Bad performance of simple regular expression - why??

[MarcL]

hi everyone, 

first of all i want to say that i'm not a professional programmer  - so the problem i have might be 
caused by my own  lack of experience. Nevertheless i want to describe it, hoping that someone in this 
group might be able to tell me what's wrong. I am a molecular biologist and i often have to deal with 
larger amounts of DNA and protein sequence data (which is in principle text). I am mainly using Perl to 
process these DNA files, and Perl generally performs very well (regular expressions are actually the killer 
tool for working with DNA sequences). Unfortunately not everything in Perl is a fast as the regular 
expressions and so i started trying to learn a language that can be compiled to produce fast 
executables : C++ - and went crazy because everything is so complicated. All the ugly details that Perl 
takes care of for the user have to be organized manually and that really gave me the creeps. Then i 
learned about D and it sounded like it the solution to my problem: A compilable language that supports 
associative arrays, garbage collection and (most importantly for me) regular expressions! Great! I 
experimented a bit and actually managed to write small working programlet directly. I was delighted! 
But now comes the reason why i write all this: Being enthusiastic about this new nice language i started 
to write a module that should implement basic functions for working with the most common DNA 
sequence file formats. To parse these files i planned to use regular expressions. So far so good. When 
testing my module with a small DNA file everything seemed OK -then i tried to use it to parse a more 
real world-sized DNA file (~155000 characters of DNA sequence plus about the same amount of textual 
information) and had to find out that a simple std.regexp.split call took about 59 seconds!!! I could not 
believe it and wrote a little Perl script doing the same thing and it took less than 1s!! What's wrong 
here??? This can't really be true, can it? Is the implementation of regular expressions in the phobos 
library so bad or preliminary that it is so much less performant than the Perl regex engine? It's actually 
not usable for me like this (which is a sad think because i really like the other features of D and would 
like to use it). Am i making mistakes or do i simply have to wait for a better version of phobos? 

Any comments or suggestions would be great. 

cheers