[Bioperl-l] Getting started with Bio::Perl

[Catherine Letondal]

On Jan 13, 2005, at 6:24 PM, Kat Hull wrote:

> *Dear Users,
> I have a newbie question!  I am interested in the following module 
> 'Bio::Tools::Run::PiseApplication::codonw' but really don't
> know how to start to use it.  I have looked at the documentation etc 
> but am confused about how to pass my array of sequences to
> the module and then how to call the individual functions to perform 
> the calculations (e.g. gc, cai, fop...).
>
> Does anyone have a simple script showing how to run this module with 
> the input as an array of fasta format sequences?
> Many thanks,
>
> Kat
> *

Hi again,

As Jason already answered, first look at 
Bio::Tools::Run::PiseApplication where there is an example of use. You 
can also look at the examples/pise directory.
Regarding the parameters of a specific program (codonw), I suggest to 
first look at the interactive service 
(http://bioweb.pasteur.fr/seqanal/interfaces/codonw.html), for it's 
exactly the same that the one that is run through bioperl). You will 
get a better understanding of the available values and the output files 
of interest (which differ from on program to another).

--
Catherine Letondal -- Institut Pasteur