X BOL wishing you a very and Happy New year

Alternative content

Our Sponsors



Download BioinformaticsOnline(BOL) Apps in your chrome browser.




Raku script to find overlaps between two bed files !

  • Public
By LEGE 329 days ago
#!/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.";