Re: [Gmod-ajax] How can I display each feature name/tag/id/description next to it?

[Mitch S. <mit...@be...>]

On 07/02/2010 09:57 AM, David Breimann wrote:
> Thank you!
>
> 1. Is it possible to call a subroutine defined in extraData from label
> (e.g. "label": "load_id")? I tried playing with the syntax, but
> couldn't figure it out.
>    

The "label" callback and the "extraData" callback both operate on 
bioperl feature objects.  So data doesn't go from the extraData outputs 
to the label callback, as you seem to be assuming.  Instead, in your 
"label" callback you get data straight from the source.  So, for 
example, you could so something like

"label": "sub { return \"foo\" . $_[0]->attributes(\"load_id\"); }",

to get whatever information you wanted, directly from the bioperl 
feature object.

> 2. What is the structure of a feature object (read from a GFF)?
>    

That's a bioperl thing; refer to the bioperl documentation.  When I want 
to experiment to learn a perl API, I often use Devel::REPL (installed 
from cpan), something like this:

$ re.pl

$ use Bio::DB::SeqFeature::Store

$ my $db = Bio::DB::SeqFeature::Store->new(-dsn => "dbi:mysql:dmel_5_13")
$Bio_DB_SeqFeature_Store_DBI_mysql1 = 
Bio::DB::SeqFeature::Store::DBI::mysql=HASH(0x97cae84);

$ my @genes = $db->features(-seq_id => "4", -type => "gene")

$ $genes[0]->attributes("load_id")
FBgn0040037


Mitch