Bio::Matrix::PSM InstanceSite
SummaryPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Matrix::PSM::InstanceSite - A PSM site occurance
Package variables
No package variables defined.
Included modules
Bio::LocatableSeq
Bio::Matrix::PSM::InstanceSiteI
Bio::Matrix::PSM::SiteMatrix
Bio::Root::Root
strict
Synopsis
  use Bio::Matrix::PSM::InstanceSite;

  #You can get an InstanceSite object either from a file:

  my ($instances,$matrix)=$SomePSMFile->parse_next;

  #or from memory

  my %params=(seq=>'TATAAT',
    id=>"TATAbox1", accession=>'ENSG00000122304', mid=>'TB1',
    desc=>'TATA box, experimentally verified in PRM1 gene',
    relpos=>-35);
Description
Abstract interface to PSM site occurrence (PSM sequence
match). InstanceSite objects may be used to describe a PSM (See
Bio::Matrix::PSM::SiteMatrix) sequence matches. The usual
characteristic of such a match is sequence coordinates, score,
sequence and sequence (gene) identifier- accession number or other id.
This object inherits from Bio::LocatableSeq (which defines the real
sequence) and might hold a SiteMatrix object, used to detect the CRE
(cis-regulatory element), or created from this CRE.
While the documentation states that the motif id and gene id
(accession) combination should be unique, this is not entirely true-
there might be more than one occurrence of the same cis-regulatory
element in the upstream region of the same gene. Therefore relpos
would be the third element to create a really unique combination.
Methods
newDescriptionCode
midDescriptionCode
scoreDescriptionCode
minstanceDescriptionCode
relposDescriptionCode
Methods description
newcode    nextTop
 Title   : new
 Usage   : my $isntance=new Bio::Matrix::PSM::InstanceSite 
                         (-seq=>'TATAAT', -id=>"TATAbox1",
                          -accession_number='ENSG00000122304', -mid=>'TB1',
                          -desc=>'TATA box, experimentally verified in PRM1 gene',
			  -relpos=>-35)
 Function: Creates an InstanceSite object from memory.
 Throws  :
 Example :
 Returns : Bio::Matrix::PSM::InstanceSite object
 Args    : hash
midcodeprevnextTop
 Title   : mid
 Usage   : my $mid=$instance->mid;
 Function: Get/Set the motif id
 Throws  :
 Example :
 Returns : scalar
 Args    : scalar
scorecodeprevnextTop
 Title   : score
 Usage   : my $score=$instance->score;
 Function: Get/Set the score (mismatches) between the instance and the attached (or
            initial) PSM
 Throws  :
 Example :
 Returns : real number
 Args    : real number
minstancecodeprevnextTop
 Title   : minstance
 Usage   : my $minstance=$misntance->score;
 Function: Get/Set the unique identifier- sequence id/motif id, for example PRM1_TATAbox.
          Not necessarily human readable.
 Throws  :
 Example :
 Returns : string
 Args    : string
relposcodeprevnextTop
 Title   : relpos
 Usage   : my $seqpos=$instance->relpos;
 Function: Get/Set the relative position of the instance with respect to the transcription start
            site (if known). Can and usually is negative.
 Throws  :
 Example :
 Returns : integer
 Args    : integer
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my %args = @args; #Too many things to rearrange, and I am creating >1K such objects routinely, so this is a performance issue    
    $args{'-start'} ||= 1;
    my $end = $args{'-start'} + length($args{-seq});
    if (!defined($args{-strand})) {
	$args{-strand}=1;
	@args=%args;
    }
    my $self = $class->SUPER::new(@args,'-end',$end);
    
    while( @args ) {
	(my $key = shift @args) =~ s/-//gi; #deletes all dashes (only dashes)!
	$args{$key} = shift @args;
    }
#should throw exception if seq is null, for now just warn
    if (($args{seq} eq '') || (!defined($args{seq}))) {
	$args{seq}="AGCT";
	warn "No sequence?!\n";
    }
    $self->{mid}=$args{mid};
    $self->seq($args{seq});
    $self->desc($args{desc});
    $self->{score}=$args{score};
    $self->{relpos}=$args{relpos};
    return $self;
}
middescriptionprevnextTop
sub mid {
    my $self = shift;
    my $prev = $self->{mid};
    if (@_) { $self->{mid} = shift; }
    return $prev;
}
scoredescriptionprevnextTop
sub score {
    my $self = shift;
    my $prev = $self->{score};
    if (@_) { $self->{score} = shift; }
    return $prev;
}
minstancedescriptionprevnextTop
sub minstance {
    my $self = shift;
    my $prev = $self->{minstance};
    if (@_) { $self->{minstance} = shift; }
    return $prev;
}
relposdescriptionprevnextTop
sub relpos {
    my $self = shift;
    my $prev = $self->{relpos};
    if (@_) { $self->{relpos} = shift; }
    return $prev;
}
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://bio.perl.org/MailList.html     - About the mailing lists
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 email or the web:
  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/
DescriptionTop
Bio::Matrix::PSM::InstanceSiteI implementation
AUTHOR - Stefan KirovTop
Email skirov@utk.edu
APPENDIXTop
startTop
 Title   : start
 Usage   : my $start=$instance->start;
 Function: Get/Set the position of the instance on the sequence used
 Throws  :
 Example :
 Returns : integer
 Args    : integer