Raw content of Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor
<![CDATA[package Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor;
use strict;
use Bio::EnsEMBL::Compara::Homology;
use Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor;
use Bio::EnsEMBL::Utils::Exception;
our @ISA = qw(Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor);
=head2 fetch_by_Member
DEPRECATED: use fetch_all_by_Member instead
=cut
sub fetch_by_Member {
my ($self, @args) = @_;
return $self->fetch_all_by_Member(@args);
}
=head2 fetch_all_by_Member
Arg [1] : Bio::EnsEMBL::Compara::Member $member
Example : $homologies = $HomologyAdaptor->fetch_all_by_Member($member);
Description: fetch the homology relationships where the given member is implicated
Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
Exceptions : none
Caller : general
=cut
sub fetch_all_by_Member {
my ($self, $member) = @_;
my $join = [[['homology_member', 'hm'], 'h.homology_id = hm.homology_id']];
my $constraint = "hm.member_id = " .$member->dbID;
# This internal variable is used by add_Member_Attribute method
# in Bio::EnsEMBL::Compara::BaseRelation to make sure that the first element
# of the member array is the one that has been used by the user to fetch the
# homology object
$self->{'_this_one_first'} = $member->stable_id;
return $self->generic_fetch($constraint, $join);
}
=head2 fetch_by_Member_paired_species
DEPRECATED: use fetch_all_by_Member_paired_species instead
=cut
sub fetch_by_Member_paired_species {
my ($self, @args) = @_;
return $self->fetch_all_by_Member_paired_species(@args);
}
=head2 fetch_all_by_Member_paired_species
Arg [1] : Bio::EnsEMBL::Compara::Member $member
Arg [2] : string $species
e.g. "Mus_musculus" or "Mus musculus"
Arg [3] : (optional) an arrayref of method_link types
e.g. ['ENSEMBL_ORTHOLOGUES']. Default is ['ENSEMBL_ORTHOLOGUES','ENSEMBL_PARALOGUES']
Example : $homologies = $HomologyAdaptor->fetch_all_by_Member_paired_species($member, "Mus_musculus");
Description: fetch the homology relationships where the given member is implicated
in pair with another member from the paired species. Member species and
paired species should be different.
When you give the species name the method attempts to find
the species without _ subsitution and then replacing them
for spaces. This is to help support GenomeDB objects which
have _ in their names.
Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
Exceptions : If a GenomeDB cannot be found for the given species name
Caller :
=cut
sub fetch_all_by_Member_paired_species {
my ($self, $member, $species, $method_link_types) = @_;
my $gdb_a = $self->db->get_GenomeDBAdaptor();
my $gdb1 = $member->genome_db;
my $gdb2 = eval {$gdb_a->fetch_by_name_assembly($species)};
if(!defined $gdb2) {
my $species_no_underscores = $species;
$species_no_underscores =~ tr/_/ /;
$gdb2 = eval {$gdb_a->fetch_by_name_assembly($species_no_underscores)};
if(!defined $gdb2) {
throw("No GenomeDB found with names [$species | $species_no_underscores]");
}
}
unless (defined $method_link_types) {
$method_link_types = ['ENSEMBL_ORTHOLOGUES','ENSEMBL_PARALOGUES'];
}
my $mlssa = $self->db->get_MethodLinkSpeciesSetAdaptor;
my $all_homologies = [];
foreach my $ml (@{$method_link_types}) {
my $mlss;
if ($gdb1->dbID == $gdb2->dbID) {
next if ($ml eq 'ENSEMBL_ORTHOLOGUES');
$mlss = $mlssa->fetch_by_method_link_type_GenomeDBs($ml, [$gdb1]);
} else {
$mlss = $mlssa->fetch_by_method_link_type_GenomeDBs($ml, [$gdb1, $gdb2]);
}
if (defined $mlss) {
my $homologies = $self->fetch_all_by_Member_MethodLinkSpeciesSet($member, $mlss);
push @{$all_homologies}, @{$homologies} if (defined $homologies);
}
}
return $all_homologies;
}
=head2 fetch_all_by_Member_method_link_type
Arg [1] : Bio::EnsEMBL::Compara::Member $member
Arg [2] : string $method_link_type
Example : $homologies = $HomologyAdaptor->fetch_all_by_Member_method_link_type(
$member, "ENSEMBL_ORTHOLOGUES");
Description: fetch the homology relationships where the given member is implicated
in a relationship of the type defined by $method_link_type.
Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
Exceptions : none
Caller :
=cut
sub fetch_all_by_Member_method_link_type {
my ($self, $member, $method_link_type) = @_;
unless ($member->isa('Bio::EnsEMBL::Compara::Member')) {
throw("The argument must be a Bio::EnsEMBL::Compara::Member object, not $member");
}
unless ($member->genome_db_id) {
warning("Cannot get Homologues for a Bio::EnsEMBL::Compara::Member (".$member->source_name.
"::".$member->stable_id.") with no GenomeDB");
return [];
}
throw("method_link_type arg is required\n")
unless ($method_link_type);
my $mlssa = $self->db->get_MethodLinkSpeciesSetAdaptor;
my $mlss_arrayref = $mlssa->fetch_all_by_method_link_type_GenomeDB($method_link_type,$member->genome_db);
unless (scalar @{$mlss_arrayref}) {
warning("There is no $method_link_type data stored in the database for " . $member->genome_db->name . "\n");
return [];
}
my $join = [[['homology_member', 'hm'], 'h.homology_id = hm.homology_id']];
my $constraint = " h.method_link_species_set_id in (". join (",", (map {$_->dbID} @{$mlss_arrayref})) . ")";
$constraint .= " AND hm.member_id = " . $member->dbID;
# See in fetch_by_Member what is this internal variable for
$self->{'_this_one_first'} = $member->stable_id;
return $self->generic_fetch($constraint, $join);
}
=head2 fetch_all_by_Member_MethodLinkSpeciesSet
Arg [1] : Bio::EnsEMBL::Compara::Member $member
Arg [2] : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $mlss
Example : $homologies = $HomologyAdaptor->fetch_all_by_Member_MethodLinkSpeciesSet($member, $mlsss);
Description: fetch the homology relationships for a given $member and $mlss.
Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
Exceptions : none
Caller :
=cut
sub fetch_all_by_Member_MethodLinkSpeciesSet {
my ($self, $member, $method_link_species_set) = @_;
unless ($member->isa('Bio::EnsEMBL::Compara::Member')) {
throw("The argument must be a Bio::EnsEMBL::Compara::Member object, not $member");
}
throw("method_link_species_set arg is required\n")
unless ($method_link_species_set);
# my $mlssa = $self->db->get_MethodLinkSpeciesSetAdaptor;
# my $mlss_arrayref = $mlssa->fetch_all_by_method_link_type_genome_db_id($method_link_type,$member->genome_db_id);
# unless (scalar @{$mlss_arrayref}) {
# warning("There is no $method_link_type data stored in the database for " . $member->genome_db->name . "\n");
# return [];
# }
my $join = [[['homology_member', 'hm'], 'h.homology_id = hm.homology_id']];
my $constraint = " h.method_link_species_set_id =" . $method_link_species_set->dbID;
$constraint .= " AND hm.member_id = " . $member->dbID;
# See in fetch_by_Member what is this internal variable for
$self->{'_this_one_first'} = $member->stable_id;
return $self->generic_fetch($constraint, $join);
}
=head2 fetch_by_Member_Member_method_link_type
Arg [1] : Bio::EnsEMBL::Compara::Member $member
Arg [2] : Bio::EnsEMBL::Compara::Member $member
Arg [3] : string $method_link_type
Example : $homologies = $HomologyAdaptor->fetch_by_Member_Member_method_link_type(
$member1->gene_member, $member2->gene_member, "ENSEMBL_ORTHOLOGUES");
Description: fetch the homology relationships where the given member pair is implicated
in a relationship of the type defined by $method_link_type.
Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
Exceptions : none
Caller :
=cut
sub fetch_by_Member_Member_method_link_type {
my ($self, $member1, $member2, $method_link_type) = @_;
unless ($member1->stable_id ne $member2->stable_id) {
throw("The members should be different");
}
unless ($member1->isa('Bio::EnsEMBL::Compara::Member')) {
throw("The argument must be a Bio::EnsEMBL::Compara::Member object, not $member1");
}
unless ($member2->isa('Bio::EnsEMBL::Compara::Member')) {
throw("The argument must be a Bio::EnsEMBL::Compara::Member object, not $member2");
}
$method_link_type = 'ENSEMBL_ORTHOLOGUES' unless (defined($method_link_type));
my $genome_dbs = [$member1->genome_db, $member2->genome_db];
if ($member1->genome_db_id == $member2->genome_db_id) {
$method_link_type = 'ENSEMBL_PARALOGUES';
$genome_dbs = [$member1->genome_db];
}
my $mlssa = $self->db->get_MethodLinkSpeciesSetAdaptor;
my $mlss = $mlssa->fetch_by_method_link_type_GenomeDBs($method_link_type,$genome_dbs);
unless (defined($mlss)) {
warning("There is no $method_link_type data stored in the database for " . $member1->genome_db->name . " and " . $member2->genome_db->name . "\n");
return [];
}
# my $join = [[['homology_member', 'hm'], 'h.homology_id = hm.homology_id']];
my $join = [[['homology_member', 'hm1'], 'h.homology_id = hm1.homology_id'],[['homology_member', 'hm2'], 'h.homology_id = hm2.homology_id']];
my $constraint = " h.method_link_species_set_id =" . $mlss->dbID;
$constraint .= " AND hm1.member_id = " . $member1->dbID;
$constraint .= " AND hm2.member_id = " . $member2->dbID;
# $constraint .= " AND hm1.member_id<hm2.member_id ";
# See in fetch_by_Member what is this internal variable for
$self->{'_this_one_first'} = $member1->stable_id;
return $self->generic_fetch($constraint, $join);
}
=head2 fetch_by_Member_id_Member_id
Arg [1] : int $member_id1
Arg [2] : int $member_id2
Example : $homologies = $HomologyAdaptor->fetch_by_Member_id_Member_id(
$member_id1, $member_id2);
Description: fetch the homology relationships for a given member_id pair
Returntype : a Bio::EnsEMBL::Compara::Homology object
Exceptions : none
Caller :
=cut
sub fetch_by_Member_id_Member_id {
my ($self, $member_id1, $member_id2) = @_;
unless ($member_id1 ne $member_id2) {
throw("The members should be different");
}
my $join = [[['homology_member', 'hm1'], 'h.homology_id = hm1.homology_id'],[['homology_member', 'hm2'], 'h.homology_id = hm2.homology_id']];
my $constraint .= " hm1.member_id = " . $member_id1;
$constraint .= " AND hm2.member_id = " . $member_id2;
# See in fetch_by_Member what is this internal variable for
$self->{'_this_one_first'} = $member_id1;
return $self->generic_fetch($constraint, $join);
}
=head2 fetch_all_by_MethodLinkSpeciesSet
Arg [1] : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $mlss
Example : $homologies = $HomologyAdaptor->fetch_all_by_MethodLinkSpeciesSet($mlss);
Description: fetch all the homology relationships for the given MethodLinkSpeciesSet
Since each species pair Orthologue analysis is given a unique
MethodLinkSpeciesSet, this method can be used to grab all the
orthologues for a species pair.
Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
Exceptions : none
Caller :
=cut
sub fetch_all_by_MethodLinkSpeciesSet {
my ($self, $method_link_species_set) = @_;
throw("method_link_species_set arg is required\n")
unless ($method_link_species_set);
my $constraint = " h.method_link_species_set_id =" . $method_link_species_set->dbID;
return $self->generic_fetch($constraint);
}
=head2 fetch_all_by_tree_node_id
Arg [1] : int $tree_node_id
Example : $homologies = $HomologyAdaptor->fetch_all_by_tree_node_id($tree->node_id);
Description: fetch all the homology relationships for the given tree
Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
Exceptions : none
Caller :
=cut
sub fetch_all_by_tree_node_id {
my ($self, $tree_node_id) = @_;
throw("tree_node_id arg is required\n")
unless ($tree_node_id);
my $constraint = " h.tree_node_id =" . $tree_node_id;
return $self->generic_fetch($constraint);
}
=head2 fetch_all_by_genome_pair
Arg [1] : genome_db_id
Arg [2] : genome_db_id
Example : $homologies = $HomologyAdaptor->fetch_all_by_genome_pair(22,3);
Description: fetch all the homology relationships for the a pair of genome_db_ids
This method can be used to grab all the orthologues for a species pair.
Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
Exceptions : none
Caller :
=cut
sub fetch_all_by_genome_pair {
my ($self, $genome_db_id1, $genome_db_id2) = @_;
my $join = [ [['homology_member', 'hm1'], 'h.homology_id = hm1.homology_id'],
[['member', 'm1'], 'hm1.member_id = m1.member_id'],
[['homology_member', 'hm2'], 'h.homology_id = hm2.homology_id'],
[['member', 'm2'], 'hm2.member_id = m2.member_id'],
];
my $constraint = "m1.genome_db_id= $genome_db_id1";
$constraint .= " AND m2.genome_db_id = $genome_db_id2";
$self->{'_this_one_first'} = undef; #not relevant
return $self->generic_fetch($constraint, $join);
}
=head2 fetch_all_by_MethodLinkSpeciesSet_orthology_type
Arg [1] : method_link_species_set
Arg [2] : orthology type
Example : $homologies = $HomologyAdaptor->
fetch_all_by_MethodLinkSpeciesSet_orthology_type(
$mlss, 'ortholog_one2one');
Description: fetch all the homology relationships for the given
orthology type and for a mlss (corresponding to one or
a pair of genomes). This method can be used to grab all
the orthologues for one genome paralogues or a species
pair and an orthology type.
Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
Exceptions : none
Caller :
=cut
sub fetch_all_by_MethodLinkSpeciesSet_orthology_type {
my ($self, $method_link_species_set, $orthology_type) = @_;
throw ("method_link_species_set arg is required\n")
unless ($method_link_species_set);
throw ("[$method_link_species_set] must be a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object\n")
unless (UNIVERSAL::isa($method_link_species_set, "Bio::EnsEMBL::Compara::MethodLinkSpeciesSet"));
throw ("orthology_type arg is required\n")
unless ($orthology_type);
my $constraint = " h.method_link_species_set_id =" . $method_link_species_set->dbID;
$constraint .= " AND h.description=\"$orthology_type\"";
$self->{'_this_one_first'} = undef; #not relevant
return $self->generic_fetch($constraint);
}
=head2 fetch_all_by_MethodLinkSpeciesSet_orthology_type_subtype
Arg [1] : method_link_species_set
Arg [2] : orthology type
Arg [3] : orthology subtype
Example : $homologies = $HomologyAdaptor->
fetch_all_by_MethodLinkSpeciesSet_orthology_type_subtype(
$mlss, 'ortholog_one2one','Mammalia');
Description: fetch all the homology relationships for the given
orthology type, mlss (corresponding to one or
a pair of genomes) and subtype (taxonomy level). This method can be
used to grab all the orthologues for one genome paralogues or a species
pair and an orthology type and taxonomy level.
Returntype : an array reference of Bio::EnsEMBL::Compara::Homology objects
Exceptions : none
Caller :
=cut
sub fetch_all_by_MethodLinkSpeciesSet_orthology_type_subtype {
my ($self, $method_link_species_set, $orthology_type, $subtype) = @_;
throw ("method_link_species_set arg is required\n")
unless ($method_link_species_set);
throw ("[$method_link_species_set] must be a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object\n")
unless (UNIVERSAL::isa($method_link_species_set, "Bio::EnsEMBL::Compara::MethodLinkSpeciesSet"));
throw ("orthology_type arg is required\n")
unless ($orthology_type);
my $constraint = " h.method_link_species_set_id =" . $method_link_species_set->dbID;
$constraint .= " AND h.description=\"$orthology_type\"";
$constraint .= " AND h.subtype=\"$subtype\"";
$self->{'_this_one_first'} = undef; #not relevant
return $self->generic_fetch($constraint);
}
=head2 fetch_orthocluster_with_Member
Arg [1] : Bio::EnsEMBL::Compara::Member $gene_member (must be ENSEMBLGENE type)
Example : my ($homology_list, $gene_list) =
$HomologyAdaptor->fetch_orthocluster_with_Member($gene_member);
Description: do a recursive search starting from $gene_member to find the cluster of
all connected genes and homologies via connected components clustering.
Returntype : an array pair of array references.
First array_ref is the list of Homology objects in the cluster graph
Second array ref is the list of unique gene Members in the cluster
Exceptions : none
Caller :
=cut
sub fetch_orthocluster_with_Member {
my $self = shift;
my $gene_member = shift;
my $ortho_set = {};
my $member_set = {};
$self->_recursive_get_orthocluster($gene_member, $ortho_set, $member_set, 0);
my @homologies = values(%{$ortho_set});
my @genes = values(%{$member_set});
return (\@homologies, \@genes);
}
sub _recursive_get_orthocluster {
my $self = shift;
my $gene = shift;
my $ortho_set = shift;
my $member_set = shift;
my $debug = shift;
return if($member_set->{$gene->dbID});
$gene->print_member("query gene\n") if($debug);
$member_set->{$gene->dbID} = $gene;
my $homologies = $self->fetch_by_Member($gene);
printf("fetched %d homologies\n", scalar(@$homologies)) if($debug);
foreach my $homology (@{$homologies}) {
next if($ortho_set->{$homology->dbID});
foreach my $member_attribute (@{$homology->get_all_Member_Attribute}) {
my ($member, $attribute) = @{$member_attribute};
next if($member->dbID == $gene->dbID); #skip query gene
$member->print_member if($debug);
printf("adding homology_id %d to cluster\n", $homology->dbID) if($debug);
$ortho_set->{$homology->dbID} = $homology;
$self->_recursive_get_orthocluster($member, $ortho_set, $member_set, $debug);
}
}
printf("done with search query %s\n", $gene->stable_id) if($debug);
}
#
# internal methods
#
###################
# internal methods used in multiple calls above to build homology objects from table data
sub _tables {
my $self = shift;
return (['homology', 'h']);
}
sub _columns {
my $self = shift;
return qw (h.homology_id
h.stable_id
h.method_link_species_set_id
h.description
h.subtype
h.dn
h.ds
h.n
h.s
h.lnl
h.threshold_on_ds
h.ancestor_node_id
h.tree_node_id);
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my ($homology_id, $stable_id, $description, $dn, $ds, $n, $s, $lnl, $threshold_on_ds,
$method_link_species_set_id, $subtype, $ancestor_node_id, $tree_node_id);
$sth->bind_columns(\$homology_id, \$stable_id, \$method_link_species_set_id,
\$description, \$subtype, \$dn, \$ds,
\$n, \$s, \$lnl, \$threshold_on_ds, \$ancestor_node_id, \$tree_node_id);
my @homologies = ();
while ($sth->fetch()) {
push @homologies, Bio::EnsEMBL::Compara::Homology->new_fast
({'_dbID' => $homology_id,
'_stable_id' => $stable_id,
'_description' => $description,
'_method_link_species_set_id' => $method_link_species_set_id,
'_subtype' => $subtype,
'_dn' => $dn,
'_ds' => $ds,
'_n' => $n,
'_s' => $s,
'_lnl' => $lnl,
'_threshold_on_ds' => $threshold_on_ds,
'_adaptor' => $self,
'_this_one_first' => $self->{'_this_one_first'},
'_ancestor_node_id' => $ancestor_node_id,
'_tree_node_id' => $tree_node_id});
}
return \@homologies;
}
sub _default_where_clause {
my $self = shift;
return '';
}
#
# STORE METHODS
#
################
=head2 store
Arg [1] : Bio::EnsEMBL::Compara::Homology $homology
Example : $HomologyAdaptor->store($homology)
Description: Stores a homology object into a compara database
Returntype : int
been the database homology identifier, if homology stored correctly
Exceptions : when isa if Arg [1] is not Bio::EnsEMBL::Compara::Homology
Caller : general
=cut
sub store {
my ($self,$hom) = @_;
$hom->isa('Bio::EnsEMBL::Compara::Homology') ||
throw("You have to store a Bio::EnsEMBL::Compara::Homology object, not a $hom");
$hom->adaptor($self);
if ( !defined $hom->method_link_species_set_id && defined $hom->method_link_species_set) {
$self->db->get_MethodLinkSpeciesSetAdaptor->store($hom->method_link_species_set);
}
if (! defined $hom->method_link_species_set) {
throw("Homology object has no set MethodLinkSpecies object. Can not store Homology object\n");
} else {
$hom->method_link_species_set_id($hom->method_link_species_set->dbID);
}
unless($hom->dbID) {
my $sql = "INSERT INTO homology (stable_id, method_link_species_set_id, description, subtype, ancestor_node_id, tree_node_id) VALUES (?,?,?,?,?,?)";
my $sth = $self->prepare($sql);
$sth->execute($hom->stable_id,$hom->method_link_species_set_id,$hom->description, $hom->subtype, $hom->ancestor_node_id, $hom->tree_node_id);
$hom->dbID($sth->{'mysql_insertid'});
}
foreach my $member_attribute (@{$hom->get_all_Member_Attribute}) {
$self->store_relation($member_attribute, $hom);
}
return $hom->dbID;
}
=head2 update_genetic_distance
Arg [1] : Bio::EnsEMBL::Compara::Homology $homology
Example : $HomologyAdaptor->update_genetic_distance($homology)
Description: updates the n,s,dn,ds,lnl values from a homology object into a compara database
Exceptions : when isa if Arg [1] is not Bio::EnsEMBL::Compara::Homology
Caller : Bio::EnsEMBL::Compara::Runnable::Homology_dNdS
=cut
sub update_genetic_distance {
my $self = shift;
my $hom = shift;
throw("You have to store a Bio::EnsEMBL::Compara::Homology object, not a $hom")
unless($hom->isa('Bio::EnsEMBL::Compara::Homology'));
throw("homology object must have dbID")
unless ($hom->dbID);
# We use here internal hash key for _dn and _ds because the dn and ds method call
# do some filtering based on the threshold_on_ds.
unless(defined $hom->{'_dn'} and defined $hom->{'_ds'} and defined $hom->n and defined $hom->lnl and defined $hom->s) {
warn("homology needs valid dn, ds, n, s, and lnl values to store");
return $self;
}
my $sql = "UPDATE homology SET dn=?, ds=?, n=?, s=?, lnl=?";
if (defined $hom->threshold_on_ds) {
$sql .= ", threshold_on_ds=?";
}
$sql .= " WHERE homology_id=?";
my $sth = $self->prepare($sql);
if (defined $hom->threshold_on_ds) {
$sth->execute($hom->{'_dn'},$hom->{'_ds'},$hom->n, $hom->s, $hom->lnl, $hom->threshold_on_ds, $hom->dbID);
} else {
$sth->execute($hom->{'_dn'},$hom->{'_ds'},$hom->n, $hom->s, $hom->lnl, $hom->dbID);
}
$sth->finish();
return $self;
}
=head2 fetch_all_orphans_by_GenomeDB
Arg [1] : Bio::EnsEMBL::Compara::GenomeDB $genome_db
Example : $HomologyAdaptor->fetch_all_orphans_by_GenomeDB($genome_db);
Description: fetch the members for a genome_db that have no homologs in the database
Returntype : an array reference of Bio::EnsEMBL::Compara::Member objects
Exceptions : when isa if Arg [1] is not Bio::EnsEMBL::Compara::GenomeDB
Caller : general
=cut
sub fetch_all_orphans_by_GenomeDB {
my $self = shift;
my $gdb = shift;
throw("genome_db arg is required\n")
unless ($gdb);
my $gdb_id = $gdb->dbID;
my $sql = "SELECT m.member_id from member m LEFT JOIN homology_member hm ON m.member_id=hm.member_id WHERE m.source_name='ENSEMBLGENE' AND m.genome_db_id=$gdb_id AND hm.member_id IS NULL";
my $sth = $self->dbc->prepare($sql);
$sth->execute();
my $ma = $self->db->get_MemberAdaptor;
my @members;
while ( my $member_id = $sth->fetchrow ) {
my $member = $ma->fetch_by_dbID($member_id);
push @members, $member;
}
return \@members;
}
# DEPRECATED METHODS
####################
sub fetch_by_Member_Homology_source {
my ($self, $member, $source_name) = @_;
deprecate("fetch_by_Member_Homology_source method is deprecated. Calling
fetch_all_by_Member_method_link_type instead");
return $self->fetch_all_by_Member_method_link_type($member, $source_name);
}
1;
]]>