[Bioperl-l] Puzzled...

Heikki Lehvaslaiho heikki.lehvaslaiho at gmail.com
Mon Dec 19 12:04:30 EST 2005

On Monday 19 December 2005 01:08, Brian Osborne wrote:
> Heikki,
> I don't have the time to be complete, that's a significant undertaking
> (e.g. both NCBI and EMBL and others, diffs of versions, correlating GIs to
> version numbers, dates, release numbers, "status", and so on). You may have
> correctly deduced from my examples that all I really care about is old and
> new GI numbers. But I can certainly add files in such a way as to allow
> these methods or modules to appear later if someone wanted to add them.

That is good enough.

> So in order to satisfy genericiy we could have Bio::DB::Version::ncbi. Or
> were you thinking about tying this all a bit closer to the Seq object, as
> in Bio::Seq::Version::<something> rather than Bio::DB? Or...?
Nah, the returned objects are plain old sequences. The new bit might be in the 
way you treat sets of seq ids that might be linked to time points and 
releases etc - but I have not given it much thought.

It might be clearer if you use Bio::DB::SeqVersion name space?


> Brian O.
> On 12/18/05 4:28 PM, "Heikki Lehvaslaiho" <heikki.lehvaslaiho at gmail.com>
> wrote:
> > It would be great if the bioperl implementation of nucleotide sequence
> > version retrieval could be as generic and complete as possible  ;-) .

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     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
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  _/  _/  _/  University of the Western Cape, South Africa
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