# CodonToAmino.pm                                           26apr16waw

package CodonToAmino;

use warnings
    FATAL => 'all'
    ;
use strict;


use parent 'Exporter';
our $VERSION = '0.1.0';

our @EXPORT    = qw();
our @EXPORT_OK = qw(
    XLATE_TABLE  BASES
    canonicalize  invalid_translation_table
    );


use constant BASES => 'ATCG';

# associate all possible base triplets (64) to aminos
use constant XLATE_TABLE => qw(
    GCA A    CAC H    CCA P    ACA T
    GCC A    CAT H    CCC P    ACC T
    GCG A             CCG P    ACG T
    GCT A    ATA I    CCT P    ACT T
             ATC I
    TGC C    ATT I    CAA Q    GTA V
    TGT C             CAG Q    GTC V
             AAA K             GTG V
    GAC D    AAG K    AGA R    GTT V
    GAT D             AGG R
             CTA L    CGA R    TGG W
    GAA E    CTC L    CGC R
    GAG E    CTG L    CGG R    TAC Y
             CTT L    CGT R    TAT Y
    TTC F    TTA L
    TTT F    TTG L    AGC S    TAA _
                      AGT S    TAG _
    GGA G    ATG M    TCA S    TGA _
    GGC G             TCC S
    GGG G    AAC N    TCG S
    GGT G    AAT N    TCT S
    );

my $invalid = invalid_translation_table(XLATE_TABLE);
die "invalid translation table: '$invalid'" if $invalid;


# exported subroutines #############################################

sub canonicalize { return uc $_[0]; }


sub invalid_translation_table {

    my (%xlate,  # translation hash table
        ) = @_;

    my $bases = canonicalize(BASES);
    my $codon = qr{ \A [\Q$bases\E]{3} \z }xms;

    # each key should be a codon.
    for my $k (keys %xlate) {
        return qq{'$k' is not proper codon} if $k !~ $codon;
        }

    # 64 unique groups of 3-character codons: all permutations.
    my $n_keys = keys %xlate;
    return qq{$n_keys, not 64, permutations of codons in table}
        if $n_keys != 64;

    # return aok.
    return '';  # no report of invalidity

    }  # end sub invalid_translation_table()


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