diff variant_effect_predictor/Bio/EnsEMBL/Compara/GenomeDB.pm @ 0:21066c0abaf5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Compara/GenomeDB.pm	Fri Aug 03 10:04:48 2012 -0400
@@ -0,0 +1,451 @@
+=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]>.
+
+=head1 NAME
+
+Bio::EnsEMBL::Compara::GenomeDB - DESCRIPTION of Object
+
+=head1 SYNOPSIS
+  use Bio::EnsEMBL::Compara::DnaFrag; 
+  my $genome_db = new Bio::EnsEMBL::Compara::GenomeDB();
+
+SET VALUES
+  $genome_db->dbID(22);
+  $genome_db->dba($dba);
+  $genome_db->name("Homo sapiens");
+  $genome_db->assembly("NCBI36");
+  $genome_db->taxon_id(9606);
+  $genome_db->taxon($taxon);
+  $genome_db->genebuild("2006-12-Ensembl");
+  $genome_db->assembly_default(1);
+  $genome_db->locator("Bio::EnsEMBL::DBSQL::DBAdaptor/host=???;port=???;user=???;dbname=homo_sapiens_core_51_36m;species=Homo sapiens;disconnect_when_inactive=1");
+
+GET VALUES
+  $dbID = $genome_db->dbID;
+  $genome_db_adaptor = $genome_db->adaptor;
+  $name = $genome_db->name;
+  $assembly = $genome_db->assembly;
+  $taxon_id = $genome_db->taxon_id;
+  $taxon = $genome_db->taxon;
+  $genebuild = $genome_db->genebuild;
+  $assembly_default = $genome_db->assembly_default;
+  $locator = $genome_db->locator;
+
+
+=head1 DESCRIPTION
+
+The GenomeDB object stores information about each species including the taxon_id, species name, assembly, genebuild and the location of the core database.
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::EnsEMBL::Compara::GenomeDB;
+
+use strict;
+
+use Bio::EnsEMBL::Utils::Exception qw(warning deprecate throw);
+use Bio::EnsEMBL::DBLoader;
+
+=head2 new
+
+  Example :
+    my $genome_db = new Bio::EnsEMBL::Compara::GenomeDB();
+    $genome_db->dba($dba);
+    $genome_db->name("Homo sapiens");
+    $genome_db->assembly("NCBI36");
+    $genome_db->taxon_id(9606);
+    $genome_db->dbID(22);
+    $genome_db->genebuild("2006-12-Ensembl");
+
+  Description: Creates a new GenomeDB object
+  Returntype : Bio::EnsEMBL::Compara::GenomeDB
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub new {
+  my($caller, $dba, $name, $assembly, $taxon_id, $dbID, $genebuild) = @_;
+
+  my $class = ref($caller) || $caller;
+  my $self = bless({}, $class);
+
+  $dba       && $self->db_adaptor($dba);
+  $name      && $self->name($name);
+  $assembly  && $self->assembly($assembly);
+  $taxon_id  && $self->taxon_id($taxon_id);
+  $dbID      && $self->dbID($dbID);
+  $genebuild && $self->genebuild($genebuild);
+
+  return $self;
+}
+
+=head2 new_fast
+
+  Arg [1]    : hash reference $hashref
+  Example    : 
+  Description: This is an ultra fast constructor which requires knowledge of
+               the objects internals to be used.
+  Returntype : Bio::EnsEMBL::Compara::GenomeDB
+  Exceptions : none
+  Caller     : Bio::EnsEMBL::Compara::DBSQL::GenomeDBAdaptor
+  Status     : Stable
+
+=cut
+
+sub new_fast {
+  my $class = shift;
+  my $hashref = shift;
+
+  return bless $hashref, $class;
+}
+
+
+=head2 db_adaptor
+
+  Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor $dba
+               The DBAdaptor containing sequence information for the genome
+               represented by this object.
+  Example    : $gdb->db_adaptor($dba);
+  Description: Getter/Setter for the DBAdaptor containing sequence 
+               information for the genome represented by this object.
+  Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub db_adaptor {
+    my ( $self, $dba ) = @_;
+
+    if($dba) {
+        $self->{'_db_adaptor'} = ($dba && $dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor'))
+            ? $dba
+            : undef;
+    }
+
+    unless($self->{'_db_adaptor'}) {
+        $self->{'_db_adaptor'} = $self->connect_to_genome_locator;
+    }
+
+    return $self->{'_db_adaptor'};
+}
+
+
+
+=head2 name
+
+  Arg [1]    : (optional) string $value
+  Example    : $gdb->name('Homo sapiens');
+  Description: Getter setter for the name of this genome database, usually
+               just the species name.
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub name{
+  my ($self,$value) = @_;
+
+  if( defined $value) {
+    $self->{'name'} = $value;
+  }
+  return $self->{'name'};
+}
+
+
+=head2 short_name
+
+  Example    : $gdb->short_name;
+  Description: The name of this genome in the Gspe ('G'enera
+               'spe'cies) format. Can also handle 'G'enera 's'pecies
+               's'ub 's'pecies (Gsss)
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub short_name {
+  my $self = shift;
+  my $name = $self->name;
+  $name =~ s/\b(\w)/\U$1/g;
+  $name =~ s/\_/\ /g;
+  unless( $name =~  s/(\S)\S*\s(\S)\S*\s(\S)\S*\s(\S).*/$1$2$3$4/ ){
+    unless( $name =~  s/(\S)\S*\s(\S)\S*\s(\S{2,2}).*/$1$2$3/ ){
+      unless( $name =~  s/(\S)\S*\s(\S{3,3}).*/$1$2/ ){
+        $name = substr( $name, 0, 4 );
+      }
+    }
+  }
+  return $name;
+}
+
+=head2 get_short_name
+
+  Example    : $gdb->get_short_name;
+  Description: The name of this genome in the Gspe ('G'enera
+               'spe'cies) format. Can also handle 'G'enera 's'pecies
+               's'ub 's'pecies (Gsss)
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub get_short_name {
+  my $self = shift;
+  return $self->short_name;
+}
+
+
+=head2 dbID
+
+  Arg [1]    : (optional) int $value the new value of this objects database 
+               identifier
+  Example    : $dbID = $genome_db->dbID;
+  Description: Getter/Setter for the internal identifier of this GenomeDB
+  Returntype : int
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub dbID{
+   my ($self,$value) = @_;
+   if( defined $value) {
+     $self->{'dbID'} = $value;
+   }
+   return $self->{'dbID'};
+}
+
+
+=head2 adaptor
+
+  Arg [1]    : (optional) Bio::EnsEMBL::Compara::GenomeDBAdaptor $adaptor
+  Example    : $adaptor = $GenomeDB->adaptor();
+  Description: Getter/Setter for the GenomeDB object adaptor used
+               by this GenomeDB for database interaction.
+  Returntype : Bio::EnsEMBL::Compara::GenomeDBAdaptor
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub adaptor{
+   my ($self,$value) = @_;
+   if( defined $value) {
+      $self->{'adaptor'} = $value;
+   }
+   return $self->{'adaptor'};
+}
+
+
+=head2 assembly
+
+  Arg [1]    : (optional) string
+  Example    : $gdb->assembly('NCBI36');
+  Description: Getter/Setter for the assembly type of this genome db.
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub assembly {
+  my $self = shift;
+  my $assembly = shift;
+
+  if($assembly) {
+    $self->{'assembly'} = $assembly;
+  }
+  return $self->{'assembly'};
+}
+
+=head2 assembly_default
+
+  Arg [1]    : (optional) int
+  Example    : $gdb->assembly_default(1);
+  Description: Getter/Setter for the assembly_default of this genome db.
+  Returntype : int
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub assembly_default {
+  my $self = shift;
+  my $boolean = shift;
+
+  if(defined $boolean) {
+    $self->{'assembly_default'} = $boolean;
+  }
+  $self->{'assembly_default'}='1' unless(defined($self->{'assembly_default'}));
+  return $self->{'assembly_default'};
+}
+
+=head2 genebuild
+
+  Arg [1]    : (optional) string
+  Example    : $gdb->genebuild('2006-12-Ensembl');
+  Description: Getter/Setter for the genebuild type of this genome db.
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub genebuild {
+  my $self = shift;
+  $self->{'genebuild'} = shift if (@_);
+  $self->{'genebuild'}='' unless(defined($self->{'genebuild'}));
+  return $self->{'genebuild'};
+}
+
+
+=head2 taxon_id
+
+  Arg [1]    : (optional) int
+  Example    : $gdb->taxon_id(9606);
+  Description: Getter/Setter for the taxon id of the contained genome db
+  Returntype : int
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub taxon_id {
+  my $self = shift;
+  my $taxon_id = shift;
+
+  if(defined $taxon_id) {
+    $self->{'taxon_id'} = $taxon_id;
+  }
+  return $self->{'taxon_id'};
+}
+
+=head2 taxon
+
+  Description: uses taxon_id to fetch the NCBITaxon object
+  Returntype : Bio::EnsEMBL::Compara::NCBITaxon object 
+  Exceptions : if taxon_id or adaptor not defined
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub taxon {
+  my $self = shift;
+
+  return $self->{'_taxon'} if(defined $self->{'_taxon'});
+
+  unless (defined $self->taxon_id and $self->adaptor) {
+    throw("can't fetch Taxon without a taxon_id and an adaptor");
+  }
+  my $ncbi_taxon_adaptor = $self->adaptor->db->get_NCBITaxonAdaptor;
+  $self->{'_taxon'} = $ncbi_taxon_adaptor->fetch_node_by_taxon_id($self->{'taxon_id'});
+  return $self->{'_taxon'};
+}
+
+
+=head2 locator
+
+  Arg [1]    : string
+  Description: Returns a string which describes where the external genome (ensembl core)
+               database base is located. Locator format is:
+               "Bio::EnsEMBL::DBSQL::DBAdaptor/host=ecs4port=3351;user=ensro;dbname=mus_musculus_core_20_32"
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub locator {
+  my $self = shift;
+  $self->{'locator'} = shift if (@_);
+  $self->{'locator'}='' unless(defined($self->{'locator'}));
+  return $self->{'locator'};
+}
+
+=head2 connect_to_genome_locator
+
+  Arg [1]    : string
+  Description: uses the locator string to connect to the external genome database
+  Returntype : DBConnection/DBAdaptor defined in locator string
+              (usually a Bio::EnsEMBL::DBSQL::DBAdaptor)
+              return undef if locator undefined or unable to connect
+  Exceptions : none
+  Caller     : internal private method 
+  Status     : Stable
+
+=cut
+
+sub connect_to_genome_locator {
+  my $self = shift;
+
+  return undef if($self->locator eq '');
+
+  my $genomeDBA = undef;
+  eval {$genomeDBA = Bio::EnsEMBL::DBLoader->new($self->locator); };
+  warn "The locator could not be loaded because: $@" if $@;
+  return $genomeDBA;
+}
+
+
+=head2 toString
+
+  Args       : (none)
+  Example    : print $dbID->toString()."\n";
+  Description: returns a stringified representation of the object
+  Returntype : string
+
+=cut
+
+sub toString {
+    my $self = shift;
+
+    return ref($self).": dbID=".($self->dbID || '?')
+        .", name='".$self->name
+        ."', assembly='".$self->assembly
+        ."', genebuild='".$self->genebuild
+        ."', taxon_id='".$self->taxon_id
+        ."', locator='".$self->locator
+        ."'";
+}
+
+
+1;