Raw content of Bio::EnsEMBL::Compara::DBSQL::DomainAdaptor
<![CDATA[#
# BioPerl module for Bio::EnsEMBL::Compara::DBSQL::DomainAdaptor
#
# Cared by Abel Ureta-Vidal <abel@ebi.ac.uk>
#
# Copyright EnsEMBL
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
DomainAdaptor
=head1 SYNOPSIS
use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
my $db = new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(-user => 'myusername',
-dbname => 'mycompra_db',
-host => 'myhost');
my $da = $famdb->get_DomainAdaptor;
my $dom = $da->fetch_by_stable_id('PR00262');
my $ma = $db->get_MemberAdaptor;
my $member = $ma->fetch_by_source_stable_id('SWISSPROT', 'YSV4_CAEEL')};
my @dom = @{$da->fetch_by_Member($member)};
@dom = @{$da->fetch_by_description_with_wildcards('interleukin',1)};
@dom = @{$da->fetch_all};
=head1 DESCRIPTION
This module is an entry point into a database of protein families,
clustering SWISSPROT/TREMBL and ensembl protein sets using the TRIBE MCL algorithm.
The clustering neatly follows the SWISSPROT DE-lines, which are
taken as the description of the whole family.
The objects can be read from and write to a compara database.
=head1 CONTACT
Abel Ureta-Vidal <abel@ebi.ac.uk>
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Compara::DBSQL::DomainAdaptor;
use strict;
use Bio::EnsEMBL::Compara::Domain;
use Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor;
our @ISA = qw(Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor);
=head2 fetch_by_Member
Arg [1] : string $dbname
Arg [2] : string $member_stable_id
Example : $fams = $FamilyAdaptor->fetch_of_source_stable_id('SPTR', 'P01235');
Description: find the family to which the given database and member_stable_id belong
Returntype : an array reference of Bio::EnsEMBL::Compara::Family objects
(could be empty or contain more than one Family in the case of ENSEMBLGENE only)
Exceptions : when missing arguments
Caller : general
=cut
sub fetch_by_Member {
my ($self, $member) = @_;
unless ($member->isa('Bio::EnsEMBL::Compara::Member')) {
$self->throw("The argument must be a Bio::EnsEMBL::Compara::Member object, not $member");
}
my $join = [[['domain_member', 'dm'], 'd.domain_id = dm.domain_id']];
my $constraint = "dm.member_id = " .$member->dbID;
return $self->generic_fetch($constraint, $join);
}
sub fetch_by_Member_Domain_source {
my ($self, $member, $source_name) = @_;
unless ($member->isa('Bio::EnsEMBL::Compara::Member')) {
$self->throw("The argument must be a Bio::EnsEMBL::Compara::Member object, not $member");
}
$self->throw("source_name arg is required\n")
unless ($source_name);
my $join = [[['domain_member', 'dm'], 'd.domain_id = dm.domain_id']];
my $constraint = "s.source_name = '$source_name'";
$constraint .= " AND dm.member_id = " . $member->dbID;
return $self->generic_fetch($constraint, $join);
}
=head2 fetch_by_description_with_wildcards
Arg [1] : string $description
Arg [2] : int $wildcard (optional)
if set to 1, wildcards are added and the search is a slower LIKE search
Example : $fams = $FamilyAdaptor->fetch_by_description_with_wildcards('REDUCTASE',1);
Description: simplistic substring searching on the description to get the families
matching the description. (The search is currently case-insensitive;
this may change if SPTR changes to case-preservation)
Returntype : an array reference of Bio::EnsEMBL::Compara::Family objects
Exceptions : none
Caller : general
=cut
sub fetch_by_description_with_wildcards{
my ($self,$desc,$wildcard) = @_;
my $constraint;
if ($wildcard) {
$constraint = "d.description LIKE '"."%"."\U$desc"."%"."'";
}
else {
$constraint = "d.description = '$desc'";
}
return $self->generic_fetch($constraint);
}
#
# INTERNAL METHODS
#
###################
# internal method used in multiple calls above to build domain objects from table data
sub _tables {
my $self = shift;
return (['domain', 'd'], ['source', 's']);
}
sub _columns {
my $self = shift;
return qw (d.domain_id
d.stable_id
d.description
s.source_id
s.source_name);
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my ($domain_id, $stable_id, $description, $source_id, $source_name);
$sth->bind_columns(\$domain_id, \$stable_id, \$description,
\$source_id, \$source_name);
my @domains = ();
while ($sth->fetch()) {
push @domains, Bio::EnsEMBL::Compara::Domain->new_fast
({'_dbID' => $domain_id,
'_stable_id' => $stable_id,
'_description' => $description,
'_source_id' => $source_id,
'_source_name' => $source_name,
'_adaptor' => $self});
}
return \@domains;
}
sub _default_where_clause {
my $self = shift;
return 'd.source_id = s.source_id';
}
#
# STORE METHODS
#
################
=head2 store
Arg [1] : Bio::EnsEMBL::ExternalData:Family::Family $fam
Example : $FamilyAdaptor->store($fam)
Description: Stores a family object into a family database
Returntype : int
been the database family identifier, if family stored correctly
Exceptions : when isa if Arg [1] is not Bio::EnsEMBL::Compara::Family
Caller : general
=cut
sub store {
my ($self,$dom) = @_;
$dom->isa('Bio::EnsEMBL::Compara::Domain') ||
$self->throw("You have to store a Bio::EnsEMBL::Compara::Domain object, not a $dom");
my $sql = "SELECT domain_id from domain where stable_id = ?";
my $sth = $self->prepare($sql);
$sth->execute($dom->stable_id);
my $rowhash = $sth->fetchrow_hashref;
$dom->source_id($self->store_source($dom->source_name));
if ($rowhash->{domain_id}) {
$dom->dbID($rowhash->{domain_id});
} else {
$sql = "INSERT INTO domain (stable_id, source_id, description) VALUES (?,?,?)";
$sth = $self->prepare($sql);
$sth->execute($dom->stable_id,$dom->source_id,$dom->description);
$dom->dbID($sth->{'mysql_insertid'});
}
foreach my $member_attribute (@{$dom->get_all_Member_Attribute}) {
$self->store_relation($member_attribute, $dom);
}
return $dom->dbID;
}
1;
]]>