Bio::Matrix::PSM Psm
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Summary
Bio::Matrix::PSM::Psm - handle combination of site matricies
Package variables
No package variables defined.
Included modules
Bio::Matrix::PSM::InstanceSite
strict
Inherit
Bio::Annotation::Collection Bio::Matrix::PSM::PsmI Bio::Matrix::PSM::SiteMatrix
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. 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.
Methods
newDescriptionCode
instancesDescriptionCode
headerDescriptionCode
matrixDescriptionCode
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)
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...)
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
Methods code
newdescriptionprevnextTop
sub new {
    my ($caller,@args) = @_;
    my $class = ref($caller) || $caller;
    my $self = $class->SUPER::new(@args);
    $self->{'_annotation'} = {};  #Init from Annotation::Collection
$self->_typemap(Bio::Annotation::TypeManager->new()); #same
($self->{instances})=$self->_rearrange(['INSTANCES'], @args); return $self;
}
instancesdescriptionprevnextTop
sub instances {
    my $self = shift;
    my $prev = $self->{instances};
    if (@_) { $self->{instances} = shift; }
    return $prev;
}
headerdescriptionprevnextTop
sub header {
    my $self = shift;
    return  if ($self->{end});
    my %header;
    if (@_) {my $key=shift; return $self->{$key}; }
    foreach my $key (@Bio::Matrix::PSM::Psm::HEADER) {
	$header{$key}=$self->{$key};
    }
    return %header;
}
matrixdescriptionprevnextTop
sub matrix {
    my $self = shift;
    my $prev = Bio::Matrix::PSM::SiteMatrix->new(-pA=>$self->{probA}, 
						-pC=>$self->{probC},
						-pG=>$self->{probG},
						-pT=>$self->{probT},
						-lA=>$self->{logA},
						-lC=>$self->{logC},
						-lG=>$self->{logG},
						-lT=>$self->{logT},
						-IC=>$self->{IC},
						-e_val=>$self->{e_val},
						-id=>$self->{id});
    if (@_) {
	my $matrix=shift;
	$self->{IC} = $matrix->IC;
	$self->{probA}=$matrix->{probA};
	$self->{probC}=$matrix->{probC};
	$self->{probG}=$matrix->{probG};
	$self->{probT}=$matrix->{probT};
	$self->{e_val}=$matrix->e_val;
	$self->{id}=$matrix->id;
    }
    return $prev;
}
 
1;
}
General documentation
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.
SEE ALSOTop
SiteMatrix, meme, transfac, InstanceSite
APPENDIXTop