[Bioperl-l] Re: Bio::Matrix::PSM::PsmHeader

[Stefan Kirov]

First, you need to send e-mails not to my personal one, but to the 
bioperl list.
You need to look at Bio::Matrix::PSM::IO, Bio::Matrix::PSM::Psm and 
Bio::Matrix::PSM::Bio::Matrix::PSM::InstanceSite objects. First one 
parses the data in your mast report and the next_psm method returns Psm 
object which contains section III as well as some other information. 
Then you get the InstanceSite objects:
my $psmio=new Bio::Matrix::PSM::IO(-format=>'mast', -file=>$file);
while (my $psm=$psmio->next_psm) {
    my %instances=$psm->instances; #Indexed by the sequence identifier
    foreach my $hit (@instances) {
      print $hit->start; #Do something with the object- get the sequence 
id, score, start, end, etc.
    }
}
 C'est tout.
Hope this helps, let me know if you have further questions. Also you may 
want to upgrade to bioperl-live if you are using bioperl-1.4
Stefan

simon118 at etumail.uhp-nancy.fr wrote:

>Hi,
>
>I worke with MAST, and I need a parser to analyse my results, with a perl
>program.
>Before to use Bio::Matrix::PSM::PsmHeader, I want to be sure of results.
>
>From mast_result.txt, I need to extract each motif and for each, its position on
>the input sequence, its score (p-value) and its strand.
>To resume, I want the section III on a table.
>
>Is it possible with your parser?
>
>
>Thanks
>
>  
>