http://benchmarksgame.alioth.debian.org/u32/performance.php?test=knucleotide

Based on the submission for Perl 5.

USAGE: perl6 k-nucleotide.p6 k-nucleotide.input

Expected output

A 30.298
    T 30.157
    C 19.793
    G 19.752

AA 9.177
    TA 9.137
    AT 9.136
    TT 9.094
    AC 6.000
    CA 5.999
    GA 5.986
    AG 5.985
    TC 5.970
    CT 5.970
    GT 5.957
    TG 5.956
    CC 3.915
    CG 3.910
    GC 3.908
    GG 3.902

14717GGT
    4463GGTA
    472GGTATT
    902GGTATTTTAATT
    902GGTATTTTAATTGGTATTTTAATTTATAGT

use v6;



sub MAIN($input-file = $*SPEC.catdir($*PROGRAM-NAME.IO.dirname, "k-nucleotide.input")) {
    my $fh = open $input-file.IO;

    # Read FASTA file and extract DNA sequence THREE.
    my $sequence = '';
    my $lines;

    while $fh.get -> $line {
        last if ($line.substr(0,6) eq '>THREE');
    }
    while $fh.get -> $line {
        last if ($line.substr(0,1) eq '>');
        $sequence = $sequence ~ lc $line.subst(/\n/,'');
    }

    # Count nucleotide sequences
    my $len = $sequence.chars;
    my (@keys,%table,$sum,$frame_size);
    for 1..2 -> $frame_size {
        %table = ();
        update_hash($frame_size);

        # Print.
        $sum = $len - $frame_size + 1;
        for %table.sort: {$^b.value <=> $^a.value||$^a.key leg $^b.key} {
            printf "%s %.3f\n", .key, .value*100/$sum;
        }
        print "\n";
    }

    for <ggt ggta ggtatt ggtattttaatt ggtattttaatttatagt> -> $seq {
        %table = ();
        update_hash($seq.chars);
        printf "%3d    $seq\n", (%table{$seq} || 0);
    }

    # Procedure to update a hashtable of k-nucleotide keys and count values
    # for a particular reading-frame.
    sub update_hash($frame_size) {
        for 0..($len - $frame_size) -> $i {
            %table{$sequence.substr($i,$frame_size)}++;
        }
    }
}

# vim: expandtab shiftwidth=4 ft=perl6