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

[Lincoln Stein]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Todd,

Maybe I've made a mistake.  Let me know which way works.

Lincoln

On Monday 08 March 2004 01:12 pm, Jason Stajich wrote:
> err - I don't think you should be calling attach_seq really, but
> rather add_feature on the seq object
>
>  $seq_object->add_SeqFeature($feature);
>
> This is really the right way to do this - it will properly update
> the seqfeature and call attach_feature for you.
>
> -jason
>
> On Mon, 8 Mar 2004, Lincoln Stein wrote:
> > -----BEGIN PGP SIGNED MESSAGE-----
> > Hash: SHA1
> >
> > 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.p
> > >m 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
> > -----BEGIN PGP SIGNATURE-----
> > Version: GnuPG v1.2.1 (GNU/Linux)
> >
> > iD8DBQFATLTt0CIvUP7P+AkRAgrqAJ9YLCuetr50r704+MyFo1+H7Py+4wCeOXeM
> > YiFetRZeCf+misFV4omy+f0=
> > =sLUm
> > -----END PGP SIGNATURE-----
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> _______________________________________________
> 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
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.2.1 (GNU/Linux)

iD8DBQFATL+x0CIvUP7P+AkRAh2bAJwIEXstWUJYdwAYuJ/O0nG87I7hyACfZWxR
mGai9ckUJFQb6sAozxuxJBk=
=OPAW
-----END PGP SIGNATURE-----