Raw content of Bio::EnsEMBL::Map::DitagFeature
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::Map::DitagFeature
=head1 SYNOPSIS
my $feature = Bio::EnsEMBL::Map::DitagFeature->new(
-slice => $slice,
-start => $qstart,
-end => $qend,
-strand => $qstrand,
-hit_start => $tstart,
-hit_end => $tend,
-hit_strand => $tstrand,
-ditag_id => $ditag_id,
-ditag_side => $ditag_side,
-ditag_pair_id => $ditag_pair_id,
-cigar_line => $cigar_line,
-analysis => $analysis,
);
=head1 DESCRIPTION
Represents a mapped ditag object in the EnsEMBL database. These are
the original tags separated into start ("L") and end ("R") parts if
applicable, successfully aligned to the genome. Two DitagFeatures
usually relate to one parent Ditag. Alternatively there are CAGE tags
e.g. which only have a 5\'tag ("F").
=head1 METHODS
=cut
package Bio::EnsEMBL::Map::DitagFeature;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Utils::Exception qw( throw );
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
@ISA = qw(Bio::EnsEMBL::Feature);
=head2 new
Arg [1] : (optional) int dbID
Arg [2] : (optional) Bio::EnsEMBL::DitagFeatureAdaptor $adaptor
Arg [3] : int start
Arg [4] : int end
Arg [5] : int strand
Arg [6] : Bio::EnsEMBL::Slice $slice
Arg [7] : (optional) Bio::EnsEMBL::Analysis
Arg [8] : int hit_start
Arg [9] : int hit_end
Arg [10] : int hit_strand
Arg [11] : int ditag_id
Arg [12] : string ditag_side
Arg [13] : (optional) sring cigar_line
Arg [14] : (optional) int ditag_pair_id
Arg [15] : (optional) int tag_count, only used for imported mappings where
identical positions where collapsed into into one feature.
Default: 1
Arg [16] : (optional) ditag object
Example : $ditag = Bio::EnsEMBL::Map::DitagFeature->new
(-dbID => 123, -adaptor => $adaptor, ...);
Description: Creates a new DitagFeature
Returntype : Bio::EnsEMBL::Map::DitagFeature
Caller : general
Status : At Risk
=cut
sub new {
my ($caller, @args) = @_;
my ( $dbID, $adaptor, $start, $end, $strand, $slice, $analysis, $hit_start, $hit_end,
$hit_strand, $ditag_id, $ditag_side, $cigar_line, $ditag_pair_id, $tag_count, $ditag ) =
rearrange( [ 'dbid', 'adaptor' ,'start', 'end', 'strand', 'slice', 'analysis', 'hit_start',
'hit_end', 'hit_strand', 'ditag_id', 'ditag_side', 'cigar_line', 'ditag_pair_id' ,'tag_count', 'ditag'],
@args );
my $class = ref($caller) || $caller;
if($analysis) {
if(!ref($analysis) || !$analysis->isa('Bio::EnsEMBL::Analysis')) {
throw('-ANALYSIS argument must be a Bio::EnsEMBL::Analysis not '.
$analysis);
}
}
if(defined($strand)) {
if(!($strand =~ /^-?\d$/) or !($strand == 1) && !($strand == -1) && !($strand == 0)) {
throw('-STRAND argument must be 1, -1, or 0');
}
}
if(defined($hit_strand)) {
if(!($hit_strand == 1) && !($hit_strand == -1) && !($hit_strand == 0)) {
throw('-HIT_STRAND argument must be 1, -1, or 0 not '.$hit_strand);
}
}
if(defined($start) && defined($end)) {
if($end+1 < $start) {
throw('Start must be less than or equal to end+1.');
}
}
else{
throw('Need start and end location.');
}
if(!(defined($hit_start) && defined($hit_end))) {
throw('Need hit start and hit end location.');
}
if(!defined($tag_count) or (!$tag_count =~ /^[\d]+$/)){
$tag_count = 1;
}
my $self = bless( {'dbID' => $dbID,
'analysis' => $analysis,
'adaptor' => $adaptor,
'slice' => $slice,
'start' => $start,
'end' => $end,
'strand' => $strand,
'hit_start' => $hit_start,
'hit_end' => $hit_end,
'hit_strand' => $hit_strand,
'ditag_id' => $ditag_id,
'ditag_pair_id' => $ditag_pair_id,
'ditag_side' => $ditag_side,
'cigar_line' => $cigar_line,
'tag_count' => $tag_count,
'ditag' => $ditag,
}, $class);
return $self;
}
=head2 fetch_ditag
Description: Deprecated, use ditag() instead
=cut
sub fetch_ditag {
throw("Deprecated method, please use ditag() instead.\n")
}
=head2 ditag
Arg [1] : (optional) ditag object
Description: Get/Set the ditag object of this DitagFeature
Returntype : Bio::EnsEMBL::Map::Ditag
Exceptions : none
Caller : general
Status : At Risk
=cut
sub ditag {
my $self = shift;
if(@_) {
$self->{'ditag'} = shift;
} elsif(!$self->{'ditag'}) {
if($self->{'ditag_id'}) {
#lazy load the ditag
my $ditag_adaptor = $self->analysis->adaptor->db->get_DitagAdaptor;
$self->{'ditag'} = $ditag_adaptor->fetch_by_dbID($self->ditag_id);
}
else{
throw "Could not get Ditag for DitagFeature ".$self->dbID;
}
}
return($self->{'ditag'});
}
=head2 get_ditag_location
Arg [1] : none
Description: Get the start and end location (and strand ) of the start-end pair
this DitagFeature belongs to.
If it is not a paired ditag, these will be identical
to DitagFeature->start() & DitagFeature->end().
Please note that the returned start/end are min/max locations.
Returntype : int (start, end, strand)
Exceptions : throws if the 2 features of a pair are found on different strands
or if the second one cannot be found.
Caller : general
Status : At Risk
=cut
sub get_ditag_location {
my $self = shift;
my ($start, $end, $strand);
if($self->ditag_side eq "F"){
$start = $self->start;
$end = $self->end;
}
else{
my ($ditag_a, $ditag_b, $more);
eval{
($ditag_a, $ditag_b, $more) = @{$self->adaptor->fetch_all_by_ditagID($self->ditag_id,
$self->ditag_pair_id,
$self->analysis->dbID)};
};
if($@ or !defined($ditag_a) or !defined($ditag_b)){
throw("Cannot find 2nd tag of pair (".$self->dbID.", ".$self->ditag_id.", ".
$self->ditag_pair_id.", ".$self->analysis->dbID.")\n".$@);
}
else{
# if(defined $more){
# throw("More than two DitagFeatures were returned for ".$self->dbID.", ".$self->ditag_id
# .", ".$self->ditag_pair_id);
# }
($ditag_a->start < $ditag_b->start) ? ($start = $ditag_a->start) : ($start = $ditag_b->start);
($ditag_a->end > $ditag_b->end) ? ($end = $ditag_a->end) : ($end = $ditag_b->end);
if($ditag_a->strand != $ditag_b->strand){
throw('the strands of the two ditagFeatures are different! '.$ditag_a->strand.'/'.$ditag_b->strand);
}
}
}
return($start, $end, $self->strand);
}
=head2 ditag_id
Arg [1] : (optional) value
Description: Getter/Setter for the ditag_id
of this DitagFeature
Returntype : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub ditag_id {
my $self = shift;
if(@_) {
$self->{'ditag_id'} = shift;
}
return $self->{'ditag_id'};
}
=head2 slice
Arg [1] : (optional) value
Description: Getter/Setter for the slice
of this DitagFeature
Returntype : slice object
Exceptions : none
Caller : general
Status : At Risk
=cut
sub slice {
my $self = shift;
if(@_) {
$self->{'slice'} = shift;
}
return $self->{'slice'};
}
=head2 ditag_pair_id
Arg [1] : (optional) value
Description: Getter/Setter for the ditag_pair_id
of this DitagFeature
Returntype : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub ditag_pair_id {
my $self = shift;
if(@_) {
$self->{'ditag_pair_id'} = shift;
}
return $self->{'ditag_pair_id'};
}
=head2 ditag_side
Arg [1] : (optional) value
Description: Getter/Setter for the ditag_side
of this DitagFeature
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub ditag_side {
my $self = shift;
if(@_) {
$self->{'ditag_side'} = shift;
}
return $self->{'ditag_side'};
}
=head2 hit_start
Arg [1] : (optional) value
Description: Getter/Setter for the hit_start
of this DitagFeature
Returntype : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub hit_start {
my $self = shift;
if(@_) {
$self->{'hit_start'} = shift;
}
return $self->{'hit_start'};
}
=head2 hit_end
Arg [1] : (optional) value
Description: Getter/Setter for the hit_end
of this DitagFeature
Returntype : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub hit_end {
my $self = shift;
if(@_) {
$self->{'hit_end'} = shift;
}
return $self->{'hit_end'};
}
=head2 hit_strand
Arg [1] : (optional) value
Description: Getter/Setter for the hit_strand
of this DitagFeature
Returntype : 1/-1/0
Exceptions : none
Caller : general
Status : At Risk
=cut
sub hit_strand {
my $self = shift;
if(@_) {
$self->{'hit_strand'} = shift;
}
return $self->{'hit_strand'};
}
=head2 cigar_line
Arg [1] : (optional) value
Description: Getter/Setter for the cigar_line
of this DitagFeature
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub cigar_line {
my $self = shift;
if(@_) {
$self->{'cigar_line'} = shift;
}
return $self->{'cigar_line'};
}
=head2 start
Arg [1] : (optional) value
Description: Getter/Setter for the start
of this DitagFeature
Returntype : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub start {
my $self = shift;
if(@_) {
$self->{'start'} = shift;
}
return $self->{'start'};
}
=head2 end
Arg [1] : (optional) value
Description: Getter/Setter for the end
of this DitagFeature
Returntype : int or string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub end {
my $self = shift;
if(@_) {
$self->{'end'} = shift;
}
return $self->{'end'};
}
=head2 strand
Arg [1] : (optional) value
Description: Getter/Setter for the strand
of this DitagFeature
Returntype : 1/-1/0
Exceptions : none
Caller : general
Status : At Risk
=cut
sub strand {
my $self = shift;
if(@_) {
$self->{'strand'} = shift;
}
return $self->{'strand'};
}
=head2 dbID
Arg [1] : (optional) value
Description: Getter/Setter for the dbID
of this DitagFeature
Returntype : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub dbID {
my $self = shift;
if(@_) {
$self->{'dbID'} = shift;
}
return $self->{'dbID'};
}
=head2 sequence
Arg [1] : (optional) value
Description: Getter/Setter for the sequence
of this DitagFeature
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub sequence {
my $self = shift;
$self->{'sequence'} = $self->adaptor->sequence($self->dbID());
return $self->{'sequence'};
}
=head2 tag_count
Arg [1] : (optional) value
Description: Getter/Setter for the tag_count
of this DitagFeature
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub tag_count {
my $self = shift;
if(@_) {
$self->{'tag_count'} = shift;
}
return $self->{'tag_count'};
}
1;
]]>