[Bioperl-l] Re: entrezgene binary ASN

[Mingyi Liu]

Yelp, I agree with pretty much all the points Hilmar raised.  I don't 
think all the opinions on pipes or index/seek differ that much.

Just want to note that Bio::ASN1::EntrezGene::Indexer (included in the 
download of Bio::ASN1::EntrezGene and a child class of 
Bio::Index::AbstractSeq) already does the indexing and retrieval of 
Bio::Seq object of entrez gene using id.  And Bio::ASN1::EntrezGene 
returns filehandle through function fh, which can be used for seeking 
(and in fact, Bio::ASN1::EntrezGene::Indexer uses the function to do 
seeking for a non-bio-perl-standard function it provides).  So seeking 
possibility is already provided by the fh function in the low-level 
parser of entrezgene, but not directly handled in parser (though used in 
indexer).

Mingyi

Stefan Kirov wrote:

> Yes, Hilmar is right- there should be Bio::Index::entrezgene to do 
> that. I agree this functionality is better kept separated from 
> Bio::SeqIO parser.
> Stefan