Bio::Matrix::PSM::Psm.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Matrix::PSM::Psm - handle combination of site matricies

SYNOPSIS

   use Bio::Matrix::PSM::IO;
 
   #To get a Psm object from a file use the Psm parser:
   my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'meme', -file=>$file);
 
   # Now go through all entities in the file with next_psm, which
   # returns a Psm object see Bio::Matrix::PSM::IO for detailed
   # documentation (matrix predictions or matrix sequence matches or
   # both):
 
   while (my $psm=$psmIO->next_psm) {
     my %psm_header=$psm->header;
     my $ic=$psm_header{IC};
     my $sites=$psm_header{sites};
     my $width=$psm_header{width};
     my $score=$psm_header{e_val};
     my $IUPAC=$psm->IUPAC;
     my $instances=$psm->instances;
     foreach my $instance (@{$instances}) {
       my $id=$instance->primary_id;
       #Do something with the id
     }
   }
 
  #or create from memmory:
   my $psm= Bio::Matrix::PSM::Psm->new( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,-pT=>\@pT,
        -id=>$id,
        -instances=>$instances, -e_val=>$e_val,
        -IC=>$ic, -width=>$width, -sites=>$sites)
 
   # where pA through pG are the respective frequencies of the matrix (see also
   # Bio::Matrix::PSM::SiteMatrix), and everything else is self-explenatory, 
   # except for -instances (reference to an array of 
   #  Bio::Matrix::PSM::InstanceSite objects) which is documented bellow.
 
 

DESCRIPTION

To handle a combination of site matrices and/or their corresponding sequence matches (instances). This object inherits from Bio::Matrix::PSM::SiteMatrix, so you can use the respective methods. It may hold also an array of Bio::Matrix::PSM::InstanceSite object, but you will have to retrieve these through Bio::Matrix::PSM::Psm->instances method (see below). To some extent this is an expanded SiteMatrix object, holding data from analysis that also deal with sequence matches of a particular matrix.

DESIGN ISSUES

This does not make too much sense to me I am mixing PSM with PSM sequence matches Though they are very closely related, I am not satisfied by the way this is implemented here. Heikki suggested different objects when one has something like meme But does this mean we have to write a different objects for mast, meme, transfac, theiresias, etc.? To me the best way is to return SiteMatrix object + arrray of InstanceSite objects and then mast will return undef for SiteMatrix and transfac will return undef for InstanceSite. Probably I cannot see some other design issues that might arise from such approach, but it seems more straightforward. Hilmar does not like this beacause it is an exception from the general BioPerl rules Should I leave this as an option? Also the header rightfully belongs the driver object, and could be retrieved as hashes. I do not think it can be done any other way, unless we want to create even one more object with very unclear content.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably
 to one of the Bioperl mailing lists. Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Stefan Kirov

Email skirov@utk.edu

DISCLAIMER

This software is provided ``as is'' without warranty of any kind.

SEE ALSO

SiteMatrix, meme, transfac, InstanceSite

APPENDIX

new

  Title   : new
  Usage   : my $psm= Bio::Matrix::PSM::Psm->new( -pA=>\@pA,-pC=>\@pC,
                                                -pG=>\@pG,-pT=>\@pT,-id=>$id,
                                                -instances=>$instances, 
                                                -e_val=>$e_val,
                                                -IC=>$ic, -width=>$width, 
                                                -sites=>$sites)
  Function: Creates a new Bio::Matrix::PSM::Psm object
  Throws  :
  Example :
  Returns :  Bio::Matrix::PSM::Psm object
  Args    :  hash
 
 

instances

  Title   : instances
  Usage   :   my @instances=@{$psm->instances};
  Function: Gets/sets the instances (Bio::Matrix::PSM::InstanceSite objects)
             associated with the Psm object
  Throws  :
  Example :
  Returns :  array reference (Bio::Matrix::PSM::InstanceSite objects)
  Args    :  array reference (Bio::Matrix::PSM::InstanceSite objects)
 
 

header

  Title   : header
  Usage   :  my %header=$psm->header;
             my $ic=$psm->header('IC');
  Function: Gets the general information, common for most files,
            dealing with PSM such as information content (IC), score
            (e-value, etc.), number of sites (sites) and width. This
            list may expand. The current list should be in
            @Bio::Matrix::PSM::Psm::HEADER. Returns undef if an
            argument is supplied that is not in
            @Bio::Matrix::PSM::meme::HEADER.
  Throws  :
  Example :
  Returns :  hash or string
  Args    :  string (IC, e_val...)
 
 

matrix

  Title   :  matrix
  Usage   :  my $matrix=$psm->matrix;
  Function:  Gets/sets the SiteMatrix related information
  Throws  :
  Example :
  Returns :  Bio::Matrix::PSM::SiteMatrix objects
  Args    :  Bio::Matrix::PSM::SiteMatrix objects