[Bioperl-l] ASN.1 and BioPerl ?

[Stephen L. Mathias]

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
> 
> http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn

You also need:
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/seqfeat/seqfeat.asn
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/general/general.asn
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/seqloc/seqloc.asn
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/pub/pub.asn
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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