[Bioperl-l] Bio::Seq, search for specific features

[Chris Fields]

Well, no move has been concretely made yet.  It would be nice to abstract the backend, so one could use possibly any db or memory adaptor.  This is essentially the direction I would like to take the alignment data as well (part of the GSoC project for BioPerl this year was to tackle this very thing).

chris

On Sep 8, 2010, at 3:42 AM, Frank Schwach wrote:

> Hi Jason,
> 
> Yes, I guess that would be the simplest way of doing it - basically just
> doing it the way the docs suggest for getting at a specific feature but
> hiding the grep behind a Bio::Seq method with search parameters. But we
> could also build a hash of feature tags as the Bio::Seq is built so that
> retrieval is more efficient. This could also be used to implement a bin
> indexing scheme for range queries, similar to what Bio::DB::GFF does.
> Is a move to an sqlite backend planend for the near future? 
> 
> Frank
> 
> 
> 
> On Tue, 2010-09-07 at 10:36 -0700, Jason Stajich wrote:
>> And the implementation would just be something like this?
>> 
>> my @features = grep { $_->has_tag('id') && ($_->get_tag_values('id'))[0] 
>> eq 'my_gene' } $seq->get_SeqFeatures();
>> 
>> I think any implementation would be if we moved from the in-memory 
>> arrays & hash-based system to a sqlite db on the back-end for how 
>> Sequence and Feature objects are stored.
>> This would be a somewhat slower but wouldn't have performance/memory 
>> problems we get for sequences with many annotations.
>> 
>> -jason
>> Frank Schwach wrote, On 9/7/10 5:09 AM:
>>> I am working a lot with feature-rich Bio::Seq objects these days and
>>> thought that it would be really nice if I could do something like:
>>> 
>>> my @features = $bio_seq_obj->get_SeqFeatures(-by_id =>  'my_gene');
>>> 
>>> instead of having to grep for the feature every time.
>>> There could then be 'by_tag' and 'by_region' options as well.
>>> 
>>> According to the Bio::Seq docs, something like this seems to be planned
>>> at some stage. I would be willing to contribute to this feature if I can
>>> and if this isn't already being implemented by somebody else.
>>> Does anybody know the state of this feature?
>>> 
>>> Frank
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
> 
> 
> 
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