[Bioperl-l] Entrez Gene and bioperl-db

[Hilmar Lapp]

On Thursday, January 6, 2005, at 06:33  PM, Stefan A Kirov wrote:

> Hilmar,
> Getting back to your post, I have some concern about automatic
> parsing of multiple files (if I got this right...). Say if one 
> downloads
> the whole Entrez Gene stuff and all is OK I don't see why this can't be
> done. But if something goes wrong (and occasionally it will), it will 
> be
> really hard for the user to understand he misses parts of the data.

By going wrong you mean partial downloads resulting from interrupted 
file transfer sessions? If so, then this is no different from parsing 
other (e.g. Genbank) downloaded and therefore possibly truncated files. 
If by wrong you mean certain files are absent, then yes, I mean that 
there presence is optional, and certainly the parser could warn, unless 
warnings are suppressed.

> [...]
> Another issue that comes to mind is the approach of a stream is fine 
> for
> people with the whole DB on their minds. But of you need particular
> record, I guess you you could index the files, but this totally 
> different
> game.

right. You'd write a Bio::Index::<name> module for this.

	-hilmar
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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