Perl script to find overlaps between two bed files !

LEGE — Thu, 01 Feb 2024 02:04:04 -0600

#!/usr/bin/perl

use strict;
use warnings;

# Check if the correct number of arguments are provided
if (@ARGV != 2) {
    die "Usage: $0 file1.bed file2.bed\n";
}

# Read the contents of the two BED files
my $file1 = shift @ARGV;
my $file2 = shift @ARGV;

open my $fh1, '<', $file1 or die "Error opening $file1: $!";
open my $fh2, '<', $file2 or die "Error opening $file2: $!";

# Iterate over each interval in the first BED file
while (my $line1 = <$fh1>) {
    chomp $line1;
    my @fields1 = split /\t/, $line1;
    my $chr1 = $fields1[0];
    my $start1 = $fields1[1];
    my $end1 = $fields1[2];

    # Check for overlaps with intervals in the second BED file
    while (my $line2 = <$fh2>) {
        chomp $line2;
        my @fields2 = split /\t/, $line2;
        my $chr2 = $fields2[0];
        my $start2 = $fields2[1];
        my $end2 = $fields2[2];

        # Check for chromosome match and overlap
        if ($chr1 eq $chr2 && $start1 < $end2 && $end1 > $start2) {
            print "Overlap found:\n";
            print "File 1: $line1\n";
            print "File 2: $line2\n\n";
        }
    }

    # Rewind file2 to the beginning for the next iteration
    seek $fh2, 0, 0;
}

close $fh1;
close $fh2;

print "Comparison completed.\n";

BOL: Perl script to find overlaps between two bed files !

Perl script to find overlaps between two bed files !