[Bioperl-l] Bio::DB::GFF::Aggregator problem, new wormbase models.

Todd Harris todd.harris at cshl.edu
Tue Feb 17 17:10:48 EST 2004

Hi Phillip - 

You need to aggregate the separate parts of the CDS.  Create a wormbase_cds
(or whatever you wish to call it), aggregating the following features using
the CDS group: coding_exon,5_UTR,3_UTR.

The following stanza should do the trick.

$dbgff = (-adaptor => 'dbi::mysql',
          -dsn     => 'dbi:mysql:database=your_database;host=your_host',
          -aggregators => [qw(wormabse_cds{coding_exon,5_UTR,3_UTR/CDS})],
          -user    => 'your_username',
          -pass    => 'your_dbgff_pass');

This should do the trick for properly aggregating genes under the new
WormBase CDS class.

Todd Harris

> On 2/17/04 2:18 PM, Philip MacMenamin wrote:

> I cannot get things to aggregate properly in the new wormbase models.
> Previously this worked:
> $aggregator = Bio::DB::GFF::Aggregator->new(-method    => 'test',
>       -sub_parts => ['UTR','CDS:curated']
>      );
> (Or I could of more simply used the 'processed_transcript' aggregator that
> Linoln wrote.)
> And one feature, with the UTRs "aggregated" together with the curated CDS's,
> was returned:
> test:5_UTR(AH6.5), start->9524078 end->9526248
> This could be fed to some kind of glyph, and would draw a nice picture of
> UTRs hanging off a coding seq.
> [--------------]    [----------]  [---->
> (You have to use your imaginatio a bit here)
> With the new models of wormbase, this is not the case, so I am re-writing
> code to accomadate these changes.
> Now I am returned for example 3 features: a 3 prime UTR, a prime, and a CDS.
> test:UTR(5_UTR:AH6.5)9524078 9524086
> test:UTR(3_UTR:AH6.5)9525782 9526248
> test:curated(AH6.5)9524087 9525781
> The glyph then draws these things on two planes.
> []                [------->
> [---------]  [------------] [----------]
> My assumption is that a single feature can be rendered as a single glyph. And
> if you have >1 feature, then >1 glyphs are needed. Therefore, I assume the
> problem stems from my failure to aggregate UTR and CDS features.
> I have noticed that the new SQL GFF Db used to have two fmethods for UTRs,
> one for both 3 and 5 primes. The new one has only one. There are other
> changes of course, but I think this is important.
> So, essentially I want to draw UTRs with CDS's attached... with the new
> wormbase models. If anyone knows how to do this, i'd like to hear from them.
> Thanks :)

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