|Bill Allombert on Tue, 24 Feb 2004 20:47:45 +0100|
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|Re: Pattern Match within PARI/GP|
On Tue, Feb 24, 2004 at 10:55:29AM -0800, Paulo Ney de Souza wrote: > > There is a subtle difference between the two problems, you see the > Human Genome data is static, generated by some sequencing machines, > it stays put, and written to a disk after it is found. You can then > go there with any tools and try to find patterns, etc ... Our example > problem here is "dynamic" in the sense that I want to generate the > first 1 million digits and depending on the sequences found, go look > a bit further in the "second" million digit set, etc ... Well, computing 1 million digits of Pi with PARI is likely to take several minutes on a fast box. > That going in between PARI and Perl and then back to PARI is exactly > what is breaking my neck in terms of speed... and my reason to try > to do this inside PARI. Then you should probably try Math::PARI which is a PARI interface for perl. This way you can do everything inside of perl. Another alternative is to write your custom C plug-in to PARI and install() them under GP, so you can call your new functions inside of GP. such custom C plug-in could use a regexp library like libpcre to make the test. It is easy to implement. Cheers, Bill.