[Bioperl-l] Re: Bioperl MEME parsing information

[Sumit Middha]

Hello,
I am sorry for the direct email. But thanks for your response.
Sumit


Quoting Stefan Kirov <skirov at utk.edu>:

> 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
> 
> 
>