Raw content of Bio::EnsEMBL::ExternalData::Expression::LibraryAdaptor
<![CDATA[#
# EnsEMBL module for Bio::EnsEMBL::ExternalData::Expression::ExpressionAdaptor
#
# Cared for by EnsEMBL (www.ensembl.org)
#
# Copyright GRL and EBI
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::ExternalData::Expression::LibraryAdaptor
=head1 SYNOPSIS
my $dbname='expression';
my $lib_ad=Bio::EnsEMBL::ExternalData::Expression::LibraryAdaptor->new($obj);
$lib_ad->dbname($dbname);
# pass in a list of synonyms
my @libs=$lib_ad->fetch_by_SeqTag_SynonymList("ENSG00000080561");
my @tgs=("AAAAAAAAAA","AAAAAAAAAC");
my @libs=$lib_ad->fetch_by_SeqTagList(@tgs);
=head1 DESCRIPTION
Represents information on one Clone
=head1 CONTACT
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::ExternalData::Expression::LibraryAdaptor;
use Bio::EnsEMBL::ExternalData::BaseAdaptor;
use Bio::EnsEMBL::ExternalData::Expression::Library;
use Bio::EnsEMBL::ExternalData::Expression::SeqTagAdaptor;
use vars qw(@ISA);
use strict;
@ISA = qw(Bio::EnsEMBL::ExternalData::BaseAdaptor);
# new in Bio::EnsEMBL::ExternalData::BaseAdaptor
=head2 fetch_all
Title : fetch_all
Usage : $obj->fetch_all
Function:
Example :
Returns : array of library objects
Args :
=cut
sub fetch_all {
my ($self)=shift;
my $statement="select library_id,source,cgap_id,
dbest_id,name,
tissue_type,description,total_seqtags
from library";
return $self->_fetch($statement);
}
=head2 fetch_by_dbID
Title : fetch_by_dbID
Usage : $obj->fetch_by_dbID
Function:
Example :
Returns : library object
Args :
=cut
sub fetch_by_dbID {
my ($self,$id)=@_;
$self->throw("need a library id") unless $id;
my $statement="select library_id,source,cgap_id,
dbest_id,name,
tissue_type,description,total_seqtags
from library where library.library_id=$id";
my @libs=$self->_fetch($statement);
if (defined $libs[0]){
return $libs[0];
}else{return;}
}
=head2 fetch_by_Name
Title : fetch_by_Name
Usage : $obj->fetch_by_Name
Function:
Example :
Returns : library object
Args :
=cut
sub fetch_by_Name {
my ($self,$name)=@_;
$self->throw("need a library name") unless $name;
my $statement="select library_id,source,cgap_id,
dbest_id,name,
tissue_type,description,total_seqtags
from library where library.name='$name'";
my @libs=$self->_fetch($statement);
if (defined $libs[0]){
return $libs[0];
}else{return;}
}
=head2 fetch_by_SeqTag_Name
Title : fetch_by_SeqTag_Name
Usage : $obj->fetch_by_SeqTag_Name
Function:
Example :
Returns : array of library objects
Args : seqtag name
=cut
sub fetch_by_SeqTag_Name {
my ($self,$name)=@_;
$self->throw("need a seqtag name") unless $name;
my $statement="select l.library_id,l.source,l.cgap_id,
l.dbest_id,l.name,
l.tissue_type,l.description,l.total_seqtags
from library l,seqtag_alias a,frequency f
where l.library_id=f.library_id
and f.seqtag_id=a.seqtag_id
and a.external_name='$name'";
return $self->_fetch($statement);
}
=head2 fetch_by_SeqTagList
Title : fetch_by_SeqTagList
Usage : $obj->fetch_by_SeqTagList
Function:
Example :
Returns : array of library objects
Args : array of seqtag names
=cut
sub fetch_by_SeqTagList {
my ($self,@seqtags)=@_;
$self->throw("need a seqtag name") unless @seqtags && $#seqtags>=0;
my $list=$self->_prepare_list(@seqtags);
my $statement="select l.library_id,l.source,l.cgap_id,
l.dbest_id,l.name,
l.tissue_type,l.description,l.total_seqtags
from library l,seqtag s,frequency f
where l.library_id=f.library_id
and f.seqtag_id=s.seqtag_id
and s.name in $list";
print "$statement\n";
return $self->_fetch($statement);
}
=head2 fetch_by_SeqTag_SynonymList
Title : fetch_by_SeqTag_SynonymList
Usage : $obj->fetch_by_SeqTag_SynonymList
Function:
Example :
Returns : array of library objects
Args : array of seqtag synonyms
=cut
sub fetch_by_SeqTag_SynonymList {
my ($self,@seqtags)=@_;
$self->throw("need a seqtag name") unless @seqtags && $#seqtags>=0;
my $list=$self->_prepare_list(@seqtags);
my $statement="select l.library_id,l.source,l.cgap_id,
l.dbest_id,l.name,
l.tissue_type,l.description,l.total_seqtags
from library l,seqtag_alias a,frequency f
where l.library_id=f.library_id
and f.seqtag_id=a.seqtag_id
and a.external_name in $list";
return $self->_fetch($statement);
}
=head2 fetch_SeqTag_by_dbID
Title : fetch_SeqTag_by_dbID
Usage : $obj->fetch_SeqTag_by_dbID
Function:
Example :
Returns : seqtag object
Args :
=cut
sub fetch_SeqTag_by_dbID {
my ($self,$library_id,$id)=@_;
$self->throw("need a library id") unless $library_id;
$self->throw("need a seqtag id") unless $id;
my $seqtag_ad=Bio::EnsEMBL::ExternalData::Expression::SeqTagAdaptor->new($self->db);
my $seqtag=$seqtag_ad->fetch_by_Library_dbID_SeqTag_dbID($library_id,$id);
if (defined $seqtag){
return $seqtag;
}else{
return;
}
}
=head2 fetch_SeqTag_by_Name
Title : fetch_SeqTag_by_Name
Usage : $obj->fetch_SeqTag_by_Name
Function:
Example :
Returns : seqtag object
Args :
=cut
sub fetch_SeqTag_by_Name {
my ($self,$library_id,$synonym)=@_;
$self->throw("need a library id") unless $library_id;
$self->throw("need a seqtag synonym") unless $synonym;
my $seqtag_ad=Bio::EnsEMBL::ExternalData::Expression::SeqTagAdaptor->new($self->db);
return $seqtag_ad->fetch_by_Name($library_id,$synonym);
}
=head2 fetch_all_SeqTags
Title : fetch_all_SeqTags
Usage : $obj->fetch_all_SeqTags
Function:
Example :
Returns : array of seqtags objects
Args :
=cut
sub fetch_all_SeqTags {
my ($self,$id)=@_;
$self->throw("need a library id") unless $id;
my $seqtag_ad=Bio::EnsEMBL::ExternalData::Expression::SeqTagAdaptor->new($self->db);
return $seqtag_ad->fetch_by_Library_dbID($id);
}
=head2 fetch_all_SeqTags_above_frequency
Title : fetch_all_SeqTags_above_frequency
Usage : $obj->fetch_all_SeqTags_above_frequency
Function: returns seqtags with expression above given level
Example :
Returns : array of seqtags objects
Args :
=cut
sub fetch_all_SeqTags_above_frequency {
my ($self,$id,$frequency)=@_;
$self->throw("need a library id") unless $id;
$self->throw("need a frequency value") unless $frequency;
my $seqtag_ad=Bio::EnsEMBL::ExternalData::Expression::SeqTagAdaptor->new($self->db);
return $seqtag_ad->fetch_by_Library_dbID_above_frequency($id,$frequency);
}
=head2 fetch_all_SeqTags_above_relative_frequency
Title : fetch_all_SeqTags_above_relative_frequency
Usage : $obj->fetch_all_SeqTags_above_realtive_frequency
Function: returns seqtags with expression above given level
Example :
Returns : array of seqtags objects
Args :
=cut
sub fetch_all_SeqTags_above_relative_frequency {
my ($self,$id,$frequency,$multiplier)=@_;
$self->throw("need a library id") unless $id;
$self->throw("need a frequency value") unless $frequency;
$multiplier=$self->multiplier unless $multiplier;
my $seqtag_ad=Bio::EnsEMBL::ExternalData::Expression::SeqTagAdaptor->new($self->db);
return $seqtag_ad->fetch_by_Library_dbID_above_relative_frequency($id,$frequency,$multiplier);
}
=head2 fetch_all_SeqTags_below_relative_frequency
Title : fetch_all_SeqTags_below_relative_frequency
Usage : $obj->fetch_all_SeqTags_below_realtive_frequency
Function: returns seqtags with expression below given level
Example :
Returns : array of seqtags objects
Args :
=cut
sub fetch_all_SeqTags_below_relative_frequency {
my ($self,$id,$frequency,$multiplier)=@_;
$self->throw("need a library id") unless $id;
$self->throw("need a frequency value") unless $frequency;
$multiplier=$self->multiplier unless $multiplier;
my $seqtag_ad=Bio::EnsEMBL::ExternalData::Expression::SeqTagAdaptor->new($self->db);
return $seqtag_ad->fetch_by_Library_dbID_below_relative_frequency($id,$frequency);
}
=head2 multiplier
Title : multiplier
Usage : $obj->multiplier($newval)
Function:
Example :
Returns : value of multiplier
Args : newvalue (optional)
=cut
sub multiplier {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_multiplier'} = $value;
} elsif (!defined$obj->{'_multiplier'}) {
$obj->{'_multiplier'}=1000000;
}
return $obj->{'_multiplier'};
}
sub _fetch {
my ($self,$statement)=@_;
my @libs;
my $sth = $self->prepare($statement);
$sth->execute();
my ($library_id,$source,$cgap_id,$dbest_id,
$name,$tissue_type,$description, $total_seqtags);
$sth->bind_columns(undef,\$library_id,\$source,\$cgap_id,\$dbest_id,
\$name,\$tissue_type,\$description,\$total_seqtags);
while ($sth->fetch){
my @args=($library_id,$source,$cgap_id,$dbest_id,$name,$tissue_type,$description,$total_seqtags);
push @libs,Bio::EnsEMBL::ExternalData::Expression::Library->new($self,@args);
}
return @libs;
}
sub _prepare_list {
my ($self,@ids)=@_;
my $string;
foreach my $id(@ids){
$string .= $id . "\',\'";
}
$string="\'".$string;
chop $string;
chop $string;
if ($string) { $string = "($string)";}
return $string;
}
]]>