[Bioperl-l] help for parsing MAST output

Stefan Kirov skirov at utk.edu
Fri Feb 11 16:30:05 EST 2005


I am confused. Are you trying to parse MAST or MEME output?
Something like this should work for you:

use Bio::Matrix::PSM::IO;

 my $psmIO= new Bio::Matrix::PSM::IO(-file=>$file, -format=>'meme');
 while (my $psm=$psmIO->next_psm) {
 my $instances=$psm->instances;
 foreach my $instance (@{$instances}) {
   print $instance->primary_id," is found at position 

Sameet wrote:

>Dear all,
>let me thank you in advance for such a nice discussion group.  Though i have 
>not posted anything to the group, the discussions have been very helpful to 
>me.  I need some help with the parsing of MAST output, because i want to find 
>the start site of the match for certain motifs that i produced earlier using 
>MEME.  Is there a way to do it.  I read the documentation at 
>http://search.cpan.org/~birney/bioperl-1.4/Bio/Matrix/PSM/IO.pm, however it 
>was a bit confusing, because i havent used perl in a long time.

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