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Perl script to find overlaps between two bed files !
By LEGE 296 days ago
#!/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";
