[Bioperl-l] Re: BioGraphics tutorial problem

[Scott Cain]

Laurence and Wes,

While I am sure there is another way to fix this problem, I can't seem
to figure it out this morning.  Installing from CVS will fix it, and it
is not particularly painful to do (at least, not on a unix-like
system).  You can go to 

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/?cvsroot=bioperl

and click the "Download tarball" link to get bioperl-live. 

If you don't want to install the "bleeding edge" version of bioperl, you
can wait either until I shake the cold I've got, or until Lincoln gets
back from vacation :-)

Scott


On Thu, 2003-08-07 at 05:08, Laurence Amilhat wrote:
> Dear Scott, 
> 
> Thank you very much for your answer.
> The http://www.gmod.org/BioGraphicsTest.png is what am I expecting.
> I installed the BioPerl-1.2.2 version. I used the tutorial from
> Lincoln Stein at :
> http://stein.cshl.org/genome_informatics/BioGraphics
> 
> So, the only way to get my script working is to use bio-perl-live from
> CVS?
> I saw that I need a secure ssh (I have one), a CVS and an account to
> run script on bioperl live.
> but I don't know what is CVS?
> 
> Thank you,
> 
> Sincerely,
> 
> Laurence
> 
> 
> 
> 
> 
> 
> At 15:52 06/08/2003 -0400, you wrote:
> > Laurence,
> > 
> > I ran a script very similar to what you are using (the code I used
> > is
> > below), and I didn't have any problems, at least not if what is
> > expected
> > is the same as this: http://www.gmod.org/BioGraphicsTest.png.
> > 
> > I suspect you are having a version problem.  I am using bioperl-live
> > (from CVS), but when I installed bioperl-1.2.2, it failed in the way
> > you
> > describe.  Where is the tutorial you are reading?  Perhaps it is not
> > in
> > sync with the most recent version of released bioperl.
> > 
> > Here is the script I used:
> > #!/usr/local/bin/perl -w
> > 
> > use strict;
> > 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 (<DATA>)
> > {
> >          chomp;
> >          next if /^\#/;
> >          my ($name,$score,$start,$end)=split /\s+/;
> >          warn "$name\n";
> >          my $feature=
> > Bio::SeqFeature::Generic->new(-display_name=>$name,-score=>$score,-start=>$start,-end=>$end);
> >          $track->add_feature($feature);
> > }
> > 
> > print $panel->png;
> > 
> > __DATA__
> > #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
> > 
> > Scott
> > 
> > On Wed, 2003-08-06 at 13:31, bioperl-l-request at portal.open-bio.org
> > wrote:
> > > 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?
> > 
> > -- 
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D.                                        
> > cain at cshl.org
> > GMOD Coordinator (http://www.gmod.org/)                    
> > 216-392-3087
> > Cold Spring Harbor Laboratory
> 
> 
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory