[Bioperl-l] ASN.1 and BioPerl ?
Stephen L. Mathias
smathias at poblano.health.unm.edu
Mon Feb 14 10:32:23 EST 2005
On Sat, 2005-02-12 at 14:37, Peter.Robinson at t-online.de wrote:
> On Sat, Feb 12, 2005 at 01:20:30PM -0800, Hilmar Lapp wrote:
> > The ASN.1 parser would be very useful, in particular for implementing
> > the NCBI Gene parser I suppose.
> > I do suggest though that you publish this as a separate module on CPAN,
> > as supposedly it is (or meant to be?) generically useful, so I
> > completely agree with Chris on this.
> I also agree that it would be better to have the module on CPAN; if you
> been inspired to use the module to incorporate Entrez Gene into BioPerl I
> would be happy to help out as I can. My initial experiences with this suggest it will not be easy.
> > I need an NCBI Gene parser implemented in the Bio::SeqIO framework
> > returning compatible Bio::SeqI objects within the next few weeks. The
> > speed needs to be at least several records per second, ideally 10/s or
> > higher.
> > My understanding is that Peter has a grammar-based parser in Java
> > (speed I don't know), and Steve has a Parse::RecDescent-based parser in
> > perl (not bioperl) which is (expectedly) slow.
> > I've seen Graham Barr's module on CPAN but haven't tried it yet; it
> > seemed to me that you need the ASN model definition to start with,
> > which I haven't seen at any obvious or not-so-obvious place on the NCBI
> > ftp site, so I either missed something or you have to download the
> > entire toolkit or something else.
> You might want to take a look at this
You also need:
which contain definitions imported by the above file.
( Stephen L. Mathias, Ph.D. ( s m a t h i a s (
) Office of Biocomputing ) @ p o b l a n o )
( UNM School of Medicine ( . h e a l t h . (
) ) u n m . e d u )
( http://poblano.health.unm.edu/ (
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