Re: [MLUG] String manipulation in C

[Mike Miller <EMAIL:PROTECTED>]

On Sun, 1 Jul 2007, Jack Smith wrote:

> Yes, it sure is. The gene sequence files are in FASTA format, which has 
> some MATLAB import scripts that go with it. (FASTA is still plaintext 
> and the files are easily grepped and read into other programs) I would 
> have stuck with MATLAB as it was pretty quick and easy to get running 
> and it works but it runs far too slow and uses too much RAM to be very 
> useful. That is why I was going to try to perform the operations using 
> something else other than MATLAB if at all possible. But my knowledge of 
> the different languages and utilities is not complete and such I ran 
> into a little stumbling block and had to ask for help.

If you are doing things in MATLAB, I recommend checking out Octave and the 
Octave Help list.  Those guys are really good at coming up with efficient 
ways of doing things in that kind of environment.


> So I suppose using Perl would be what I want to do to get my output? I 
> can try to hack my way though some Perl if need be. I just need to get 
> my output and get it done in a reasonable amount of time and with a 
> reasonable amount of RAM- something less than weeks and something less 
> than four gigs. HDD space is no problem as this machine has a 
> half-terabyte RAID 5 in it.

Perl is fantastic for this kind of thing.  I'm sure there are scripts 
already available.  Also, it wouldn't be hard to figure out how to do what 
you need.

Mike

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