scripts to vizualize a feature distribution on genome

viz/gff_to_chromsummary.pl

@@ -0,0 +1,77 @@
+#!/usr/bin/perl -w
+use strict;
+
+use Getopt::Long;
+use Bio::DB::Fasta;
+use Bio::SeqFeature::Generic;
+use File::Spec;
+use Bio::Graphics;
+
+my $WIDTH = 1000;
+
+my $dir = 'graphics';
+my $type_filter;
+GetOptions('d|dir:s' => \$dir,
+	   't|type:s' => \$type_filter,
+	   );
+my $db = shift;
+my $gff = shift;
+
+mkdir($dir) unless -d $dir;
+my $dbh = Bio::DB::Fasta->new($db);
+open(my $fh => $gff) || die $!;
+my %dat;
+while(<$fh>) {
+    next if /^\#/;
+    my ($chrom,$src,$type,$start,$stop,$score,$strand,$frame,
+	$group) = split;
+    next if( defined $type_filter && $type_filter ne $type);
+
+    my %group = map { split(/=/,$_) } split(/;/,$group);
+    push @{$dat{$chrom}}, Bio::SeqFeature::Generic->new(-start => $start,
+							-end   => $stop,
+							-primary_tag => $type,
+							-source_tag  => $src,
+							-tag => { Note => $group{Note} },
+							-display_name => $group{Name});
+}
+my $limit = $type_filter || 'all';
+for my $chrom ( keys %dat ) {    
+    my $ofname = File::Spec->catfile($dir,"$chrom.$limit.png");
+    my $chrom_length = $dbh->length($chrom);
+    my $panel = Bio::Graphics::Panel->new(-length=> $chrom_length,
+					  -width  => $WIDTH,
+					  -pad_left => 0,
+					  -pad_right => 0);
+
+    my $top_length = Bio::SeqFeature::Generic->new
+	(-start => 1,
+	 -end   => $chrom_length,
+	 -display_name => $chrom);
+
+    $panel->add_track($top_length,
+		      -glyph   => 'arrow',
+		      -tick    => 2,
+		      -fgcolor => 'black',
+		      -double  => 1,
+		      -label   => 1,
+		      );
+    $panel->add_track($dat{$chrom},
+		      -glyph => 'transcript',
+		      -label => 0,
+		      -bump  => 0,
+		      -bgcolor => 'blue',
+		      -fgcolor => 'blue',
+		      -height => 5,
+#		      -description => \&desc,
+		      -font2color => 'red');    
+    open(my $ofh => ">$ofname") || die $!;
+    binmode($fh);
+    print $ofh $panel->png;
+}
+
+sub desc {
+    my $ft = shift;
+    my ($n) = $ft->get_tag_values('Note');
+    $n;
+}