perl/etc/WoodyMiaoLin/Tiger/draw_linkagemap.pl

   1 #!/usr/bin/perl
   2 use strict;
   3 use warnings;
   4
   5 open I75, "<", "scaffold188SNP.16.gt";
   6 open O, ">", "scaffold188_linkage_map.svg";
   7
   8 my @ra75;
   9 while (<I75>) {
  10   chomp;
  11   my @a = split /\t/;
  12   my @b;
  13   $b[0] = $a[0];
  14   $b[1] = $a[1];
  15   foreach (4..12) {
  16     my ($a1, $a2) = split /\//, $a[$_];
  17     if (($a1 eq "N") and ($a2 eq "A")) {
  18       push @b, "none";
  19     } elsif (($a1 eq "0") and ($a2 eq "0")) {
  20       push @b, $a[2];
  21     } elsif (($a1 eq "1") and ($a2 eq "1")) {
  22       push @b, $a[3];
  23     } else {
  24       push @b, "$a[2]$a[3]";
  25     }
  26   }
  27   my $b0 = 0;
  28   my $b1 = 0;
  29   foreach (13..19) {
  30     my ($a1, $a2) = split /\//, $a[$_];
  31     if (($a1 eq "N") and ($a2 eq "A")) {
  32       push @b, "none";
  33     } elsif (($a1 eq "0") and ($a2 eq "0")) {
  34       ++$b0;
  35       push @b, $a[2];
  36     } elsif (($a1 eq "1") and ($a2 eq "1")) {
  37       ++$b1;
  38       push @b, $a[3];
  39     } else {
  40       push @b, "$a[2]$a[3]";
  41     }
  42   }
  43   if ($b0 > $b1) {
  44     push @b, $a[2];
  45   } elsif ($b0 < $b1) {
  46     push @b, $a[3];
  47   } else {
  48     push @b, "equal"
  49   }
  50   push @ra75, \@b;
  51 }
  52 close I75;
  53
  54 print O "<?xml version=\"1.0\"?>\n\n<svg xmlns=\"http://www.w3.org/2000/svg\">\n\n";
  55
  56 my $yy;
  57 foreach my $a (@ra75) {
  58   ++$yy;
  59   my $y = 10*$yy;
  60   print O "<text x=\"0\" y=\"$y\" font-family=\"Courier\" font-size=\"8\" fill=\"black\">${$a}[0]</text>\n";
  61   print O "<text x=\"70\" y=\"$y\" font-family=\"Courier\" font-size=\"8\" fill=\"black\">${$a}[1]</text>\n";
  62   foreach (2..17) {
  63     my $xt = 30*$_ + 60;
  64     my $yt = 10*$yy;
  65     my $xr = 30*$_ + 50;
  66     my $yr = 10*$yy - 8;
  67     my $h = length ${$a}[$_];
  68     my $color;
  69     if ($h == 2) {
  70       $color = "green";
  71     } elsif ($h == 1) {
  72       if (${$a}[18] eq "equal") {
  73         $color = "pink";
  74       } elsif (${$a}[18] eq ${$a}[$_]) {
  75         $color = "yellow";
  76       } else {
  77         $color = "blue";
  78       }
  79     } else {
  80       $color = "white";
  81     }
  82     print O "<rect x=\"$xr\" y=\"$yr\" width=\"30\" height=\"10\" fill=\"$color\" stroke-width=\"0.5\" stroke=\"black\"/>\n";
  83     print O "<text x=\"$xt\" y=\"$yt\" font-family=\"Courier\" font-size=\"8\" fill=\"black\">${$a}[$_]</text>\n";
  84   }
  85 }
  86
  87 print O "\n</svg>\n";
  88 close O;