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

Jason Stajich jason at bioperl.org
Tue Sep 7 13:36:07 EDT 2010


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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