I have a subroutine for a basic one frame translation that is giving me an error for "Use of uninitialized value $codon in hash element" and "substr outside of string". I think my problem is I need to modify the subroutine's for loop to account for nucleotide sequences with odd numbers of acids (i.e. not in multiples of 3).

Does anyone have suggestions for how to modify the code properly?

Here is the subroutine I'm using in a simple example:

use strict;
use warnings; 

my $amino_acid='';
my $s1 = 'ATGCCCGTAC';     ## Sequence 1
my $s2 = 'GCTTCCCAGCGC';   ## Sequence 2

print "Sequence 1 Translation:";
OneFrameTranslation ($s1);        ## Calls subroutine
print "$amino_acid\n";

print "Sequence 2 Translation:";
OneFrameTranslation ($s2);       ## Calls subroutine
print "$amino_acid\n";

### Subroutine ###

sub OneFrameTranslation {
    my ($seq) = shift;
    my $amino_acid='';
    my $seqarray='';
    
my %genetic_code = (
     'TTT' => 'F', 'TTC' => 'F', 'TTA' => 'L', 'TTG' => 'L',
     'CTT' => 'L', 'CTC' => 'L', 'CTA' => 'L', 'CTG' => 'L', 
     'ATT' => 'I', 'ATC' => 'I', 'ATA' => 'I', 'ATG' => 'M',
     'GTT' => 'V', 'GTC' => 'V', 'GTA' => 'V', 'GTG' => 'V',
     'TCT' => 'S', 'TCC' => 'S', 'TCA' => 'S', 'TCG' => 'S',
     'CCT' => 'P', 'CCC' => 'P', 'CCA' => 'P', 'CCG' => 'P',
     'ACT' => 'T', 'ACC' => 'T', 'ACA' => 'T', 'ACG' => 'T',
     'GCT' => 'A', 'GCC' => 'A', 'GCA' => 'A', 'GCG' => 'A',
     'TAT' => 'Y', 'TAC' => 'Y', 'TAA' => '*', 'TAG' => '*',
     'CAT' => 'H', 'CAC' => 'H', 'CAA' => 'Q', 'CAG' => 'Q',
     'AAT' => 'N', 'AAC' => 'N', 'AAA' => 'K', 'AAG' => 'K',
     'GAT' => 'D', 'GAC' => 'D', 'GAA' => 'E', 'GAG' => 'E',
     'TGT' => 'C', 'TGC' => 'C', 'TGA' => '*', 'TGG' => 'W',
     'CGT' => 'R', 'CGC' => 'R', 'CGA' => 'R', 'CGG' => 'R',
     'AGT' => 'S', 'AGC' => 'S', 'AGA' => 'R', 'AGG' => 'R',
     'GGT' => 'G', 'GGC' => 'G', 'GGA' => 'G', 'GGG' => 'G' 
    );
    
         ## '---' = 3 character codon in hash above
         ## '-' = one letter amino acid abbreviation in hash above

    my @seqarray = split(//,$seq);   ## Explodes the string

    for (my $i=0; $i<=$#seqarray-2; $i=$i+3) {
        my $codon = substr($seqarray,$i,3);
        $amino_acid = $genetic_code{$codon};
    }
    return ($amino_acid);
}
[download]