[Bioperl-l] GenBankParser comparison to bioperl parser

[John Pearson]

On Thu, 12 Sep 2002, Ewan Birney wrote:

> On Thu, 12 Sep 2002, Ian Korf wrote:
>
> > I'll de-lurk for this.
> >
> > I, for one, think that a bio-util-perl project would be a good
> > idea. Not everyone wants or needs the whole of bioperl.
> > Sometimes, a small utility outside the framework is useful.
> > Analogously, I use a full-featured text editor that counts
> > letters, words, paragraphs etc, but I still find myself using wc
> > from time to time.
> >
> > I think that if something is going to be part of bioperl, it
> > ought to have the same consistent interface. But I like what
> > John has done, both at the interface and implementation level.
> > Is it possible to leave John's parser the way it is and offer a
> > bioperl interface to it?

Another de-lurk.

I'm guessing there might be other lurkers with good code that is functional
but not written to mesh with the bioperl framework so it never sees the
light of day.  I know we have some useful-but-tightly-targeted modules but
they are just not abstracted to the bioperl level.

A bioperl-util repository might catch some good stuff and if some GREAT
code turns up, maybe the bioperl-gods would be able to tutor the authors
on how to re-jig/re-think their code to bring it into bioperl proper.  :)

John

-- 
John Pearson
Senior Scientific Programmer, Digicon Corporation
Bioinformatics and Scientific Programming Core,
NIH / National Human Genome Research Institute
50 South Drive
Bldg 50 Rm 5228
Bethesda, MD 20892-8004
Office: (301)402-7038        Fax: (301)480-1109