Re: s/// only replacing most of the time...

[Thelonius]

Can you give an example where it's not doing what you want? Specifically can you include info like this:

print STDERR "\$hystackPatt[$j] = $haystackPatt[$j]\n";
print STDERR "\$rxHaystack[$j] = $rxHaystack[$j]\n";
print STDERR "BEFORE: \$text_seqs[$i] = $text_seqs[$i]\n";
$text_seqs[$i] =~ s{$rxHaystack[$j]}{<span class=$class[$a]>$1</span>}
+gmx;
print STDERR "AFTER: \$text_seqs[$i] = $text_seqs[$i]\n";

I had to delete the "e" from the "gemx" on the end of your substitution.