Bio::Matrix::PSM ProtPsm
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Summary
Bio::Matrix::PSM::ProtPsm - 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::ProtMatrix Bio::Matrix::PSM::PsmI
Synopsis
  use Bio::Matrix::PSM::IO;
#To get a ProtPsm object from a file use the Psm parser: my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'psiblast', -file=>$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 } }
Description
To handle a combination of site matrices and/or their corresponding sequence
matches (instances). This object inherits from Bio::Matrix::PSM::ProtMatrix, so
you can methods from that class. It may hold also an array of
Bio::Matrix::PSM::InstanceSite object, but you will have to retrieve these
through Bio::Matrix::PSM::ProtPsm->instances method (see below). To some
extent this is an expanded ProtMatrix 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::ProtPsm->new(
-pS => [ '0', '33', '0', '16', '1', '12', '11', '25' ],
-pF => [ '0', '0', '2', '0', '3', '0', '0', '0' ],
-pT => [ '0', '8', '7', '10', '1', '2', '7', '8' ],
-pN => [ '0', '0', '2', '13', '0', '36', '1', '4' ],
-pK => [ '0', '5', '0', '13', '1', '15', '0', '2' ],
-pY => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
-pE => [ '0', '41', '1', '12', '0', '0', '0', '15' ],
-pV => [ '0', '3', '9', '0', '2', '0', '3', '1' ],
-pQ => [ '0', '0', '0', '15', '0', '4', '0', '3' ],
-pM => [ '100', '0', '66', '0', '2', '0', '0', '0' ],
-pC => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
-pL => [ '0', '0', '8', '0', '25', '0', '4', '0' ],
-pA => [ '0', '10', '1', '9', '2', '0', '22', '16' ],
-pW => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
-pP => [ '0', '0', '0', '0', '3', '1', '45', '0' ],
-pH => [ '0', '0', '0', '0', '0', '0', '1', '0' ],
-pD => [ '0', '0', '1', '7', '2', '2', '0', '22' ],
-pR => [ '0', '0', '0', '3', '0', '27', '0', '0' ],
-pI => [ '0', '0', '3', '0', '59', '1', '2', '3' ],
-pG => [ '0', '0', '0', '1', '0', '0', '4', '1' ],
-IC => $ic,
-sites => $istes,
-width => $width,
-e_val => $e_val,
-instances => $instances,
}
Function: Creates a new Bio::Matrix::PSM::ProtPsm object Throws : Example : Returns : Bio::Matrix::PSM::Psm object Args : hash
instancescodeprevnextTop
 Title   : instances
Usage : my @instances=@{$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 an epty list 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::ProtPsm::HEADER) {
	$header{$key}=$self->{$key};
    }
    return %header;
}
matrixdescriptionprevnextTop
sub matrix {
   my $self = shift;

   if (@_) {
      my $matrix = shift;
      my @alphabet = $self->alphabet;

      foreach my $char (@alphabet) {
         $self->{"log$char"}  = $matrix->{"log$char"};
         $self->{"prob$char"} = $matrix->{"prob$char"};
      }
      $self->{IC}    = $matrix->IC;
      $self->{e_val} = $matrix->e_val;
      $self->{id}    = $matrix->id;
    }

    return $self;
}

1;
}
General documentation
FEEDBACKTop
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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
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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 - James ThompsonTop
Email tex@biosysadmin.com
DISCLAIMERTop
This software is provided "as is" without warranty of any kind.
SEE ALSOTop
ProtMatrix, meme, transfac, psiblast, InstanceSite
APPENDIXTop