[Bioperl-l] Glyph question

[Lincoln Stein]

Hi Olly,

Do you want the subfeatures to appear at all, or just suppress them?  If you 
just want to suppress them, then it is easy to subclass the transcript glyph 
--- you can do it in the same file as your main script if you like:

package Bio::Graphics::Glyph::mytranscript;

use base 'Bio::Graphics::Glyph::transcript';

sub _subseq {  # override the method that produces subparts
	my $self = shift;
	my $feature = shift;
	my @subseq = $self->SUPER::_subseq($feature);
	return grep {$_->primary_tag eq 'exon'} @subseq;
}

Then refer to the glyph named "mytranscript".

Alternatively there is a new glyph named "processed_transcript" that -- I 
think -- will only display subfeatures of type "exon", "CDS" and "UTR". I 
haven't tested it with other types of subfeatures, however, so I might be 
wrong.

Lincoln

On Thursday 05 May 2005 08:35, Oliver Burren wrote:
> Hi Developers,
>
> I'm trying to render some transcripts and I'm using objects in
> Bio::SeqFeature::Gene as well as Bio::Graphics::Panel and Glyph.
>
> I have added some subfeatures (Of type SeqFeature::Generic) to the exon
> objects that exist within these transcripts. Unfortunately when I render
> using the Bio::Graphics::Glyph::transcript glyph it treats these
> seqfeatures as exons so I get an odd transcript out. Is there anyway
> without creating a custom glyph to get Bio::Graphics::Glyph::transcript
> to use only exon subFeatures when rendering ?
>
> I'm using bioperl 1.4
>
> Thanks very much
>
> Olly Burren
>
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