Bio::Matrix::PSM PsmI
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Summary
Bio::Matrix::PSM::PsmI - abstract interface to handler of site matricies
Package variables
No package variables defined.
Included modules
Bio::Matrix::PSM::InstanceSite
Bio::Matrix::PSM::SiteMatrix
strict
Inherit
Bio::Matrix::PSM::SiteMatrixI
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
Supposed 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. This design is a bit of a compromise, so it might be a temporary
solution 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.
Methods
newDescriptionCode
instancesDescriptionCode
matrixDescriptionCode
headerDescriptionCode
Methods description
newcode    nextTop
 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=>$sites)
Function: Creates a new Bio::Matrix::PSM::Psm object
Throws :
Example :
Returns : Bio::Matrix::PSM::Psm object
Args : hash
instancescodeprevnextTop
 Title   : instances
Usage : my @instances=@{$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)
matrixcodeprevnextTop
 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
headercodeprevnextTop
 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...)
Methods code
newdescriptionprevnextTop
sub new {
     my $self = shift;
    $self->throw_not_implemented();
}
instancesdescriptionprevnextTop
sub instances {
    my $self = shift;
    $self->throw_not_implemented();
}
matrixdescriptionprevnextTop
sub matrix {
    my $self = shift;
    $self->throw_not_implemented();
}
headerdescriptionprevnextTop
sub header {
    my $self = shift;
    $self->throw_not_implemented();
 }

 
1;
}
General documentation
SEE ALSOTop
Bio::Matrix::PSM::SiteMatrix, Bio::Matrix::PSM::IO::meme,
Bio::Matrix::PSM::IO::transfac, Bio::Matrix::PSM::InstanceSite
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Stefan KirovTop
Email skirov@utk.edu
DISCLAIMERTop
This software is provided "as is" without warranty of any kind.
APPENDIXTop