Raku script to find overlaps between two bed files !

LEGE — Thu, 01 Feb 2024 02:02:46 -0600

#!/usr/bin/env raku

# Check if the correct number of arguments are provided
if @*ARGS.elems != 2 {
    say "Usage: ./compare_bed_files.raku file1.bed file2.bed";
    exit 1;
}

# Read the contents of the two BED files
my @bed1 = slurp(@*ARGS[0]).lines;
my @bed2 = slurp(@*ARGS[1]).lines;

# Iterate over each interval in the first BED file
for my $line1 (@bed1) {
    my @fields1 = $line1.split("\t");
    my $chr1 = @fields1[0];
    my $start1 = @fields1[1];
    my $end1 = @fields1[2];

    # Check for overlaps with intervals in the second BED file
    for my $line2 (@bed2) {
        my @fields2 = $line2.split("\t");
        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 {
            say "Overlap found:";
            say "File 1: $line1";
            say "File 2: $line2";
            say "";
        }
    }
}

say "Comparison completed.";

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

Raku script to find overlaps between two bed files !