[Bioperl-l] Searching by source in Bio::DB::SeqFeature::Store?

[Lincoln Stein]

Hi Sendu,

This may be a glaring omission on my part. Try searching for:

 @feats = $db->get_features_by_type(":$source");

Remove the colon in front of $source.

This might not work, but give it a try.

Lincoln

On 10/10/07, Sendu Bala <bix at sendu.me.uk> wrote:
>
> Once I store a feature like so:
>
> $db = Bio::DB::SeqFeature::Store->new( # mysql );
> $db->new_feature(-primary_tag  => 'X',
>                   -seq_id       => 'Y',
>                   #...
>                  -source       => 'Z');
>
> How do I search for it again? I could have sworn that in the past the
> source somehow became one of the feature's attributes so that I could do:
>
> @feats = $db->features(-attributes => {source => 'Z'});
>
> (Or does/did some other feature-related module store source as an
> attribute, and in the past I stored those features in my db?)
>
> The obvious isn't implemented:
>
> @feats = $db->features(-source => 'Z');
>
> Looking at the code I see I can do type and source at the same time:
>
> @feats = $db->features(-type => 'X:Z');
>
> which works, but how do I just search for all Z, regardless of type?
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Lincoln D. Stein
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