[Bioperl-l] Sorting Bio:Graphics::Glyphs

Oliver Burren oliver.burren at cimr.cam.ac.uk
Wed Dec 3 09:14:46 EST 2003


Hi,

I have a lot of transcripts that I'm rendering using the excellent
Bio::Graphics module. I want to sort these by the last two characters in
the display_name attribute. I used the following callback 

sub sort_trans($$){substr($_[0]->display_name,-2)<=>
                  substr($_[1]->display_name,-2)} 
# the last two chars are numbers therefore using <=>

I then added 
the following  track glyph

my $ttrack=$panel->add_track(\@transcripts,
                        -glyph=>'transcript',
                        #......more options here
                        -sort_order=>&sort_trans # should this be 						
# \&sort_trans ?
                        );

If i then run this I get the following error

Can't call method "display_name" on unblessed reference at gene_page.cgi
line 93, <DATA> line 191.

In the pod documentation for Glyphs it says to use $a and $b vars if I
use these though i get an exception that tells me to use a ($$)
prototype (which I think I'm doing by using a call back with
prototype).  

I'm using Version 1.3 of bioperl.

Can anyone point out what I should be doing or am doing wrong ?

Thanks, 

Olly Burren

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