What about this?
use Modern::Perl;
use Data::Dump qw /dump/;

my @results;

while (<DATA>) {
    my @codon = split '', (split /\s+/)[1];
    while (my ($seq, $char) = each @codon) {
        $results[$seq]{$char}++;
    }
}
say dump(@results);

__DATA__
first  ACGATT--GAT
second AGTTAAC-TTT
third  TTAGCAGG-TA

[download]
Output:
(
  { A => 2, T => 1 },
  { C => 1, G => 1, T => 1 },
  { A => 1, G => 1, T => 1 },
  { A => 1, G => 1, T => 1 },
  { A => 1, C => 1, T => 1 },
  { A => 2, T => 1 },
  { "-" => 1, "C" => 1, "G" => 1 },
  { "-" => 2, "G" => 1 },
  { "-" => 1, "G" => 1, "T" => 1 },
  { A => 1, T => 2 },
  { A => 1, T => 2 },
)

[download]
Alternatively you can write the while loop more compact (but less easy to read)
while (<DATA>) {
    my $seq;
    $results[$seq++]{$_}++ for split '', (split /\s+/)[1];
}

[download]

CountZero

A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James

My blog: Imperial Deltronics

In reply to Re: What is wrong in this code??? by CountZero
in thread What is wrong in this code??? by Anonymous Monk

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