Bio::Matrix::PSM
InstanceSite
Summary
Bio::Matrix::PSM::InstanceSite - A PSM site occurance
Package variables
No package variables defined.
Inherit
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, -anchor=>'CHR7', -start=>35000921, -end=>35000926);
#Last 2 arguments are passed to create a Bio::LocatableSeq object
#Anchor shows the coordinates system for the Bio::LocatableSeq object
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
Methods description
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, -anchor=>'CHR7', -start=>35000921, -end=>35000926, strand=>1)
Function: Creates an InstanceSite object from memory.
Throws :
Example :
Returns : Bio::Matrix::PSM::InstanceSite object
Args : hash |
Title : mid
Usage : my $mid=$instance->mid;
Function: Get/Set the motif id
Throws :
Example :
Returns : scalar
Args : scalar |
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 |
Title : anchor
Usage : my $anchor=$instance->anchor;
Function: Get/Set the anchor which shows what coordinate system start/end use
Throws :
Example :
Returns : string
Args : string |
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 |
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 |
Title : species
Usage : $species = $seq->species() or $seq->species($species)
Function: Gets or sets the species
Returns : Bio::Species object
Args : None or Bio::Species object
See Bio::Species for more information |
Title : frame
Usage : my $frane=$instance->frame;
Function: Get/Set the frame of a DNA instance with respect to a protein motif used.
Returns undef if the motif was not protein or the DB is protein.
Throws :
Example :
Returns : integer
Args : integer (0, 1, 2) |
Methods code
sub new
{ my ($class, @args) = @_;
my %args = @args;
$args{'-start'} ||= 1;
my $end = $args{'-start'} + length($args{-seq}) -1;
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;
$args{$key} = shift @args;
}
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};
$self->{frame}=$args{frame};
$self->{anchor}=$args{anchor};
return $self;} | sub mid
{ my $self = shift;
my $prev = $self->{mid};
if (@_) { $self->{mid} = shift; }
return $prev;} | sub score
{ my $self = shift;
my $prev = $self->{score};
if (@_) { $self->{score} = shift; }
return $prev;} | sub anchor
{ my $self = shift;
my $prev = $self->{anchor};
if (@_) { $self->{anchor} = shift; }
return $prev;} | sub minstance
{ my $self = shift;
my $prev = $self->{minstance};
if (@_) { $self->{minstance} = shift; }
return $prev;} | sub relpos
{ my $self = shift;
my $prev = $self->{relpos};
if (@_) { $self->{relpos} = shift; }
return $prev;} | sub annotation
{ my ($obj,$value) = @_;
if( defined $value ) {
$obj->throw("object of class ".ref($value)." does not implement ".
"Bio::AnnotationCollectionI. Too bad.")
unless $value->isa("Bio::AnnotationCollectionI");
$obj->{'_annotation'} = $value;
} elsif( ! defined $obj->{'_annotation'}) {
$obj->{'_annotation'} = new Bio::Annotation::Collection();
}
return $obj->{'_annotation'};} | sub species
{ my ($self, $species) = @_;
if ($species) {
$self->{'species'} = $species;
} else {
return $self->{'species'};
}} | sub frame
{ my $self = shift;
my $prev = $self->{frame};
if (@_) { $self->{frame} = shift; $self->throw("This is not a legitimate frame") unless (grep(/$self->{frame}/,qw[0 1 2])); }
return $prev;} | General documentation
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
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/
Bio::Matrix::PSM::InstanceSiteI implementation
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