Consensus and Profile

Author: L. Grondin

Finding a Most Likely Common Ancestor

http://rosalind.info/problems/cons/

Sample input

ATCCAGCT
GGGCAACT
ATGGATCT
AAGCAACC
TTGGAACT
ATGCCATT
ATGGCACT

Sample output

ATGCAACT
A: 5 1 0 0 5 5 0 0
C: 0 0 1 4 2 0 6 1
G: 1 1 6 3 0 1 0 0
T: 1 5 0 0 0 1 1 6

Source code: cons-grondilu.pl

use v6;

my @default-data = qw{
    ATCCAGCT
    GGGCAACT
    ATGGATCT
    AAGCAACC
    TTGGAACT
    ATGCCATT
    ATGGCACT
};

my \N = @default-data.pick.chars;

my %profile;
%profile{$_} = [0 xx N] for <A C G T>;

for @default-data[] {
    my @dna = .comb;
    my %dna-index-map = classify { @dna[$_] }, ^@dna;
    for %dna-index-map.kv -> $k, $v {
        %profile{$k}[$v[]]»++;
    }
}
my @profile = %profile<A C G T>;

say my $consensus = [~] gather
for ^N -> \c {
    my $max = max map { @profile[$_][c] }, ^4;
    take <A C G T>[$_] given first { @profile[$_][c] == $max }, ^4;
}

say [~] .key, ': ', @profile[.value] for enum <A C G T>.sort;