[Bioperl-l] Re: Bioperl MEME parsing information

[Stefan Kirov]

Sumit,
First ALWAYS send your questions to bioperl list, not to me directly.
What you need is in the docs for:

Bio::Matrix::PSM::InstanceSite
Bio::Matrix::PSM::SiteMatrix
Bio::Matrix::PSM::PsmI

so do

perldoc Bio::Matrix::PSM::InstanceSite

or look at the web description at 
http://doc.bioperl.org/releases/bioperl-1.4/

Sumit Middha wrote:

>Hi,
>I would like to know the source for all possible methods related with parsing of
>a MEME output. For instance 
>
>my $psmIO =  new Bio::Matrix::PSM::IO(-format=>'meme', 
>				      -file=>$file);
>    while (my $psm = $psmIO -> next_psm) {
>        my $instances = $psm -> instances;
>        my $pid = $psm -> id;
>        my $c = $psm -> IUPAC;
>........
>
>
>So what all options do I have, for instance retrieving the 'Motifs in block
>format' sequences, etc.
>  
>
You need to look at Bio::Matrix::PSM::InstanceSite and work with the 
$instances.

>Thanks,
>Sumit
>  
>
Stefan