[Bioperl-l] Bio::Graphics::Glyph::translation how to show the correct sequences

[Scott Cain]

Hi Christine,

Can you provide the sample data and complete script?  Nothing looks
particularly wrong, but I can't tell from you image that anything is wrong
either.  Presumably there is something in the data making you think it is
wrong though.

Scott



On Tue, Mar 18, 2014 at 2:15 AM, Christine Hoogland <
christine.hoogland at gmail.com> wrote:

> Hi,
>
> I'm trying to display the frame translation sequences into images built
> with Bio::Graphics showing exons, introns, CDS... like the example shown in
> figure 13a and 13b on this page:
> http://chlamycyc.mpimp-golm.mpg.de/gbrowse/tutorial/dbgff/tutorial.html
>
> Currently sequences shown are always the same, whatever the CDS (see image
> attached), although sequences printed in the console for debugging are fine.
>
> my @CDS = sort {$a->start <=> $b->start} $mRNA->CDS;
> my $cdsft=Bio::Graphics::Feature->new();
> for my $cds (@CDS) {
>         $cdsft->add_segment(Bio::Graphics::Feature->new(
>                                 -start=> $cds->start,
>                                 -end  => $cds->end,
>                                 -seq  => Bio::Seq->new(-seq=> $cds->dna,
> -alphabet => 'dna'),
>                                 -strand => $cds->strand,
>                                 -phase => $cds->phase
>                                ));
>
> }
>
> $panel->add_track($cdsft,
>             -glyph      => 'translation',
>             -show_sequence => 'true',
>             -key        => 'Sequence',
>             -height   => 64,
>             -bump     => +1,
>             -translation => '3frame',
>             -label    => 1,
>             -description    => 1,
>          );
>
> Is anybody able to see what's wrong with this code?
>
> Thanks a lot!
> Christine
>
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research