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

[Heikki Lehvaslaiho]

On Thursday 09 February 2006 23:25, Chris Fields wrote:
> 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.

Looking forwart to them!

	-Heikki

> 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
> > > > ___
> > > > _/_/_/_/_/________________________________________________________
> > > > _______________________________________________
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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
> > ___
> > _/_/_/_/_/________________________________________________________
>
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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
___ _/_/_/_/_/________________________________________________________