[Bioperl-l] problem for Bio::Tools::Run::RNAMotif

Chris Fields cjfields at uiuc.edu
Thu Mar 8 13:36:39 EST 2007


Let me know if you have any suggestions.  Thanks!

chris

On Mar 8, 2007, at 2:13 AM, bertrand beckert wrote:

> yes, it seems to  work!
>
> thank.
>
> Bertrand
>
> 2007/3/7, Chris Fields <cjfields at uiuc.edu>: If you're running  
> Bio::Tools::Run::RNAMotif (which is only in CVS
> currently) and BioPerl 1.5.2 you're essentially mixing versions, so I
> think you'll need to update your core bioperl from CVS.  I can't
> remember precisely but I think _set_from_args() was committed to CVS
> after the last BioPerl release (1.5.2); the last bioperl-run release
> was also 1.5.2, which lacked my wrapper modules for RNAMotif,
> Infernal, etc.
>
> Note I'm still working on those modules (Infernal, RNAMotif, ERPIN,
> etc), hence the reason they weren't in the last release.  It's
> possible I may change some of the interface design to make it more
> straightforward (ERPIN and Infernal in particular).
>
> chris
>
> PS- let me know how it works out.
>
> On Mar 7, 2007, at 10:26 AM, bertrand beckert wrote:
>
> > hello,
> >
> > I am using RNAmotif suite of programs...
> > I just try the module Bio::Tools::Run::RNAMotif, the lastest  
> version (
> > RNAMotif.pm,v 1.4 2007/02/07--)
> >
> > In order to  test how it function i just try the short example...
> > but as
> > you can imagine it don't work....
> >
> > error:
> > laptop:~/rnamot_test$ ./test_rnamotif.pl
> > Can't locate object method "_set_from_args" via package
> > "Bio::Tools::Run::RNAMotif" at
> > /usr/local/share/perl/5.8.8/Bio/Tools/Run/RNAMotif.pm line 176,
> > <GEN0> line
> > 1.
> > laptop:~/rnamot_test$
> >
> > could you help me?
> >
> > thanks
> >
> >
> > Bertrand BECKERT
> > IBMC - UPR 9002 du CNRS - ARN
> > 15, rue Rene Descartes
> > F-67084 STRASBOURG Cedex
> >
> > bertrand.beckert at gmail.com
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
> -- 
> Bertrand BECKERT
> PhD student
> IBMC - UPR 9002 du CNRS - ARN
> 15, rue Rene Descartes
> F-67084 STRASBOURG Cedex
>
> b.beckert at ibmc.u-strasbg.fr
> bertrand.beckert at gmail.com

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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