DotPlot with Perl
By Abhimanyu Singh 2676 days ago
#!/usr/bin/perl
use strict;use warnings;
my $i;my $j;my $a;
open (FH1,'<', "s.fa");
open (FH2,'<', "s.fa");
my $seq1 = do { local $/; <FH1> };
my $seq2 = do { local $/; <FH2> };
my @s1=split('',$seq1);
my @s2=split('',$seq2);
my @matrix=();
for($i=0;$i<scalar(@s2);$i++)
{
for($j=0;$j<scalar(@s1);$j++)
{
if($s2[$i] eq $s1[$j])
{
$matrix[$i][$j]=".";
}
else
{
$matrix[$i][$j]=" ";
}
}
}
#Printing matrix of dot plot
open (FHOUT,">dotplot.txt") or die "cannot open outfile\n";
for($a=0;$a<scalar(@s1);$a++)
{
print FHOUT "$s1[$a]";
}
print FHOUT "\n";
#print"\n\n";
for($i=0;$i<scalar(@s2);$i++)
{
print FHOUT "$s2[$i]";
for($j=0;$j<scalar(@s1);$j++)
{
print FHOUT "$matrix[$i][$j]";
}
print FHOUT "\n";
#print"\n\n";
}
close FH1;
close FH2;
close FHOUT;
