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

[Heikki Lehvaslaiho]

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
> > ___ _/_/_/_/_/________________________________________________________
> > _______________________________________________
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>
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-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  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
___ _/_/_/_/_/________________________________________________________