dipeptide

use strict;
use warnings;
use Bio::SeqIO;

my @amino=qw/A C D E F G H I K L M N P Q R S T U V W X Y/;
my @comb=();
foreach my $a (@amino){
    foreach my $b (@amino){
        push (@comb,$a.$b)
    }
}
my $in  = Bio::SeqIO->new(-file => "myfile.fasta" , '-format' => 'Fasta');
while ( my $seq= $in->next_seq ) {
my @dipeps=($seq->seq()=~/(?=(.{2}))/g);
my %di_count=();
$di_count{$_}++ for @dipeps;
print ">",$seq->id();
map{exists $di_count{$_}?print " ",$_,",",$di_count{$_}:print " ",$_,",",0}sort @comb;
print "\n";

}