[Bioperl-l] Bio::Graphics::Glyph::translation.pm

[Lincoln Stein]

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You need to attach a Bio::PrimarySeqI to the Bio::SeqFeature::Generic, 
not a Bio::SeqI.  I know this is confusing, but I think that you can 
get the effect you want by changing this line to read:

	$feature->attach_seq($seq_object->seq);

Lincoln

On Wednesday 03 March 2004 04:03 pm, Dr. Todd Naumann wrote:
> Hi,
>
> I am trying to use the translation glyph and I am running into
> problems. When I run the program below with glyph=>'dna' I get a
> picture of double stranded DNA sequence as I expected. When I try
> to use
> glyph=>'translation' I get the following error message:
>
> Can't locate object method "translate" via package
> "Bio::SeqFeature::Generic" at
> /usr/lib/perl5/site_perl/5.8.2/Bio/Graphics/Glyph/translation.pm
> line 134, <GEN0> line 118.
>
> I tried to find another SeqFeature object that has a translate
> method but did not have any luck. If someone could point me in the
> right direction I would really appreciate it.
>
> -Todd
>
> #!/usr/bin/perl
>
> use strict;
> use warnings;
>
> use Bio::Graphics;
> use Bio::SeqFeature::Generic;
> use Bio::SeqIO;
>
> # initialize the graphics panel
> my $panel = Bio::Graphics::Panel->new(-length => 80,
> -width => 800,
> -pad_left => 10,
> -pad_right => 10,
> );
>
> # make the feature object
> my $feature = Bio::SeqFeature::Generic->new(-start=>1,
> -end=>60,
> );
>
> # create a sequence object
> my $seqIO_object = Bio::SeqIO->new(-file => 'test_sequence.gb',
> -format => 'genbank',
> );
>
> my $seq_object = $seqIO_object->next_seq();
>
> # attach sequence object to feature
> $feature->attach_seq($seq_object);
>
> # add track to panel
> $panel->add_track($feature,
> -glyph => 'translation',
> -fgcolor => 'black',
> );
>
> print $panel->png;
>
> exit;
> ============================
> Todd Naumann
> Dept. of Chemistry
> Penn State University
> University Park, PA  16802
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

- -- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
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