Your original string contains 9 characters. The form you are compressing to packs 4 characters to a byte, but with no way of knowing how many characters in the last byte are significant.
Update: FWIW you can speed this up considerably by banging 4 characters at a time -- code enclosed, below. However, in my experience a little bit of C will do a lot better -- particularly when reading big chunks of file and getting the C to process many strings at a time.
# ACGT String compression and decompression
#
# We compress to fixed length string, 2 bits per symbol -- zero fill i
+n last byte.
my %compress ; # string of up to 4 characters to compressed item
my @expand ; # compressed value to string
BEGIN {
my @ACGT = qw(A C G T) ;
my $s = '' ;
my $v = 0 ;
foreach my $a (@ACGT) {
$s = $a ; $compress{$s."\n"} = $compress{$s} = chr($v) ;
foreach my $b (@ACGT) {
$s = $a.$b ; $compress{$s."\n"} = $compress{$s} = chr($v) ;
foreach my $c (@ACGT) {
$s = $a.$b.$c ; $compress{$s."\n"} = $compress{$s} = chr($v) ;
foreach my $d (@ACGT) {
$s = $a.$b.$c.$d ;
$compress{$s} = chr($v) ;
$expand[$v++] = $s ;
} ;
} ;
} ;
} ;
$compress{"\n"} = '' ;
$compress{''} = '' ;
} ;
# Compress ACGT string (all upper case) with or without trailing "\n"
#
# $compressed = acgt_compress(ACGT_STRING)
sub acgt_compress {
my $c = '' ;
$c .= $compress{$_} for unpack('(a4)*', $_[0]) ;
return $c ;
} ;
# Decompress compressed ACGT, and cut to required length
#
# $acgt_string = acgt_expand(COMPRESSED, LENGTH)
sub acgt_expand {
my $e = '' ;
$e .= $expand[$_] for unpack('C*', $_[0]) ;
return substr($e, 0, $_[1]) ;
} ;
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