The following provides a not-very-elegant but executable implementation of the hash-counting that others have been hinting at:

use strict;
use Data::Dumper;

my @simple_pairs = qw(ag at ta cg gc);

#'mirrored pairs' are pairs that will (eventually)
#increment a 'base pair' w/ the same index;
my @base_pairs = qw(ac tg tt cc ga);
my @mirrored_pairs = qw(gt ca aa gg tc);

my %counts;
#the three arrays will be 'flattened' in the for loop
$counts{$_} = 0
  for (@simple_pairs, @base_pairs, @mirrored_pairs);

while (<DATA>) {
  chomp;
  my $seq = $_;
  #use if-else to warn of unwanted/bad sequences
  if (exists $counts{$seq}) {
    $counts{$seq}++;
  } else {
    warn "Unknown pair: $_\n";
  }
}

print "Before consolidating mirrored pairs:\n";
print Dumper(%counts);

for (0..$#base_pairs) {
  $counts{$base_pairs[$_]} += $counts{$mirrored_pairs[$_]};
  delete $counts{$mirrored_pairs[$_]};
}

print "\nAfter consolidating mirrored pairs:\n";
print Dumper(%counts);

1;
__DATA__
ag
gc
qa
gt
ca
cg
gt
ca

[download]

This should be quite a bit peppier than the if-else blocks that you were using.

Hanlon's Razor - "Never attribute to malice that which can be adequately explained by stupidity"

In reply to Re: how can I speed up this perl?? by Art_XIV
in thread how can I speed up this perl?? by Anonymous Monk

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