[BioPython] LCC function coded.

[Iddo Friedberg]

That's great!

I am currently working hard (sampling the beer) at Monterey, CA in CASP5.
So I will get around to it only on next week. 

Best,

Iddo

--
Iddo Friedberg
The Burnham Institute
10901 North Torrey Pines Road
La Jolla, CA 92037
USA

Tel: +1 (858) 646 3100  x3516
Fax: +1 (858) 646 3171

On Mon, 2 Dec 2002, Sebastian Bassi wrote:

> Hi Iddo,
> 
> I've just coded 2 functions to calculate LCC.
> lcc_mult and lcc_simp. Both calculates LCC (Local composition content),
> lcc_mult is optimized for speed in several runs. It returns a list of
> LCC values.
> lcc_simp is for 1 LCC value (you can get more calling the function using
> a for loop). If you need more LCC values than the size of the LCC
> window, is recomended lcc_mult.
> lcc_mult calculates in forehand all logs to save time. It also calculate
> the "next" window lcc by comparing the next nucleotide on the window
> (head) and the nucleotide that leaves the window (tail), if they are the
> same, the LCC is the same so it is not calculated.
> 
> lcc_mult(seq,wsize,start,end):
> seq: String of the sequence.
> wsize: Windows size
> start: Where to start "walking".
> end: Where to end "walking"
> it returns a list, all elements float values.
> 
> lcc_simp(seq,start,end):
> seq: String of the sequence.
> start: Where to start calculating LCC.
> end: Where to end calculating LCC.
> it returns one float value.
> 
> I did an informal benchmark and, for a large list of LCC values, 
> lcc_simp took 54 secs. and lcc_mult took just 12.
> 
> I don't know how to make a module, so I give the code here for you to
> adapt it according the BioPython standarts. I hopw it make it to the
> BioPython.
> 
> -- 
> Best regards,
> 
> //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ   //=\
> \=// IT Manager Advanta Seeds - Balcarce Research Center -      \=//
> //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\
> \=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 -     \=//
> 
>                 Linux para todos: http://Linuxfacil.info
> 
>