diff variant_effect_predictor/Bio/EnsEMBL/IdentityXref.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/IdentityXref.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,522 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 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
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=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;