[Biopython-dev] Active projects list? (BOSC Biopython Project Update)

[Peter]

On Wed, Jul 21, 2010 at 4:43 PM, Andrea Pierleoni
<andrea at biocomp.unibo.it> wrote:
>>
>> Well, I went and did the basics to be consistent with the existing limited
>> dict like support in BioSeqDatabase. Would you mind testing it?
>>
>> This can be improved by iterating over the cursor rather than building a
>> list of identifiers in memory. Likewise __len__ and __contains__ can be
>> turned into SQL statements to be more efficient. Do you fancy trying that?
>>
>> Peter
>>
>
> I've tested the new BioSeqDatabase in postgres BioSQL db containing 50000
> bioentry, and it works very fast (I'm using python 2.6) even in this way.

Good :)

> howver using SQL will be much better of course. I will take a try, as soon
> as I fix the DAS client and UniprotIO.

I had time this afternoon to do __len__ and __contains__ with SQL, and
add a couple of tests here too. Memory efficient Iteration can wait for
another day - I'm going home now.

We should probably have started a new thread for this BioSQL discussion.

Peter