Algorithm to do numeric profile of the string - algorithm

Question

I have few file similar to below, and I am trying to do numeric profiling as mentioned in the image
>File Sample
attttttttttttttacgatgccgggggatgcggggaaatttccctctctctctcttcttctcgcgcgcg
aaaaaaaaaaaaaaagcgcggcggcgcggasasasasasasaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
I have to map each substring of size 2 and then map it to 33 value for different ptoperties and then add as per the window size of 5.
my %temp = (
aCount => {
aa =>2
}
cCount => {
aa => 0
}
);
My current implementation include as per below ,
while (<FILE>) {
my $line = $_;
chomp $line;
while ($line=~/(.{2})/og) {
$subStr = $1;
if (exists $temp{aCount}{$subStr}) {
push #{$temp{aCount_array}},$temp{aCount}{$subStr};
if (scalar(#{$temp{aCount_array}}) == $WINDOW_SIZE) {
my $sum = eval (join('+',#{$temp{aCount_array}}));
shift #{$temp{aCount_array}};
#Similar approach has been taken to other 33 rules
}
}
if (exists $temp{cCount}{$subStr}) {
#similar approach
}
$line =~s/.{1}//og;
}
}
is there any other approach to increase the speed of the overall process

Answer 1

Regular expressions are awesome, but they can be overkill when all you need are fixed width substrings. Alternatives are substr
$len = length($line);
for ($i=0; $i<$len; $i+=2) {
$subStr = substr($line,$i,2);
...
}
or unpack
foreach $subStr (unpack "(A2)*", $line) {
...
}
I don't know how much faster either of these will be than regular expressions, but I know how I would find out.