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

Philip MacMenamin pm66 at nyu.edu
Wed Feb 18 11:41:46 EST 2004

Thanks very much Todd...

What version of wormbase are you using? I am using WS118. I am not able to 
get this aggregator to return me the UTR bits. 

For instance, I connect to the db using your agg:
my $db = new Bio::DB::GFF(-adaptor=>'dbi::mysqlopt',
#			  -dsn=>'dbi:mysql:wormbase110;host=localhost',
			  -aggregator => [qw(wormabse_cds{coding_exon,5_UTR,3_UTR/CDS})],
			 ) or die();

#...ask for a segment in the AH6.5 region:
my $panelSeg = $db->segment(CDS=>'AH6.5');

#...make a searchSegment a little larger to pick everything:
my $searchSeg =$db->segment($panelSeg->sourceseq, 
($panelSeg->abs_start-1000), ($panelSeg->abs_end+1000));

#and, then get the features that wormabse_cds pulls:
my @all_transcripts = $searchSeg->features('wormabse_cds');
foreach my $transcript ( @all_transcripts )
    print $transcript, $transcript->abs_start,' ', $transcript->abs_end,"\n";

I assume this is the right way to do things. But, the problem is that this 
does not get my UTRs. This does:
my @UTRs = $searchSeg->features('UTR:UTR');
foreach my $UTR (@UTRs)
    print $UTR," ",$UTR->start," ",$UTR->end,"\n";
But, these are not aggregated obviously.

This is the output of the little script above:

UTR:UTR(5_UTR:AH6.5) 9524078 9524086
UTR:UTR(3_UTR:AH6.5) 9525782 9526248
wormabse_cds:curated(AH6.5)9524087 9525781

And you can see that the wormabse_cds does not overlap with the UTRs.

Sorry about this. I have been trying all sorts of things... it just keeps on 
missing the UTRs in the new wormbase models. And we can't re-sync the site 
here till this works.

On Tuesday 17 February 2004 05:10 pm, Todd Harris wrote:
> 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

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