examples/quality/svgtrace.pl

   1 #! /usr/bin/perl
   2
   3 use warnings;
   4 use strict;
   5 use Bio::SeqIO;
   6 use SVG;
   7
   8 my $USAGE = <<END_USAGE;
   9 $0 <file>
  10
  11 This simple example script reads the ABI data and uses the trace data to
  12 generate a SVG-formatted chromatogram. Requires the CPAN SVG module and
  13 Bio::SeqIO::staden::read (from bioperl-ext), which itself requires io_lib from
  14 the Staden package.
  15
  16 END_USAGE
  17
  18 my $file = shift || die $USAGE;
  19
  20 my $img_width = 6000;
  21 my $img_height = 200;
  22
  23 my $svg = SVG->new(width => $img_width, height => $img_height, xmlns => "http://www.w3.org/2000/svg");
  24
  25 my $seq_io = Bio::SeqIO->new( -file => $file, -format => 'abi', -get_trace_data => 1);
  26
  27 my $seq = $seq_io->next_seq;
  28
  29 my $points = scalar($seq->get_trace_graph( -trace => 'a' ));
  30
  31 my @xdata = map { $_ / $points * $img_width } (0..$points-1);
  32
  33 my %colours = ( 'a' => 'green', 'c' => 'blue', 'g' => 'black', 't' => 'red' );
  34 foreach my $element ('a', 'c', 'g', 't')
  35 {
  36         my @trace = $seq->get_trace_graph( -trace => $element, -scale => $img_height);
  37         @trace = map { $img_height - $_ } @trace;
  38         my $points = $svg->get_path(-type => 'polyline', -closed => 0, x => \@xdata, y => \@trace);
  39         $svg->polyline(%$points, id=> $element, 'stroke-width' => 0.5, stroke => $colours{$element}, 'fill-opacity' => 0, 'fill' => 'white');
  40 }
  41
  42 my $count = 0;
  43 my $text_group = $svg->group( id => 'text_layer');
  44 foreach my $base_loc (@{$seq->trace})
  45 {
  46         $text_group->text(x => ($base_loc / $points * $img_width), y => 50, 'text-anchor' => 'middle', fill => 'black', 'font-size' => '5pt')->cdata(substr($seq->seq,$count,1));
  47         ++$count;
  48 }
  49
  50 print $svg->xmlify();