[Bioperl-l] Bio::Graphics::Glyph::dna

Paul Boutros paul.boutros at utoronto.ca
Sat Dec 23 22:36:59 EST 2006


Hi,

I've been trying to get the dna glyph working and have had some  
problems.  I'm using a fasta file, and am having some problems.  This  
is ActiveState perl 5.8.8 (build 819) and BioPerl 1.5.2 on WinXP.  I'm  
starting with a FASTA file, so I've tried:
$panel->add_track(
	$seq,
	-glyph     =>   'dna',
	-do_gc     =>   'true',
	-gc_window =>   'auto'
	);

where $seq is a Bio::Seq object

and I've tried it using a GFF $segment:
my $db = Bio::DB::GFF->new(
          -adaptor=>    'berkeleydb',
          -create =>    1,
          -dsn    =>    'temp'
          );

$db->load_sequence_string(
           $seq->primary_id(),
           $seq->seq()
           );

my $segment = Bio::DB::GFF::Segment->new(
           $db,
           $seq->primary_id(),
           $seq->primary)_id(),
           1,
           $seq->length()
           );

$panel->add_track(
	$segment,
	-glyph     =>   'dna',
	-do_gc     =>   'true',
	-gc_window =>   'auto'
	);




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