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

[David B. <dav...@gm...>]

Thanks a lot Mitch.

On Fri, Jul 2, 2010 at 7:26 PM, Mitch Skinner
<mit...@be...> wrote:
> 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
>