[Bioperl-l] Bio::Graphics

[Lincoln Stein]

Are you sure that you are using the same version of bioperl on both boxes?  
The fonts are compiled in and LANG is ignored by Bio::Graphics.

Lincoln

On Friday 29 August 2003 01:27 pm, Christopher Fields wrote:
> I tried the tutorial on RedHat Linux 9.0 and it works, but I tried it on
> my wife's IBook (Mac OSX 10.2.6) and couldn't get the labels to come up
> either.  I posted a reply here (bioperl-l) a while back about it but
> didn't get a reply.  Could it be a font problem or LANG setting?  My RH
> 9.0 system has LANG=en_US, but I think the IBook (OS X) has LANG=C
> (neither set to UTF-8; I had problems with this in the past on both
> systems).
>
> On Fri, 2003-08-29 at 10:39, Lincoln Stein wrote:
> > Sorry for responding so late to this e-mail.  You were looking at an out
> > of date tutorial that no longer matches the code base.  However, the
> > tutorial has now been updated and the examples should work.
> >
> > Lincoln
> >
> > On Wednesday 06 August 2003 03:09 am, Laurence Amilhat wrote:
> > > Hi,
> > >
> > > I try to learn how to use the module Bio::Graphics.
> > > I found he How To from Lincoln Stein on the web. I try to practice with
> > > the examples, it's working except for the labels of the features that
> > > don't appear on my figure.
> > > Does anybody ever use this module?
> > >
> > > This is the example:
> > > #!/usr/local/public/bin/perl
> > >
> > > use strict;
> > > use lib
> > > '/homej/bioinf/lamilhat/PERL_MODULE/lib/perl5/site_perl/5.005/BIOPERL/l
> > >ib/s ite_perl/5.6.1/'; use Bio::Graphics;
> > > use Bio::SeqFeature::Generic;
> > >
> > > my $panel= Bio::Graphics::Panel->new(-length =>1000,-width =>800);
> > > my $track=$panel->add_track(-glyph =>'generic',-label =>1);
> > >
> > >
> > > while (<>)
> > > {
> > >          chomp;
> > >          next if /^\#/;
> > >          my ($name,$score,$start,$end)=split /\t+/;
> > >          print STDERR "$name\n";
> > >          my $feature=
> > > Bio::SeqFeature::Generic->new(-display_name=>$name,-score=>$score,-star
> > >t=>$ start,-end=>$end); $track->add_feature($feature);
> > > }
> > >
> > > print $panel->png;
> > >
> > >
> > > And this is the Data to parse with the example:
> > > #hit    score   start   end
> > > truc1   381     2       200
> > > truc2   210     2       210
> > > truc3   800     2       200
> > > truc4   1000    380     921
> > > truc5   812     402     972
> > > truc6   1200    400     970
> > > bum     400     300     620
> > > pres1   127     310     700
> > >
> > >
> > > Thanks,
> > >
> > > Laurence.
> > >
> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > > INRA, UMR INRA/UBP Amélioration et Santé des Plantes
> > > 234 avenue du Brézet
> > > 63039 Clermont-Ferrand Cedex 2
> > >
> > > Tel 04 73 62 48 37
> > > Fax 04 73 62 44 53
> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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