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

Chris Fields cjfields at uiuc.edu
Wed Mar 7 11:55:31 EST 2007


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





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