[Bioperl-l] Puzzled...

Brian Osborne osborne1 at optonline.net
Mon Dec 19 14:10:36 EST 2005


Yes, this is my preference as well. Very good, I'll get started, see where
it takes me...

Brian O.

On 12/19/05 12:04 PM, "Heikki Lehvaslaiho" <heikki.lehvaslaiho at gmail.com>

> 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?
> -Heikki
>> 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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