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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/UnmappedObject.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,485 @@
+=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::UnmappedObject - A object representing why a particular entity
+was NOT mapped to the ensembl.
+
+=head1 SYNOPSIS
+
+  use Bio::EnsEMBL::UnmappedObject;
+
+  my $uo = Bio::EnsEMBL::UnmappedObject->new(
+    -type           => 'xref',
+    -analysis       => $analysis,
+    -external_db_id => 4100,
+    -identifier     => "Q12345",
+    -query_score    => 45.5,
+    -target_score   => 29.2,
+    -ensembl_id     => 122346,
+    -ensembl_type   => "Translation",
+    -summary        => "match failed for exonerate",
+    -full_desc      => "match failed for the xref exonerate run "
+      . "as match was below threshold of 90"
+  );
+
+=head1 DESCRIPTION
+
+UnmappedObjects represent entities NOT mapped to ensembl. Therefore this
+should help users to find out why certain accessions etc can not be
+found.
+
+=head1 METHODS
+
+=cut
+
+
+
+package Bio::EnsEMBL::UnmappedObject;
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::Utils::Exception qw(throw);
+use Bio::EnsEMBL::Storable;
+
+use vars qw(@ISA);
+
+@ISA = qw(Bio::EnsEMBL::Storable);
+
+
+=head2 new
+
+  Arg [TYPE]           : the type of mapping i.e. 'xref','cDNA' 
+  Arg [ANALYSIS]       : Analysis object. 
+  Arg [EXTERNAL_DB_ID] : id for the external db id this identifier is from
+  Arg [IDENTIFIER]     : name of the identifier i.e. accession
+  Arg [QUERY_SCORE]    : (optional) The query score
+  Arg [TARGET_SCORE]   : (optional) The target score
+  Arg [SUMMARY]        : The summary reason for not mapping.
+  Arg [FULL_DESC]      : The Full description of why it did not map.
+  Arg [ENSEMBL_ID]     : (optional) internal ensembl id for the best match
+  Arg [ENSEMBL_OBJECT_TYPE] : (optional) the type of object for the best match
+  Example              : see SYNOPSIS
+  Returntype           : Bio::EnsEMBL::UnmappedObject
+  Exceptions           : If any of the none optional args are missing
+  Caller               : general
+  Status               : At Risk
+
+=cut
+
+sub new {
+  my $caller = shift;
+
+  #allow constructor to be called as class or object method
+  my $class = ref($caller) || $caller;
+
+
+
+  my ($dbID, $unmapped_reason_id, $type, $analysis, $ex_db_id, $identifier, 
+      $query_score, $target_score, $summary, $full_desc,
+      $ensembl_id, $ensembl_object_type, $adaptor ) = 
+    rearrange([qw(UNMAPPED_OBJECT_ID UNMAPPED_REASON_ID TYPE ANALYSIS 
+		  EXTERNAL_DB_ID IDENTIFIER QUERY_SCORE TARGET_SCORE 
+		  SUMMARY FULL_DESC ENSEMBL_ID ENSEMBL_OBJECT_TYPE ADAPTOR)], @_);
+
+  my $self = $class->SUPER::new(@_);
+  if(defined($analysis)) {
+    if(!ref($analysis) || !$analysis->isa('Bio::EnsEMBL::Analysis')) {
+      throw('-ANALYSIS argument must be a Bio::EnsEMBL::Analysis not '.
+            $analysis);
+    }
+  }
+  else{
+    throw('-ANALYSIS argument must be given');
+  }
+  $self->{'analysis'} = $analysis;
+  $self->{'dbID'} = $dbID if (defined($dbID));
+  $self->{'description'} = $full_desc   || throw('FULL_DESC must be given');
+  $self->{'summary'} = $summary         || throw('SUMMARY must be given');
+  $self->{'type'} = $type               || throw('TYPE must be given');
+  $self->{'external_db_id'} = $ex_db_id;
+
+  if (lc($type) eq "xref") {
+    throw('EXTERNAL_DB_ID must be given') if ! defined $ex_db_id;
+  }
+
+  $self->{'identifier'} = $identifier   || throw('IDENTIFIER must be given');
+  $self->{'query_score'} = $query_score  if(defined($query_score));
+  $self->{'target_score'} = $target_score  if(defined($target_score));
+  $self->{'ensembl_id'} = $ensembl_id  if(defined($ensembl_id));
+  $self->{'ensembl_object_type'} = $ensembl_object_type  
+    if(defined($ensembl_object_type));
+  $self->{'unmapped_reason_id'} = $unmapped_reason_id 
+    if(defined($unmapped_reason_id));
+  $self->adaptor($adaptor)  if(defined($adaptor));
+  return $self;
+}
+
+=head2 new_fast
+
+  Arg [...]  : none
+  Example    : $feature = Bio::EnsEMBL::UnmappedObject->new_fast();
+  Description: Creates a new Unmapped Object.
+  Returntype : Bio::EnsEMBL::UnmappedObject
+  Exceptions : none
+  Caller     : general
+  Status     : At Risk
+
+=cut
+
+sub new_fast{
+  my $caller = shift;
+
+  #allow constructor to be called as class or object method
+  my $class = ref($caller) || $caller;
+
+  my $self = $class->SUPER::new(@_);
+
+  return $self;
+}
+
+=head2 description
+
+  Arg [1]     : (optional) * to be set to
+  Example     : print $unmappedObject->description."\n";
+  Description : Basic getter/setter for description
+  ReturnType  : String
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+
+=cut
+
+sub description{
+  my $self = shift;
+
+  if(@_) {
+    my $des = shift;
+    $self->{'description'} = $des;
+  }
+
+  return $self->{'description'};
+}
+
+=head2 summary
+
+  Arg [1]     : (optional) summary to be set to
+  Example     : print $unmappedObject->summary."\n";
+  Description : Basic getter/setter for summary
+  ReturnType  : String
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+
+=cut
+
+sub summary{
+  my $self = shift;
+
+  if(@_) {
+    my $des = shift;
+    $self->{'summary'} = $des;
+  }
+
+  return $self->{'summary'};
+}
+
+=head2 type
+
+  Arg [1]     : (optional) type to be set to
+  Example     : print $unmappedObject->type."\n";
+  Description : Basic getter/setter for type
+  ReturnType  : String
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+
+=cut
+
+sub type{
+  my $self = shift;
+
+  if(@_) {
+    my $arg = shift;
+    $self->{'type'} = $arg;
+  }
+
+  return $self->{'type'};
+}
+
+=head2 ensembl_object_type
+
+  Arg [1]     : (optional) ensembl object type to be set to
+  Example     : print $unmappedObject->ensembl_object_type."\n";
+  Description : Basic getter/setter for ensembl object type
+  ReturnType  : String
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+
+=cut
+
+sub ensembl_object_type{
+  my $self = shift;
+
+  if(@_) {
+    my $arg = shift;
+    $self->{'ensembl_object_type'} = $arg;
+  }
+
+  return $self->{'ensembl_object_type'};
+}
+
+=head2 ensembl_id
+
+  Arg [1]     : (optional) ensembl id to be set to
+  Example     : print $unmappedObject->ensembl_id."\n";
+  Description : Basic getter/setter for ensembl id
+  ReturnType  : String
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+
+=cut
+
+sub ensembl_id{
+  my $self = shift;
+
+  if(@_) {
+    my $arg = shift;
+    $self->{'ensembl_id'} = $arg;
+  }
+
+  return $self->{'ensembl_id'};
+}
+
+=head2 external_db_id
+
+  Arg [1]     : (optional) external_db_id to be set to
+  Example     : print $unmappedObject->external_db_id."\n";
+  Description : Basic getter/setter for external_db_id
+  ReturnType  : int
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+
+=cut
+
+sub external_db_id{
+  my $self = shift;
+
+  if(@_) {
+    my $arg = shift;
+    $self->{'external_db_id'} = $arg;
+  }
+  
+  return $self->{'external_db_id'};
+}
+
+=head2 external_db_name
+
+  Example     : print $unmappedObject->external_db_name()."\n";
+  Description : Basic getter for external_db_name
+  ReturnType  : int
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+
+=cut
+
+sub external_db_name{
+  my $self = shift;
+
+  my $handle = $self->adaptor;
+  if(defined($handle) and defined($self->{'external_db_id'})){
+    my $sth = $handle->prepare("select db_name from external_db where external_db_id = ".$self->{'external_db_id'});
+    $sth->execute();
+    my $name;
+    $sth->bind_columns(\$name);
+    $sth->fetch();
+    return $name;
+  }
+  return "";
+}
+
+
+sub stable_id{
+  my ($self) = shift;
+  
+  my $handle = $self->adaptor;
+  if(defined($handle)){
+    my $sql = "select stable_id from ".lc($self->{'ensembl_object_type'})." where ".
+      lc($self->{'ensembl_object_type'})."_id = ".
+	$self->{'ensembl_id'};
+    my $sth = $handle->prepare($sql);
+    $sth->execute();
+    my $name;
+    $sth->bind_columns(\$name);
+    $sth->fetch();
+    return $name;
+  }
+  return "";
+}
+					     
+ #  my $adaptor;
+#  if($self->{'ensembl_object_type'} eq  "Transcript"){
+#    $adaptor= $self->adaptor->db->get_TranscriptAdaptor();
+#  }
+#  elsif($self->{'ensembl_object_type'} eq  "Translation"){
+#    $adaptor= $self->adaptor->db->get_TranslationAdaptor();
+#  }
+#  elsif($self->{'ensembl_object_type'} eq  "Gene"){
+#    $adaptor= $self->adaptor->db->get_GeneAdaptor();
+#  } 
+#  else{
+#    return undef;
+#  }
+#  my $object = $adaptor->fetch_by_dbID($self->{'ensembl_id'});
+#  if(defined($object)){
+#    return $object->stable_id;
+#  }
+#  else{
+#    return undef;
+#  }
+#}
+
+ 
+=head2 identifier
+
+  Arg [1]     : (optional) identifier to be set to
+  Example     : print $unmappedObject->identifier."\n";
+  Description : Basic getter/setter for identifier
+  ReturnType  : String
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+
+=cut
+
+sub identifier{
+  my $self = shift;
+
+  if(@_) {
+    my $arg = shift;
+    $self->{'identifier'} = $arg;
+  }
+
+  return $self->{'identifier'};
+}
+
+=head2 query_score
+
+  Arg [1]     : (optional) query_score to be set to
+  Example     : print $unmappedObject->query_score."\n";
+  Description : Basic getter/setter for query_score
+  ReturnType  : float
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+
+=cut
+
+sub query_score{
+  my $self = shift;
+
+  if(@_) {
+    my $arg = shift;
+    $self->{'query_score'} = $arg;
+  }
+
+  return $self->{'query_score'};
+}
+
+=head2 target_score
+
+  Arg [1]     : (optional) target_score to be set to
+  Example     : print $unmappedObject->target_score."\n";
+  Description : Basic getter/setter for target_score
+  ReturnType  : float
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+
+=cut
+
+sub target_score{
+  my $self = shift;
+
+  if(@_) {
+    my $arg = shift;
+    $self->{'target_score'} = $arg;
+  }
+
+  return $self->{'target_score'};
+}
+
+=head2 unmapped_reason_id
+
+  Arg [1]     : (optional) unmapped_reason_id to be set to
+  Example     : print $unmappedObject->unmapped_reason_id."\n";
+  Description : Basic getter/setter for unmapped_reason_id
+  ReturnType  : int
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+
+=cut
+
+sub unmapped_reason_id{
+  my $self = shift;
+
+  if(@_) {
+    my $arg = shift;
+    $self->{'unmapped_reason_id'} = $arg;
+  }
+
+  return $self->{'unmapped_reason_id'};
+}
+
+=head2 analysis
+
+  Arg [1]     : (optional) analysis to be set to
+  Example     : print $unmappedObject->analysis->logic_name."\n";
+  Description : Basic getter/setter for analysis
+  ReturnType  : Bio::EnsEMBL::Analysis
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+
+=cut
+
+sub analysis {
+  my $self = shift;
+
+  if(@_) {
+    my $an = shift;
+    if(defined($an) && (!ref($an) || !$an->isa('Bio::EnsEMBL::Analysis'))) {
+      throw('analysis argument must be a Bio::EnsEMBL::Analysis');
+    }
+    $self->{'analysis'} = $an;
+  }
+
+  return $self->{'analysis'};
+}
+
+1;