Raw content of Bio::EnsEMBL::IdentityXref
<![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::IdentityXref
=head1 SYNOPSIS
my $xref = Bio::EnsEMBL::IdentityXref->new(
-XREF_IDENTITY => 80.4,
-ENSEMBL_IDENTITY => 90.1,
-SCORE => 90,
-EVALUE => 12,
-CIGAR_LINE => '23MD3M2I40M',
-XREF_START => 1,
-XREF_END => 68,
-ENSEMBL_START => 10,
-ENSEMBL_END => 77,
-ADAPTOR => $adaptor,
-PRIMARY_ID => $primary_id,
-DBNAME => 'SwissProt'
);
=head1 METHODS
=cut
package Bio::EnsEMBL::IdentityXref;
use vars qw(@ISA $AUTOLOAD);
use strict;
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use Bio::EnsEMBL::Utils::Exception qw( deprecate );
@ISA = qw( Bio::EnsEMBL::DBEntry );
=head2 new
Arg [...] : XREF_IDENTITY ENSEMBL_IDENTITY SCORE EVALUE CIGAR_LINE
: XREF_START XREF_END ENSEMBL_START ENSEMBL_END
: ANALYSIS pairs
Example : see synopsis
Description: Create a new Bio::EnsEMBL::IdentityXref object
Returntype : Bio::EnsEMBL::IdentityXref
Exceptions : none
Caller : general
Status : Stable
=cut
my $error_shown = 0;
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($query_identity, $target_identity, $score, $evalue,
$cigar_line, $query_start, $query_end, $translation_start,
$translation_end, $analysis, $xref_identity, $ensembl_identity,
$xref_start, $xref_end, $ensembl_start, $ensembl_end) = rearrange(
[qw(QUERY_IDENTITY TARGET_IDENTITY SCORE EVALUE CIGAR_LINE
QUERY_START QUERY_END TRANSLATION_START TRANSLATION_END
ANALYSIS XREF_IDENTITY ENSEMBL_IDENTITY XREF_START XREF_END ENSEMBL_START ENSEMBL_END)], @args);
if((defined($query_identity) or defined($target_identity) or defined($query_start) or defined ($query_end) or
defined($translation_start) or defined($translation_end)) and !$error_shown){
print STDERR "Arguments have now been changed to stop confusion so please replace the following\n";
print STDERR "\tQUERY_IDENTITY\t->\tXREF_IDENTITY\n";
print STDERR "\tTARGET_IDENTITY\t->\tENSEMBL_IDENTITY\n";
print STDERR "\tQUERY_START\t->\tXREF_START\n";
print STDERR "\tQUERY_END\t->\tXREF_END\n";
print STDERR "\tTRANSLATION_START\t->\tENSEMBL_START\n";
print STDERR "\tTRANSLATION_END\t->\tENSEMBL_END\n";
print STDERR "The old arguments will be removed in a futute release so please change your code to the new names\n";
$error_shown = 1;
}
$self->{'xref_identity'} = $query_identity || $xref_identity;
$self->{'ensembl_identity'} = $target_identity || $ensembl_identity;
$self->{'score'} = $score;
$self->{'evalue'} = $evalue;
$self->{'cigar_line'} = $cigar_line;
$self->{'xref_start'} = $query_start || $xref_start;
$self->{'xref_end'} = $query_end || $xref_start;
$self->{'ensembl_start'} = $translation_start || $ensembl_start;
$self->{'ensembl_end'} = $translation_end || $ensembl_end;
$self->{'analysis'} = $analysis;
return $self;
}
=head2 xref_identity
Arg [1] : (optional) string $value
Example : $xref_identity = $id_xref->xref_identity;
Description: Getter/Setter for xref identity
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub xref_identity{
my $obj = shift;
if( @_ ) {
my $value = shift;
$obj->{'xref_identity'} = $value;
}
return $obj->{'xref_identity'};
}
=head2 ensembl_identity
Arg [1] : (optional) string $value
Example : $ensembl_identity = $id_xref->ensembl_identity;
Description: Getter/Setter for ensembl identity
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub ensembl_identity{
my $obj = shift;
if( @_ ) {
my $value = shift;
$obj->{'ensembl_identity'} = $value;
}
return $obj->{'ensembl_identity'};
}
=head2 cigar_line
Arg [1] : string $cigar_line
Example : none
Description: get/set for attribute cigar_line
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub cigar_line {
my $self = shift;
$self->{'cigar_line'} = shift if( @_ );
return $self->{'cigar_line'};
}
=head2 ensembl_start
Arg [1] : string $ensembl_start
Example : none
Description: get/set for attribute ensembl_start
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub ensembl_start {
my $self = shift;
$self->{'ensembl_start'} = shift if( @_ );
return $self->{'ensembl_start'};
}
=head2 ensembl_end
Arg [1] : string $ensembl_end
Example : none
Description: get/set for attribute ensembl_end
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub ensembl_end {
my $self = shift;
$self->{'ensembl_end'} = shift if( @_ );
return $self->{'ensembl_end'};
}
=head2 xref_start
Arg [1] : string $xref_start
Example : none
Description: get/set for attribute xref_start
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub xref_start {
my $self = shift;
$self->{'xref_start'} = shift if( @_ );
return $self->{'xref_start'};
}
=head2 xref_end
Arg [1] : string $xref_end
Example : none
Description: get/set for attribute xref_end
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub xref_end {
my $self = shift;
$self->{'xref_end'} = shift if( @_ );
return $self->{'xref_end'};
}
=head2 score
Arg [1] : string $score
Example : none
Description: get/set for attribute score
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub score {
my $self = shift;
$self->{'score'} = shift if( @_ );
return $self->{'score'};
}
=head2 evalue
Arg [1] : string $evalue
Example : none
Description: get/set for attribute evalue
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub evalue {
my $self = shift;
$self->{'evalue'} = shift if( @_ );
return $self->{'evalue'};
}
=head2 get_mapper
Args : none
Example : none
Description: produces a mapper object that takes coordinates from one side
of the alignment to the other side. "ensembl" and "external"
are the two coordinate systems contained.
Returntype : Bio::EnsEMBL::Mapper
Exceptions : none
Caller : general, ProteinDAS subsystem
Status : Stable
=cut
sub get_mapper {
my ( $self ) = @_;
# parse the cigar_line and create a mapper ...
if( exists $self->{'_cached_mapper'} ) {
return $self->{'_cached_mapper'};
}
my ( @lens, @chars );
# if there is no cigar line, nothing is going to be loaded
if( $self->cigar_line() ) {
my @pre_lens = split( '[DMI]', $self->cigar_line() );
@lens = map { if( ! $_ ) { 1 } else { $_ }} @pre_lens;
@chars = grep { /[DMI]/ } split( //, $self->cigar_line() );
}
my $translation_start = $self->ensembl_start();
my $translation_end = $self->ensembl_end();
my $query_start = $self->xref_start();
my $query_end = $self->xref_end();
# my $hit_id = $self->display_id();
my $ensembl_id = "ensembl_id";
my $external_id = "external_id";
# now build the mapper
my $mapper = Bio::EnsEMBL::Mapper->new( "external", "ensembl" );
for( my $i=0; $i<=$#lens; $i++ ) {
my $length = $lens[$i];
my $char = $chars[$i];
if( $char eq "M" ) {
$mapper->add_map_coordinates( $external_id, $query_start,
$query_start + $length - 1, 1,
$ensembl_id, $translation_start,
$translation_start + $length - 1);
$query_start += $length;
$translation_start += $length;
} elsif( $char eq "D" ) {
$translation_start += $length;
} elsif( $char eq "I" ) {
$query_start += $length;
}
}
$self->{'_cached_mapper'} = $mapper;
return $mapper;
}
=head2 transform_feature
Arg [1] : a feature type with start and end $feature
This doesnt need to be a Bio::EnsEMBL::Feature as it doesnt
need an attached slice. We may have to introduce an appropriate
object type.
Example : my $ens_prot_feature_list =
$ident_xref->transform_feature( $swiss_prot_feature );
Description: a list of potential partial features which represent all
mappable places
of the original feature in ensembl translation coordinates.
Returntype : listref of whatever was put in
Exceptions : none
Caller : general, ProteinDAS subsystem
Status : Stable
=cut
sub transform_feature {
my $self= shift;
my $feature = shift;
my $fstart = $feature->start();
my $fend = $feature->end();
my $mapper = $self->get_mapper();
my @result;
my @coords = $mapper->map_coordinates( "external_id", $fstart, $fend,
1, "external" );
for my $coord ( @coords ) {
if( $coord->isa( "Bio::EnsEMBL::Mapper::Coordinate" )) {
my $new_feature;
%{$new_feature} = %$feature;
bless $new_feature, ref( $feature );
$new_feature->start( $coord->start() );
$new_feature->end( $coord->end() );
push( @result, $new_feature );
}
}
return \@result;
}
=head2 map_feature
Arg [1] : a start,end capable feature object
Example : none
Description:
Returntype : list of Coordinates/Gaps which represents the mapping
Exceptions : none
Caller : another way of doing ProteinDAS
Status : Stable
=cut
sub map_feature {
my $self = shift;
my $feature = shift;
my $fstart = $feature->start();
my $fend = $feature->end();
my $mapper = $self->get_mapper();
my @coords = $mapper->map_coordinates( "external_id", $fstart, $fend, 1,
"external" );
return @coords;
}
###########################
# DEPRECATED METHODS FOLLOW
###########################
=head2 query_identity
Description: DEPRECATED. Use xref_identity() instead.
Status : At Risk
=cut
sub query_identity{
deprecate("Use xref_identity instead");
xref_identity(@_);
}
=head2 target_identity
Description: DEPRECATED. Use ensembl_identity() instead.
Status : At Risk
=cut
sub target_identity{
deprecate("Use ensembl_identity instead");
ensembl_identity(@_);
}
=head2 translation_start
Description: DEPRECATED. Use ensembl_start() instead.
Status : At Risk
=cut
sub translation_start {
deprecate("Use ensembl_start instead");
ensembl_start(@_);
}
=head2 translation_end
Description: DEPRECATED. Use ensembl_end() instead.
Status : At Risk
=cut
sub translation_end {
deprecate("Use ensembl_end instead");
ensembl_end(@_);
}
=head2 query_start
Description: DEPRECATED. Use xref_start() instead.
Status : At Risk
=cut
sub query_start {
deprecate("Use xref_start instead");
xref_start(@_);
}
=head2 query_end
Description: DEPRECATED. Use xref_end() instead.
Status : At Risk
=cut
sub query_end {
deprecate("Use xref_end instead");
xref_end(@_);
}
1;
]]>