://gna.org/bugs/index.php?17276) are perfectly fine and do not
trigger the bug.  From the full data set (sent in a private email for
confidentiality), I can see that the problem is because the entries in
the peak lists are not in the same order.  If I look at the first 4
lines of a subset of the peak lists, I see:


[edau@localhost T1_relax]$ cat T10102done.list T1010done.list
T112002done.list T11200done.list
      Assignment         w1         w2       Intensity

                        A1649N-HN    xx  xx  xx
                        D1514N-HN    xx  xx  xx
      Assignment         w1         w2       Intensity

                        A1649N-HN    xx  xx  xx
                        R1615N-HN    xx  xx  xx
      Assignment         w1         w2       Intensity

                        A1649N-HN    xx  xx  xx
                        D1514N-HN    xx  xx  xx
      Assignment         w1         w2       Intensity

                        A1649N-HN    xx  xx  xx
                        R1615N-HN    xx  xx  xx

This is enough to trigger the bug.  I will change half the 'R1615N-HN'
entries to 'D1514N-HN' to catch the bug.  I would like relax to be
able to handle this data without issue, maybe warning that the peak
lists are not synchronised but still handling the residual data, but a
quick fix would be to sort out your peak lists.

Cheers,

Edward




On 3 December 2010 11:15, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> Dear Leanne,
>
> Welcome to the relax mailing lists.  The error you have found seems to
> be from a new bug in relax.  I don't think anyone has encountered this
> one before.  It would be very much appreciated if you could report
> this within the relax bug tracker
> (https://gna.org/bugs/?func=additem&group=relax).  This would allow
> others who encounter the same problem to find out what is happening.
> And it will also help me in debugging the issue, as input files, test
> data, etc. can be attached to the bug report.  If you could come up
> with a minimal set of test data (truncated, and randomised if you wish
> to hide the data) along with a script that reproduces the bug, I
> should be able to have a fix within a few minutes.  With the current
> information you sent, it is very, very difficult for me to pinpoint
> the location of the problem.
>
> Cheers,
>
> Edward
>
>
>
> On 1 December 2010 15:54, L Minall <lm7902@xxxxxxxxxxxxx> wrote:
> > Dear All,
> >
> > I am using Relax ( version relax-1.3.5.GNU-Linux) to get relaxation curves
> > from HSQC spectra. I have exported the data from analysis in Sparky
> > format. After running for a few seconds i get he following error message
> > 'List Index out of Range'.
> >
> > Below is a print screen of the problem:
> >
> >
> > relax> spectrum.replicated(spectrum_ids=['T11000done', 'T110002done'])
> >
> > relax> spectrum.replicated(spectrum_ids=['T11200done', 'T112002done'])
> >
> > relax> spectrum.error_analysis()
> > Intensity measure:  Peak heights.
> > Replicated spectra:  Yes.
> > All spectra replicated:  Yes.
> >
> > Replicated spectra:  ['T1010done', 'T10102done']
> > Standard deviation:  77677.6124466
> >
> > Replicated spectra:  ['T1020done', 'T10202done']
> > Standard deviation:  81714.9935075
> >
> > Replicated spectra:  ['T1030done', 'T10302done']
> > Standard deviation:  52174.0074096
> >
> > Replicated spectra:  ['T1050done', 'T10502done']
> > Standard deviation:  101149.864468
> >
> > Replicated spectra:  ['T1070done', 'T10702done']
> > Standard deviation:  59278.6902247
> >
> > Replicated spectra:  ['T1100done', 'T11002done']
> > Standard deviation:  41827.710636
> >
> > Replicated spectra:  ['T1150done', 'T11502done']
> > Standard deviation:  70130.6742832
> >
> > Replicated spectra:  ['T1200done', 'T12002done']
> > Standard deviation:  80696.9386138
> >
> > Replicated spectra:  ['T1300done', 'T13002done']
> > Standard deviation:  75574.7377343
> >
> > Replicated spectra:  ['T1400done', 'T14002done']
> > Standard deviation:  109708.032792
> >
> > Replicated spectra:  ['T1600done', 'T16002done']
> > Standard deviation:  96472.7940924
> >
> > Replicated spectra:  ['T1800done', 'T18002done']
> > Standard deviation:  78680.8879662
> >
> > Replicated spectra:  ['T11000done', 'T110002done']
> > Standard deviation:  263613.329907
> >
> > Replicated spectra:  ['T11200done', 'T112002done']
> > Traceback (most recent call last):
> >  File "/home/ms4225/programs/relax-1.3.5/relax", line 358, in <module>
> >    Relax()
> >  File "/home/ms4225/programs/relax-1.3.5/relax", line 126, in __init__
> >    self.interpreter.run(self.script_file)
> >  File "/home/ms4225/programs/relax-1.3.5/prompt/interpreter.py", line
> > 287, in run
> >    return run_script(intro=self.__intro_string, local=locals(),
> > script_file=script_file, quit=self.__quit_flag,
> > show_script=self.__show_script,
> > raise_relax_error=self.__raise_relax_error)
> >  File "/home/ms4225/programs/relax-1.3.5/prompt/interpreter.py", line
> > 533, in run_script
> >    return console.interact(intro, local, script_file, quit,
> > show_script=show_script, raise_relax_error=raise_relax_error)
> >  File "/home/ms4225/programs/relax-1.3.5/prompt/interpreter.py", line
> > 429, in interact_script
> >    execfile(script_file, local)
> >  File "R1_newLM.py", line 125, in <module>
> >    spectrum.error_analysis()
> >  File "/home/ms4225/programs/relax-1.3.5/prompt/spectrum.py", line 221,
> > in error_analysis
> >    spectrum.error_analysis()
> >  File "/home/ms4225/programs/relax-1.3.5/generic_fns/spectrum.py", line
> > 394, in error_analysis
> >    __errors_repl()
> >  File "/home/ms4225/programs/relax-1.3.5/generic_fns/spectrum.py", line
> > 189, in __errors_repl
> >    ave_intensity = ave_intensity + spin.intensities[indices[j]]
> > IndexError: list index out of range
> >
> > Could anyone point me in the direction of finding this error, as it the
> > message seems a bit ambiguous?
> >
> > Many Thanks
> >
> > Leanne
> >
> >
> >
> >
> > --
> >
> >
> > --
> >
> >
> >
> > _______________________________________________
> > relax (http://nmr-relax.com)
> >
> > This is the relax-users mailing list
> > relax-users@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-users