[Bioperl-l] Re: entrezgene binary ASN

Michael Seewald mseewald at gmail.com
Sun Oct 2 11:27:17 EDT 2005

On 10/2/05, Hilmar Lapp <hlapp at gmx.net> wrote:
> On Oct 1, 2005, at 1:01 PM, Stefan Kirov wrote:
> > Hilmar,
> > As of now the parser does not seek through the streem, but hopefully
> > it will as soon as I can sit down and do it
> What advantage would that have?

You could create an index and seek by gene id. Could be handy in some cases,
although I wouldn't use it (personally).

Note that not allowing streams first off makes entrezgene different
> from all other formats, and second, together with the gene2xml
> conversion requirement would require you to call it in a different
> manner than all other SeqIO parsers (i.e., just passing a string, w/ or
> w/o trailing pipe, wouldn't suffice; you'd have to do a preprocessing
> step). If seeking in the file can outweigh that with some significant
> advantages, then great, but even then it should be optional if it can
> be within reason.

The "streaming use" shouldn't be affected. BTW, there are other bioperl
modules that use indices.
Best wishes,

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