[Bioperl-l] RNAMotif module (Bio::Tools::RNAMotif)

[Chris Fields]

Thanks!  I think, as long as the tests pass everything is fine with me.  I
may be submitting another module or two in the next few weeks; just depends
on how much time I can spend on them.

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

> -----Original Message-----
> From: Heikki Lehvaslaiho [mailto:heikki at sanbi.ac.za] 
> Sent: Thursday, February 09, 2006 1:42 PM
> To: bioperl-l at lists.open-bio.org
> Cc: Chris Fields
> Subject: Re: [Bioperl-l] RNAMotif module (Bio::Tools::RNAMotif)
> 
> Chris,
> 
> I committed your file. All tests pass; code looks like 
> written by a long term bioperl contributor! Impressive.
> 
> I truncated the larger test file from 270K to 20K (200 
> lines), to not bloat the distribution unnecessarily. Tests 
> pass which is the main thing. Shout if if you disagree.
> 
> Great job!
> 
> 	-Heikki
>  
> 
> On Thursday 09 February 2006 19:53, Chris Fields wrote:
> > Heikki,
> >
> > I've added the Bio::Tools::RNAMotif module with test suite 
> (24 tests) 
> > and two test data files to bugzilla.  The first data file is needed 
> > for normal tests, the second is for testing parsing with 
> modified data 
> > in the score tag (using sprintf() in the RNAMotif 
> descriptor).  I ran 
> > 'perl t\RNAMotif.t' and they all passed.
> >
> > Thanks!
> >
> > Christopher Fields
> > Postdoctoral Researcher - Switzer Lab
> > Dept. of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> > > -----Original Message-----
> > > From: bioperl-l-bounces at lists.open-bio.org
> > > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Heikki 
> > > Lehvaslaiho
> > > Sent: Wednesday, February 08, 2006 12:54 AM
> > > To: bioperl-l at lists.open-bio.org
> > > Cc: Chris Fields
> > > Subject: Re: [Bioperl-l] RNAMotif module (Bio::Tools::RNAMotif)
> > >
> > > Chris,
> > >
> > > Post your files to bugzilla (ticket type enhancement, add 
> files to 
> > > ticket after creation)  and someone with commit ability will add 
> > > them to CVS once the code is in satisfactory condition.
> > >
> > > Thanks,
> > >
> > > 	-Heikki
> > >
> > > On Wednesday 08 February 2006 06:52, Chris Fields wrote:
> > > > I want to submit a module for parsing RNAMotif output 
> > > > (Bio::Tools::RNAMotif).  It is capable, at the moment, 
> of scanning 
> > > > output and returning Bio::SeqFeature::Generic objects with
> > >
> > > added tags
> > >
> > > > for descriptors/sequences/file info.  I'm in the process of
> > >
> > > writing up
> > >
> > > > tests and going through biodesign to make sure everything's 
> > > > kosher, but the module itself is essentially ready-to-go.  What 
> > > > should I do next?
> > > >
> > > > Christopher Fields
> > > > Postdoctoral Researcher
> > > > Lab of Dr. Robert Switzer
> > > > Dept of Biochemistry
> > > > University of Illinois Urbana-Champaign
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Bioperl-l mailing list
> > > > Bioperl-l at lists.open-bio.org
> > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > >
> > > --
> > > ______ _/      
> _/_____________________________________________________
> > >       _/      _/
> > >      _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
> > >     _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
> > >    _/  _/  _/  SANBI, South African National 
> Bioinformatics Institute
> > >   _/  _/  _/  University of Western Cape, South Africa
> > >      _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
> > > ___ 
> > > _/_/_/_/_/________________________________________________________
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/
>      _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
>     _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
>    _/  _/  _/  SANBI, South African National Bioinformatics Institute
>   _/  _/  _/  University of Western Cape, South Africa
>      _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
> ___ 
> _/_/_/_/_/________________________________________________________