From b66689ef0eb6c03d7cc623c04ae035b8f2c67f9b Mon Sep 17 00:00:00 2001
From: Patrick Meidl <pm2@sanger.ac.uk>
Date: Thu, 8 Jun 2006 11:18:06 +0000
Subject: [PATCH] fixed sql bug in fetch_by_transcript_archive_id()
---
.../EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm | 1 +
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm | 93 +-
modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm | 140 +--
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 965 +++++++++---------
.../Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm | 746 +++++++-------
5 files changed, 1021 insertions(+), 924 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
index 2ff810f49e..2ae6606ce9 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
@@ -319,6 +319,7 @@ sub fetch_by_transcript_archive_id {
FROM gene_archive ga, mapping_session m
WHERE ga.transcript_stable_id = ?
AND ga.transcript_version = ?
+ AND ga.mapping_session_id = m.mapping_session_id
);
my $sth = $self->prepare( $sql );
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index bc5b3e5e79..d5ea2cf749 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -113,7 +113,6 @@ sub fetch_by_dbID {
}
-
=head2 fetch_by_db_accession
Arg [1] : string $dbname - The name of the database which the provided
@@ -471,7 +470,6 @@ sub exists {
}
-
=head2 fetch_all_by_Gene
Arg [1] : Bio::EnsEMBL::Gene $gene
@@ -812,7 +810,7 @@ sub _fetch_by_object_type {
sub list_gene_ids_by_extids{
my ($self,$name) = @_;
- my %T = map { ($_,1) }
+ my %T = map { ($_, 1) }
$self->_type_by_external_id( $name, 'Translation', 'gene' ),
$self->_type_by_external_id( $name, 'Transcript', 'gene' ),
$self->_type_by_external_id( $name, 'Gene' );
@@ -820,7 +818,6 @@ sub list_gene_ids_by_extids{
}
-
=head2 list_transcript_ids_by_extids
Arg [1] : string $external_id
@@ -839,7 +836,7 @@ sub list_transcript_ids_by_extids{
my ($self,$name) = @_;
my @transcripts;
- my %T = map { ($_,1) }
+ my %T = map { ($_, 1) }
$self->_type_by_external_id( $name, 'Translation', 'transcript' ),
$self->_type_by_external_id( $name, 'Transcript' );
return keys %T;
@@ -860,63 +857,82 @@ sub list_transcript_ids_by_extids{
sub list_translation_ids_by_extids{
my ($self,$name) = @_;
- return $self->_type_by_external_id( $name, 'Translation' );
+ return $self->_type_by_external_id($name, 'Translation');
}
=head2 _type_by_external_id
- Arg [1] : string $name
- (dbprimary_acc)
- Arg [2] : string $ensType
- (Object_type)
- Arg [3] : string $extraType
- (other object type to be returned) - optional
- Example : $self->_type_by_external_id( $name, 'Translation' )
+ Arg [1] : string $name - dbprimary_acc
+ Arg [2] : string $ensType - ensembl_object_type
+ Arg [3] : (optional) string $extraType
+ other object type to be returned
+ Example : $self->_type_by_external_id($name, 'Translation');
Description: Gets
- Returntype : list of ensembl_IDs
+ Returntype : list of dbIDs (gene_id, transcript_id, etc.)
Exceptions : none
Caller : list_translation_ids_by_extids
translationids_by_extids
- geneids_by_extids
+ geneids_by_extids
Status : Stable
=cut
sub _type_by_external_id{
- my ($self,$name,$ensType,$extraType) = @_;
+ my ($self, $name, $ensType, $extraType) = @_;
my $from_sql = '';
my $where_sql = '';
my $ID_sql = "oxr.ensembl_id";
- if(defined $extraType) {
- if(lc($extraType) eq 'translation') {
+
+ if (defined $extraType) {
+ if (lc($extraType) eq 'translation') {
$ID_sql = "tl.translation_id";
} else {
$ID_sql = "t.${extraType}_id";
}
- if(lc($ensType) eq 'translation') {
- $from_sql = 'transcript as t, translation as tl, ';
- $where_sql = 't.transcript_id = tl.transcript_id and ' .
- 'tl.translation_id = oxr.ensembl_id and ';
+ if (lc($ensType) eq 'translation') {
+ $from_sql = 'transcript t, translation tl, ';
+ $where_sql = qq(
+ t.transcript_id = tl.transcript_id AND
+ tl.translation_id = oxr.ensembl_id AND
+ t.is_current = 1 AND
+ );
} else {
- $from_sql = 'transcript as t, ';
- $where_sql = 't.'.lc($ensType).'_id = oxr.ensembl_id and ';
+ $from_sql = 'transcript t, ';
+ $where_sql = 't.'.lc($ensType).'_id = oxr.ensembl_id AND '.
+ 't.is_current = 1 AND ';
}
}
+
+ if (lc($ensType) eq 'gene') {
+ $from_sql = 'gene g, ';
+ $where_sql = 'g.gene_id = oxr.ensembl_id AND g.is_current = 1 AND ';
+ } elsif (lc($ensType) eq 'transcript') {
+ $from_sql = 'transcript t, ';
+ $where_sql = 't.transcript_id = oxr.ensembl_id AND t.is_current = 1 AND ';
+ } elsif (lc($ensType) eq 'translation') {
+ $from_sql = 'transcript t, translation tl, ';
+ $where_sql = qq(
+ t.transcript_id = tl.transcript_id AND
+ tl.translation_id = oxr.ensembl_id AND
+ t.is_current = 1 AND
+ );
+ }
+
my @queries = (
- "select $ID_sql
- from $from_sql xref, object_xref as oxr
- where $where_sql xref.dbprimary_acc = ? and
- xref.xref_id = oxr.xref_id and oxr.ensembl_object_type= ?",
- "select $ID_sql
- from $from_sql xref, object_xref as oxr
- where $where_sql xref.display_label = ? and
- xref.xref_id = oxr.xref_id and oxr.ensembl_object_type= ?",
- "select $ID_sql
- from $from_sql object_xref as oxr, external_synonym as syn
- where $where_sql syn.synonym = ? and
- syn.xref_id = oxr.xref_id and oxr.ensembl_object_type= ?",
+ "SELECT $ID_sql
+ FROM $from_sql xref x, object_xref oxr
+ WHERE $where_sql x.dbprimary_acc = ? AND
+ x.xref_id = oxr.xref_id AND oxr.ensembl_object_type= ?",
+ "SELECT $ID_sql
+ FROM $from_sql xref x, object_xref oxr
+ WHERE $where_sql x.display_label = ? AND
+ x.xref_id = oxr.xref_id AND oxr.ensembl_object_type= ?",
+ "SELECT $ID_sql
+ FROM $from_sql object_xref oxr, external_synonym syn
+ WHERE $where_sql syn.synonym = ? AND
+ syn.xref_id = oxr.xref_id AND oxr.ensembl_object_type= ?",
);
# Increase speed of query by splitting the OR in query into three separate
@@ -929,8 +945,8 @@ sub _type_by_external_id{
foreach( @queries ) {
my $sth = $self->prepare( $_ );
- $sth->bind_param(1,"$name",SQL_VARCHAR);
- $sth->bind_param(2,$ensType,SQL_VARCHAR);
+ $sth->bind_param(1, $name, SQL_VARCHAR);
+ $sth->bind_param(2, $ensType, SQL_VARCHAR);
$sth->execute();
while( my $r = $sth->fetchrow_array() ) {
if( !exists $hash{$r} ) {
@@ -942,6 +958,7 @@ sub _type_by_external_id{
return @result;
}
+
=head2 fetch_all_by_description
Arg [1] : string description to search for. Include % etc in this string
diff --git a/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
index a56bc3898d..66c0552ad2 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
@@ -1,3 +1,5 @@
+package Bio::EnsEMBL::DBSQL::ExonAdaptor;
+
#EnsEMBL Exon reading writing adaptor for mySQL
#
# Copyright EMBL-EBI 2001
@@ -33,20 +35,16 @@ Post questions/comments to the Ensembl dev list: ensembl-dev@ebi.ac.uk
=cut
-package Bio::EnsEMBL::DBSQL::ExonAdaptor;
-
-use vars qw( @ISA );
use strict;
-
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::Exon;
use Bio::EnsEMBL::Utils::Exception qw( warning throw deprecate );
+use vars qw( @ISA );
@ISA = qw( Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor );
-
#_tables
#
# Arg [1] : none
@@ -82,22 +80,18 @@ sub _columns {
my $created_date = $self->db->dbc->from_date_to_seconds("created_date");
my $modified_date = $self->db->dbc->from_date_to_seconds("modified_date");
- return ( 'e.exon_id', 'e.seq_region_id', 'e.seq_region_start' ,'e.seq_region_end',
- 'e.seq_region_strand', 'e.phase','e.end_phase',
- 'esi.stable_id', 'esi.version',$created_date,
- $modified_date );
-# esi.stable_id esi.version UNIX_TIMESTAMP(created_date)
-# UNIX_TIMESTAMP(modified_date) );
+ return ( 'e.exon_id', 'e.seq_region_id', 'e.seq_region_start',
+ 'e.seq_region_end', 'e.seq_region_strand', 'e.phase','e.end_phase',
+ 'e.is_current',
+ 'esi.stable_id', 'esi.version', $created_date, $modified_date );
}
-
sub _left_join {
return ( [ 'exon_stable_id', "esi.exon_id = e.exon_id" ]);
}
-
# _final_clause
#
# Arg [1] : none
@@ -114,14 +108,13 @@ sub _final_clause {
}
-
=head2 fetch_by_stable_id
Arg [1] : string $stable_id
the stable id of the exon to retrieve
Example : $exon = $exon_adaptor->fetch_by_stable_id('ENSE0000988221');
Description: Retrieves an Exon from the database via its stable id
- Returntype : Bio::EnsEMBL::Exon in contig coordinates
+ Returntype : Bio::EnsEMBL::Exon in native coordinates.
Exceptions : none
Caller : general
Status : Stable
@@ -129,16 +122,36 @@ sub _final_clause {
=cut
sub fetch_by_stable_id {
- my ( $self, $stable_id ) = @_;
+ my ($self, $stable_id) = @_;
+
+ my $constraint = "esi.stable_id = '$stable_id' AND e.is_current = 1";
+ my ($exon) = @{ $self->generic_fetch($constraint) };
+
+ return $exon;
+}
+
- my $constraint = "esi.stable_id = \"$stable_id\"";
+=head2 fetch_all_versions_by_stable_id
- # should be only one :-)
- my $exons = $self->SUPER::generic_fetch( $constraint );
+ Arg [1] : String $stable_id
+ The stable ID of the exon to retrieve
+ Example : my $exon = $exon_adaptor->fetch_all_version_by_stable_id
+ ('ENSE00000309301');
+ Description : Similar to fetch_by_stable_id, but retrieves all versions of an
+ exon stored in the database.
+ Returntype : listref of Bio::EnsEMBL::Exon objects
+ Exceptions : if we cant get the gene in given coord system
+ Caller : general
+ Status : At Risk
+
+=cut
- if( ! @$exons ) { return undef }
+sub fetch_all_versions_by_stable_id {
+ my ($self, $stable_id) = @_;
- return $exons->[0];
+ my $constraint = "esi.stable_id = '$stable_id'";
+
+ return $self->generic_fetch($constraint);
}
@@ -175,14 +188,13 @@ sub fetch_all_by_Transcript {
$self->{'tables'} = \@tables;
$self->{'final_clause'} = "ORDER BY et.transcript_id, et.rank";
-
my $constraint = "et.transcript_id = ".$transcript->dbID() .
" AND e.exon_id = et.exon_id";
# fetch all of the exons
- my $exons = $self->fetch_all_by_Slice_constraint($slice,$constraint);
+ my $exons = $self->fetch_all_by_Slice_constraint($slice, $constraint);
- #un-override the table definition
+ # un-override the table definition
$self->{'tables'} = undef;
$self->{'final_clause'} = undef;
@@ -199,7 +211,6 @@ sub fetch_all_by_Transcript {
}
-
=head2 store
Arg [1] : Bio::EnsEMBL::Exon $exon
@@ -216,7 +227,7 @@ sub fetch_all_by_Transcript {
=cut
sub store {
- my ( $self, $exon ) = @_;
+ my ($self, $exon) = @_;
if( ! $exon->isa('Bio::EnsEMBL::Exon') ) {
throw("$exon is not a EnsEMBL exon - not storing.");
@@ -233,11 +244,15 @@ sub store {
throw("Exon does not have all attributes to store");
}
+ # default to is_current = 1 if this attribute is not set
+ my $is_current = $exon->is_current;
+ $is_current = 1 unless (defined($is_current));
+
my $exon_sql = q{
INSERT into exon ( seq_region_id, seq_region_start,
seq_region_end, seq_region_strand, phase,
- end_phase )
- VALUES ( ?, ?, ?, ?, ?, ? )
+ end_phase, is_current )
+ VALUES ( ?, ?, ?, ?, ?, ?, ? )
};
my $exonst = $self->prepare($exon_sql);
@@ -249,12 +264,13 @@ sub store {
($exon, $seq_region_id) = $self->_pre_store($exon);
#store the exon
- $exonst->bind_param(1,$seq_region_id, SQL_INTEGER);
- $exonst->bind_param(2,$exon->start, SQL_INTEGER);
- $exonst->bind_param(3,$exon->end, SQL_INTEGER);
- $exonst->bind_param(4,$exon->strand, SQL_TINYINT);
- $exonst->bind_param(5,$exon->phase, SQL_TINYINT);
- $exonst->bind_param(6,$exon->end_phase, SQL_TINYINT);
+ $exonst->bind_param(1, $seq_region_id, SQL_INTEGER);
+ $exonst->bind_param(2, $exon->start, SQL_INTEGER);
+ $exonst->bind_param(3, $exon->end, SQL_INTEGER);
+ $exonst->bind_param(4, $exon->strand, SQL_TINYINT);
+ $exonst->bind_param(5, $exon->phase, SQL_TINYINT);
+ $exonst->bind_param(6, $exon->end_phase, SQL_TINYINT);
+ $exonst->bind_param(7, $is_current, SQL_TINYINT);
$exonst->execute();
$exonId = $exonst->{'mysql_insertid'};
@@ -268,18 +284,10 @@ sub store {
"stable_id = ?, " .
"exon_id = ?, ";
- $statement .= "created_date = " . $self->db->dbc->from_seconds_to_date($exon->created_date()) . ",";
-# if( $exon->created_date() ) {
-# $statement .= "created_date = from_unixtime( ".$exon->created_date()."),";
-# } else {
-# $statement .= "created_date = \"0000-00-00 00:00:00\",";
-# }
- $statement .= "modified_date = " . $self->db->dbc->from_seconds_to_date($exon->modified_date()) ;
-# if( $exon->modified_date() ) {
-# $statement .= "modified_date = from_unixtime( ".$exon->modified_date().")";
-# } else {
-# $statement .= "modified_date = \"0000-00-00 00:00:00\"";
-# }
+ $statement .= "created_date = " .
+ $self->db->dbc->from_seconds_to_date($exon->created_date()) . ",";
+ $statement .= "modified_date = " .
+ $self->db->dbc->from_seconds_to_date($exon->modified_date()) ;
my $sth = $self->prepare( $statement );
@@ -319,9 +327,9 @@ sub store {
next;
}
- $sf_sth->bind_param(1,$exonId,SQL_INTEGER);
- $sf_sth->bind_param(2,$sf->dbID,SQL_INTEGER);
- $sf_sth->bind_param(3,$type,SQL_VARCHAR);
+ $sf_sth->bind_param(1, $exonId, SQL_INTEGER);
+ $sf_sth->bind_param(2, $sf->dbID, SQL_INTEGER);
+ $sf_sth->bind_param(3, $type, SQL_VARCHAR);
$sf_sth->execute();
}
@@ -382,7 +390,7 @@ sub remove {
my $sth = $self->prepare("SELECT feature_type, feature_id " .
"FROM supporting_feature " .
"WHERE exon_id = ?");
- $sth->bind_param(1,$exon->dbID,SQL_INTEGER);
+ $sth->bind_param(1, $exon->dbID, SQL_INTEGER);
$sth->execute();
while(my ($type, $feature_id) = $sth->fetchrow()){
@@ -403,21 +411,21 @@ sub remove {
# delete the association to supporting features
$sth = $self->prepare("DELETE FROM supporting_feature WHERE exon_id = ?");
- $sth->bind_param(1,$exon->dbID,SQL_INTEGER);
+ $sth->bind_param(1, $exon->dbID, SQL_INTEGER);
$sth->execute();
$sth->finish();
# delete the exon stable identifier
$sth = $self->prepare( "DELETE FROM exon_stable_id WHERE exon_id = ?" );
- $sth->bind_param(1,$exon->dbID,SQL_INTEGER);
+ $sth->bind_param(1, $exon->dbID, SQL_INTEGER);
$sth->execute();
$sth->finish();
# delete the exon
$sth = $self->prepare( "DELETE FROM exon WHERE exon_id = ?" );
- $sth->bind_param(1,$exon->dbID,SQL_INTEGER);
+ $sth->bind_param(1, $exon->dbID, SQL_INTEGER);
$sth->execute();
$sth->finish();
@@ -446,6 +454,7 @@ sub list_dbIDs {
return $self->_list_dbIDs("exon");
}
+
=head2 list_stable_ids
Arg [1] : none
@@ -492,14 +501,13 @@ sub _objs_from_sth {
my ( $exon_id, $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand, $phase,
- $end_phase, $stable_id, $version, $created_date,
+ $end_phase, $is_current, $stable_id, $version, $created_date,
$modified_date );
- $sth->bind_columns( \$exon_id, \$seq_region_id,
- \$seq_region_start,
- \$seq_region_end, \$seq_region_strand, \$phase,
- \$end_phase, \$stable_id, \$version, \$created_date,
- \$modified_date );
+ $sth->bind_columns( \$exon_id, \$seq_region_id, \$seq_region_start,
+ \$seq_region_end, \$seq_region_strand, \$phase,
+ \$end_phase, \$is_current, \$stable_id, \$version,
+ \$created_date, \$modified_date );
my $asm_cs;
my $cmp_cs;
@@ -611,8 +619,8 @@ sub _objs_from_sth {
}
#finally, create the new repeat feature
- push @exons, Bio::EnsEMBL::Exon->new
- ( '-start' => $seq_region_start,
+ push @exons, Bio::EnsEMBL::Exon->new(
+ '-start' => $seq_region_start,
'-end' => $seq_region_end,
'-strand' => $seq_region_strand,
'-adaptor' => $self,
@@ -623,7 +631,9 @@ sub _objs_from_sth {
'-created_date' => $created_date || undef,
'-modified_date' => $modified_date || undef,
'-phase' => $phase,
- '-end_phase' => $end_phase )
+ '-end_phase' => $end_phase,
+ 'is_current' => $is_current
+ );
}
@@ -663,7 +673,7 @@ sub get_stable_entry_info {
FROM exon_stable_id
WHERE exon_id = ");
- $sth->bind_param(1,$exon->dbID,SQL_INTEGER);
+ $sth->bind_param(1, $exon->dbID, SQL_INTEGER);
$sth->execute();
# my @array = $sth->fetchrow_array();
@@ -677,6 +687,7 @@ sub get_stable_entry_info {
return 1;
}
+
=head2 fetch_all_by_gene_id
Description: DEPRECATED. This method should not be needed - Exons can
@@ -695,7 +706,9 @@ sub fetch_all_by_gene_id {
if( !$gene_id ) {
$self->throw("Gene dbID not defined");
}
+
$self->{rchash} = {};
+
my $query = qq {
SELECT
STRAIGHT_JOIN
@@ -740,3 +753,4 @@ sub fetch_all_by_gene_id {
1;
+
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index a428da13b6..500556e94b 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -1,25 +1,17 @@
-#
-# Copyright EMBL-EBI 2001
-#
-# Author: Arne Stabenau
-# based on
-# Elia Stupkas Gene_Obj
-#
-# Date : 20.02.2001
-#
+package Bio::EnsEMBL::DBSQL::GeneAdaptor;
=head1 NAME
-Bio::EnsEMBL::DBSQL::GeneAdaptor - A database aware adaptor responsible for the
-retrieval and storage of Gene objects.
+Bio::EnsEMBL::DBSQL::GeneAdaptor - Database adaptor for the retrieval and
+storage of Gene objects
=head1 SYNOPSIS
use Bio::EnsEMBL::DBSQL::DBAdaptor;
- $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
+ $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
- $gene_adaptor = $db->get_GeneAdaptor();
+ $gene_adaptor = $dba->get_GeneAdaptor();
$gene = $gene_adaptor->fetch_by_dbID(1234);
@@ -31,24 +23,30 @@ retrieval and storage of Gene objects.
$slice = $slice_adaptor->fetch_by_region('chromosome', '1', 1, 1000000);
@genes = @{$gene_adaptor->fetch_all_by_Slice($slice)};
+=head1 DESCRIPTION
-=head1 CONTACT
+This is a database aware adaptor for the retrieval and storage of gene objects.
-Contact the EnsEMBL development list for questions or information:
-ensembl-dev@ebi.ac.uk
+=head1 LICENCE
-=head1 METHODS
+This code is distributed under an Apache style licence. Please see
+http://www.ensembl.org/info/about/code_licence.html for details.
-=cut
+=head1 AUTHOR
+Arne Stabenau <stabenau@ebi.ac.uk>, Ensembl core API team
+Based on Elia Stupkas Gene_Obj
-package Bio::EnsEMBL::DBSQL::GeneAdaptor;
+=head1 CONTACT
-use strict;
+Please post comments/questions to the Ensembl development list
+<ensembl-dev@ebi.ac.uk>
+=cut
-use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
+use strict;
+use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::DBSQL::SliceAdaptor;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
@@ -58,11 +56,10 @@ use vars '@ISA';
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
-
# _tables
# Arg [1] : none
-# Description: PROTECTED implementation of superclass abstract method
-# returns the names, aliases of the tables to use for queries
+# Description: PROTECTED implementation of superclass abstract method.
+# Returns the names, aliases of the tables to use for queries.
# Returntype : list of listrefs of strings
# Exceptions : none
# Caller : internal
@@ -81,8 +78,8 @@ sub _tables {
# _columns
# Arg [1] : none
# Example : none
-# Description: PROTECTED implementation of superclass abstract method
-# returns a list of columns to use for queries
+# Description: PROTECTED implementation of superclass abstract method.
+# Returns a list of columns to use for queries.
# Returntype : list of strings
# Exceptions : none
# Caller : internal
@@ -93,14 +90,15 @@ sub _columns {
my $created_date = $self->db->dbc->from_date_to_seconds("gsi.created_date");
my $modified_date = $self->db->dbc->from_date_to_seconds("gsi.modified_date");
- return ( 'g.gene_id', 'g.seq_region_id', 'g.seq_region_start', 'g.seq_region_end',
- 'g.seq_region_strand', 'g.analysis_id' ,'g.biotype', 'g.display_xref_id',
- 'g.description', 'g.status', 'g.source',
- 'gsi.stable_id', 'gsi.version', $created_date,
- $modified_date,
+
+ return ( 'g.gene_id', 'g.seq_region_id', 'g.seq_region_start',
+ 'g.seq_region_end', 'g.seq_region_strand',
+ 'g.analysis_id' ,'g.biotype', 'g.display_xref_id',
+ 'g.description', 'g.status', 'g.source', 'g.is_current',
+ 'gsi.stable_id', 'gsi.version', $created_date, $modified_date,
'x.display_label' ,'x.dbprimary_acc', 'x.description', 'x.version',
- 'exdb.db_name', 'exdb.status', 'exdb.db_release' ,'exdb.db_display_name',
- 'x.info_type', 'x.info_text');
+ 'exdb.db_name', 'exdb.status', 'exdb.db_release',
+ 'exdb.db_display_name', 'x.info_type', 'x.info_text');
}
@@ -111,15 +109,13 @@ sub _left_join {
}
-
=head2 list_dbIDs
- Arg [1] : none
Example : @gene_ids = @{$gene_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all genes in the current db
- Returntype : list of ints
+ Returntype : Listref of Ints
Exceptions : none
- Caller : ?
+ Caller : general
Status : Stable
=cut
@@ -130,14 +126,14 @@ sub list_dbIDs {
return $self->_list_dbIDs("gene");
}
+
=head2 list_stable_ids
- Arg [1] : none
Example : @stable_gene_ids = @{$gene_adaptor->list_stable_dbIDs()};
Description: Gets an listref of stable ids for all genes in the current db
Returntype : reference to a list of strings
Exceptions : none
- Caller : ?
+ Caller : general
Status : Stable
=cut
@@ -151,10 +147,11 @@ sub list_stable_ids {
=head2 fetch_by_display_label
- Arg [1] : string $label
- Example : my $gene = $geneAdaptor->fetch_by_display_label( "BRCA2" );
- Description: returns the gene which has the given display label or undef if
- there is none. If there are more than 1, only the first is reported.
+ Arg [1] : String $label - display label of gene to fetch
+ Example : my $gene = $geneAdaptor->fetch_by_display_label("BRCA2");
+ Description: Returns the gene which has the given display label or undef if
+ there is none. If there are more than 1, only the first is
+ reported.
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
Caller : general
@@ -166,7 +163,9 @@ sub fetch_by_display_label {
my $self = shift;
my $label = shift;
- my ( $gene ) = @{$self->generic_fetch( "x.display_label = \"$label\"" )};
+ my $constraint = "x.display_label = '$label' AND g.is_current = 1";
+ my ($gene) = @{ $self->generic_fetch($constraint) };
+
return $gene;
}
@@ -174,16 +173,16 @@ sub fetch_by_display_label {
=head2 fetch_by_stable_id
- Arg 1 : string $id
- The stable id of the gene to retrieve
+ Arg [1] : String $id
+ The stable ID of the gene to retrieve
Example : $gene = $gene_adaptor->fetch_by_stable_id('ENSG00000148944');
Description: Retrieves a gene object from the database via its stable id.
The gene will be retrieved in its native coordinate system (i.e.
- in the coordinate system it is stored in the database). It may
+ in the coordinate system it is stored in the database). It may
be converted to a different coordinate system through a call to
- transform() or transfer(). If the gene or exon is not found
+ transform() or transfer(). If the gene or exon is not found
undef is returned instead.
- Returntype : Bio::EnsEMBL::Gene in given coordinate system
+ Returntype : Bio::EnsEMBL::Gene or undef
Exceptions : if we cant get the gene in given coord system
Caller : general
Status : Stable
@@ -191,80 +190,96 @@ sub fetch_by_display_label {
=cut
sub fetch_by_stable_id {
- my ($self,$id) = @_;
+ my ($self, $stable_id) = @_;
- #because of the way this query is constructed (with a left join to the
- # gene_stable_id table), it is faster to do 2 queries, getting the gene_id
- # in the first query
+ my $constraint = "gsi.stable_id = '$stable_id' AND g.is_current = 1";
+ my ($gene) = @{ $self->generic_fetch($constraint) };
- my $sth = $self->prepare("SELECT gene_id from gene_stable_id " .
- "WHERE stable_id = ?");
- $sth->bind_param(1,$id,SQL_VARCHAR);
- $sth->execute();
+ return $gene;
+}
- my ($dbID) = $sth->fetchrow_array();
- $sth->finish;
+=head2 fetch_all_versions_by_stable_id
- return undef if(!$dbID);
+ Arg [1] : String $stable_id
+ The stable ID of the gene to retrieve
+ Example : $gene = $gene_adaptor->fetch_all_versions_by_stable_id
+ ('ENSG00000148944');
+ Description : Similar to fetch_by_stable_id, but retrieves all versions of a
+ gene stored in the database.
+ Returntype : listref of Bio::EnsEMBL::Gene
+ Exceptions : if we cant get the gene in given coord system
+ Caller : general
+ Status : At Risk
- return $self->fetch_by_dbID($dbID);
- }
+=cut
+
+sub fetch_all_versions_by_stable_id {
+ my ($self, $stable_id) = @_;
+
+ my $constraint = "gsi.stable_id = '$stable_id'";
+
+ return $self->generic_fetch($constraint);
+}
=head2 fetch_by_exon_stable_id
- Arg [1] : string $id
+ Arg [1] : String $id
The stable id of an exon of the gene to retrieve
Example : $gene = $gene_adptr->fetch_by_exon_stable_id('ENSE00000148944');
Description: Retrieves a gene object from the database via an exon stable id.
The gene will be retrieved in its native coordinate system (i.e.
- in the coordinate system it is stored in the database). It may
+ in the coordinate system it is stored in the database). It may
be converted to a different coordinate system through a call to
- transform() or transfer(). If the gene or exon is not found
+ transform() or transfer(). If the gene or exon is not found
undef is returned instead.
- Returntype : Bio::EnsEMBL::Gene (or undef)
+ Returntype : Bio::EnsEMBL::Gene or undef
Exceptions : none
Caller : general
Status : Stable
=cut
-sub fetch_by_exon_stable_id{
- my ( $self, $id ) = @_;
-
- my $sth = $self->prepare(
- "SELECT t.gene_id
+sub fetch_by_exon_stable_id {
+ my ($self, $stable_id, $version) = @_;
+
+ my $sql = qq(
+ SELECT t.gene_id
FROM transcript as t,
exon_transcript as et,
+ exon as e,
exon_stable_id as esi
WHERE t.transcript_id = et.transcript_id
AND et.exon_id = esi.exon_id
- AND esi.stable_id = ?");
- $sth->bind_param(1,"$id",SQL_VARCHAR);
- $sth->execute();
+ AND et.exon_id = e.exon_id
+ AND esi.stable_id = ?
+ AND e.is_current = 1
+ );
- my ($dbID) = $sth->fetchrow_array();
-
- return undef if(!defined($dbID));
+ my $sth = $self->prepare($sql);
+ $sth->bind_param(1, $stable_id, SQL_VARCHAR);
+ $sth->execute();
- my $gene = $self->fetch_by_dbID( $dbID );
+ my ($dbID) = $sth->fetchrow_array();
- return $gene;
-}
+ return undef if(!defined($dbID));
+ my $gene = $self->fetch_by_dbID($dbID);
+ return $gene;
+}
=head2 fetch_all_by_domain
- Arg [1] : string $domain
- the domain to fetch genes from
+ Arg [1] : String $domain
+ The domain to fetch genes from
Example : my @genes = $gene_adaptor->fetch_all_by_domain($domain);
- Description: retrieves a listref of genes whose translation contain interpro
- domain $domain. The genes are returned in their native coord
+ Description: Retrieves a listref of genes whose translation contain interpro
+ domain $domain. The genes are returned in their native coord
system (i.e. the coord_system they are stored in). If the coord
- system needs to be changed, then tranform
- or transfer should be called on the individual objects returned.
+ system needs to be changed, then tranform or transfer should be
+ called on the individual objects returned.
Returntype : list of Bio::EnsEMBL::Genes
Exceptions : none
Caller : domainview
@@ -275,22 +290,23 @@ sub fetch_by_exon_stable_id{
sub fetch_all_by_domain {
my ($self, $domain) = @_;
- unless($domain) {
- throw("domain argument is required");
- }
-
- my $sth = $self->prepare("SELECT tr.gene_id " .
- "FROM interpro i, " .
- " protein_feature pf, " .
- " transcript tr, " .
- " translation tl " .
- "WHERE i.interpro_ac = ? " .
- "AND i.id = pf.hit_id " .
- "AND pf.translation_id = tl.translation_id ".
- "AND tr.transcript_id = tl.transcript_id " .
- "GROUP BY tr.gene_id");
-
- $sth->bind_param(1,$domain,SQL_VARCHAR);
+ throw("domain argument is required") unless ($domain);
+
+ my $sth = $self->prepare(qq(
+ SELECT tr.gene_id
+ FROM interpro i,
+ protein_feature pf,
+ transcript tr,
+ translation tl
+ WHERE i.interpro_ac = ?
+ AND i.id = pf.hit_id
+ AND pf.translation_id = tl.translation_id
+ AND tr.transcript_id = tl.transcript_id
+ AND tr.is_current = 1
+ GROUP BY tr.gene_id
+ ));
+
+ $sth->bind_param(1, $domain, SQL_VARCHAR);
$sth->execute();
my @array = @{$sth->fetchall_arrayref()};
@@ -328,12 +344,13 @@ sub fetch_all_by_Slice {
my $self = shift;
my $slice = shift;
my $logic_name = shift;
- my $load_exons = shift;
+ my $load_transcripts = shift;
- my $genes = $self->SUPER::fetch_all_by_Slice($slice, $logic_name);
+ my $genes = $self->SUPER::fetch_all_by_Slice_constraint($slice,
+ 'g.is_current = 1', $logic_name);
# if there are 0 or 1 genes still do lazy-loading
- if(!$load_exons || @$genes < 2) {
+ if(!$load_transcripts || @$genes < 2) {
return $genes;
}
@@ -390,7 +407,7 @@ sub fetch_all_by_Slice {
$sth->finish();
my $ta = $self->db()->get_TranscriptAdaptor();
- my $transcripts = $ta->fetch_all_by_Slice($ext_slice,1);
+ my $transcripts = $ta->fetch_all_by_Slice($ext_slice, 1);
# move transcripts onto gene slice, and add them to genes
foreach my $tr (@$transcripts) {
@@ -416,119 +433,117 @@ sub fetch_all_by_Slice {
}
-
-
-
-
=head2 fetch_by_transcript_id
- Arg [1] : int $transid
- unique database identifier for the transcript whose gene should
+ Arg [1] : Int $trans_id
+ Unique database identifier for the transcript whose gene should
be retrieved. The gene is returned in its native coord
system (i.e. the coord_system it is stored in). If the coord
system needs to be changed, then tranform or transfer should
- be called on the returned object. undef is returned if the
+ be called on the returned object. undef is returned if the
gene or transcript is not found in the database.
- Example : $gene = $gene_adaptor->fetch_by_transcript_id( 1241 );
+ Example : $gene = $gene_adaptor->fetch_by_transcript_id(1241);
Description: Retrieves a gene from the database via the database identifier
of one of its transcripts.
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
- Caller : ?
+ Caller : general
Status : Stable
=cut
sub fetch_by_transcript_id {
- my ( $self, $trans_id ) = @_;
+ my ($self, $trans_id) = @_;
- # this is a cheap SQL call
- my $sth = $self->prepare("SELECT tr.gene_id " .
- "FROM transcript as tr " .
- "WHERE tr.transcript_id = ?");
- $sth->bind_param(1,$trans_id,SQL_INTEGER);
- $sth->execute();
+ # this is a cheap SQL call
+ my $sth = $self->prepare(qq(
+ SELECT tr.gene_id
+ FROM transcript tr
+ WHERE tr.transcript_id = ?
+ ));
- my ($geneid) = $sth->fetchrow_array();
+ $sth->bind_param(1, $trans_id, SQL_INTEGER);
+ $sth->execute();
- $sth->finish();
+ my ($geneid) = $sth->fetchrow_array();
- return undef if( !defined $geneid );
+ $sth->finish();
- my $gene = $self->fetch_by_dbID( $geneid );
- return $gene;
+ return undef if( !defined $geneid );
+
+ my $gene = $self->fetch_by_dbID($geneid);
+ return $gene;
}
=head2 fetch_by_transcript_stable_id
- Arg [1] : string $transid
- unique database identifier for the transcript whose gene should
- be retrieved.
- Example : none
- Description: Retrieves a gene from the database via the database identifier
- of one of its transcripts
+ Arg [1] : string $trans_stable_id
+ transcript stable ID whose gene should be retrieved
+ Example : my $gene = $gene_adaptor->fetch_by_transcript_stable_id
+ ('ENST0000234');
+ Description: Retrieves a gene from the database via the stable ID of one of
+ its transcripts
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
- Caller : ?
+ Caller : general
Status : Stable
=cut
sub fetch_by_transcript_stable_id {
- my ( $self, $trans_stable_id) = @_;
-
- # this is a cheap SQL call
- my $sth = $self->prepare(
- "SELECT tr.gene_id " .
- "FROM transcript as tr, transcript_stable_id tcl " .
- "WHERE tcl.stable_id = ? " .
- "AND tr.transcript_id = tcl.transcript_id");
- $sth->bind_param(1,"$trans_stable_id",SQL_VARCHAR);
+ my ($self, $trans_stable_id) = @_;
+
+ my $sth = $self->prepare(qq(
+ SELECT tr.gene_id
+ FROM transcript tr, transcript_stable_id tcl
+ WHERE tcl.stable_id = ?
+ AND tr.transcript_id = tcl.transcript_id
+ AND tr.is_current = 1
+ ));
+
+ $sth->bind_param(1, $trans_stable_id, SQL_VARCHAR);
$sth->execute();
my ($geneid) = $sth->fetchrow_array();
$sth->finish;
- if( !defined $geneid ) {
- return undef;
- }
- my $gene = $self->fetch_by_dbID( $geneid );
+
+ return undef if (!defined $geneid);
+
+ my $gene = $self->fetch_by_dbID($geneid);
return $gene;
}
-
-
-
=head2 fetch_by_translation_stable_id
- Arg [1] : string $translation_stable_id
- the stable id of a translation of the gene that should
- be obtained
- Example : $gene = $gene_adaptor->fetch_by_translation_stable_id
- ( 'ENSP00000278194' );
- Description: retrieves a gene via the stable id of one of its translations.
+ Arg [1] : String $translation_stable_id
+ The stable id of a translation of the gene to be obtained
+ Example : my $gene = $gene_adaptor->fetch_by_translation_stable_id
+ ('ENSP00000278194');
+ Description: Retrieves a gene via the stable id of one of its translations.
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
- Caller : geneview
+ Caller : general
Status : Stable
=cut
sub fetch_by_translation_stable_id {
- my ( $self, $translation_stable_id ) = @_;
-
- # this is a cheap SQL call
- my $sth = $self->prepare
- ("SELECT tr.gene_id " .
- "FROM transcript as tr, " .
- " translation as tl, " .
- " translation_stable_id as trs " .
- "WHERE trs.stable_id = ? " .
- "AND trs.translation_id = tl.translation_id " .
- "AND tr.transcript_id = tl.transcript_id");
-
- $sth->bind_param(1,"$translation_stable_id",SQL_VARCHAR);
+ my ($self, $translation_stable_id) = @_;
+
+ my $sth = $self->prepare(qq(
+ SELECT tr.gene_id
+ FROM transcript tr,
+ translation tl,
+ translation_stable_id as trs
+ WHERE trs.stable_id = ?
+ AND trs.translation_id = tl.translation_id
+ AND tr.transcript_id = tl.transcript_id
+ AND tr.is_current = 1
+ ));
+
+ $sth->bind_param(1, $translation_stable_id, SQL_VARCHAR);
$sth->execute();
my ($geneid) = $sth->fetchrow_array();
@@ -540,32 +555,31 @@ sub fetch_by_translation_stable_id {
}
-
=head2 fetch_all_by_external_name
- Arg [1] : string $external_id
- the external identifier for the gene to be obtained
+ Arg [1] : String $external_id
+ The external identifier for the gene to be obtained
Example : @genes = @{$gene_adaptor->fetch_all_by_external_name('BRCA2')}
- Description: retrieves a list of genes with an external database
- idenitifier $external_id. The genes returned are in their
- native coordinate system. I.e. in the coordinate system they
- are stored in the database in. If another coordinate system
+ Description: Retrieves a list of genes with an external database
+ idenitifier $external_id. The genes returned are in their
+ native coordinate system. I.e. in the coordinate system they
+ are stored in the database in. If another coordinate system
is required then the Gene::transfer or Gene::transform method
can be used.
Returntype : listref of Bio::EnsEMBL::Genes
Exceptions : none
- Caller : goview
+ Caller : goview, general
Status : Stable
=cut
sub fetch_all_by_external_name {
- my ( $self, $external_id) = @_;
+ my ($self, $external_id) = @_;
my $entryAdaptor = $self->db->get_DBEntryAdaptor();
- my ( @ids, @result );
- @ids = $entryAdaptor->list_gene_ids_by_extids( $external_id );
+ my (@ids, @result);
+ @ids = $entryAdaptor->list_gene_ids_by_extids($external_id);
my $genes = $self->fetch_all_by_dbID_list(\@ids);
@@ -576,20 +590,20 @@ sub fetch_all_by_external_name {
}
-
=head2 fetch_all_alt_alleles
Arg [1] : Bio::EnsEMBL::Gene $gene
- Example : my @alt_genes = @{$gene_adaptor->fetch_all_alt_alleles($gene);}
+ The gene to fetch alternative alleles for
+ Example : my @alt_genes = @{ $gene_adaptor->fetch_all_alt_alleles($gene) };
foreach my $alt_gene (@alt_genes) {
print "Alternate allele: " . $alt_gene->stable_id() . "\n";
}
Description: Retrieves genes which are alternate alleles to a provided gene.
Alternate alleles in Ensembl are genes which are similar and are
- on an alternative haplotype of the same region. There are not
- currently very many of these. This method will return a
+ on an alternative haplotype of the same region. There are not
+ currently very many of these. This method will return a
reference to an empty list if no alternative alleles are found.
- Returntype : reference to a list of genes
+ Returntype : listref of Bio::EnsEMBL::Genes
Exceptions : throw if incorrect arg provided
warning if gene arg does not have dbID
Caller : Gene::get_all_alt_alleles
@@ -618,8 +632,8 @@ sub fetch_all_alt_alleles {
"AND aa2.gene_id = ? " .
"AND aa1.gene_id <> ?");
- $sth->bind_param(1,$gene_id,SQL_INTEGER);
- $sth->bind_param(2,$gene_id,SQL_INTEGER);
+ $sth->bind_param(1, $gene_id, SQL_INTEGER);
+ $sth->bind_param(2, $gene_id, SQL_INTEGER);
$sth->execute();
my @alt_ids;
@@ -629,31 +643,28 @@ sub fetch_all_alt_alleles {
}
$sth->finish();
- if(@alt_ids) {
+ if (@alt_ids) {
return $self->fetch_all_by_dbID_list(\@alt_ids);
}
return [];
-
}
-
-
=head2 store_alt_alleles
Arg [1] : reference to list of Bio::EnsEMBL::Genes $genes
- Example : $gene_adaptor->store_alt_allele([$gene1, $gene2, $gene3]);
- Description: This method creates a group of alternative aleles (i.e. locus)
- from a set of genes. The genes should be genes from alternate
- haplotypes which are similar. The genes must already be stored
+ Example : $gene_adaptor->store_alt_alleles([$gene1, $gene2, $gene3]);
+ Description: This method creates a group of alternative alleles (i.e. locus)
+ from a set of genes. The genes should be genes from alternate
+ haplotypes which are similar. The genes must already be stored
in this database. At least 2 genes must be in the list reference
provided.
Returntype : none
Exceptions : throw on incorrect arguments
throw on sql error (e.g. duplicate unique id)
- Caller : ?
+ Caller : general
Status : Stable
=cut
@@ -686,12 +697,12 @@ sub store_alt_alleles {
my $gene_id = $gene->dbID();
- if(!$gene_id) {
+ if (!$gene_id) {
throw("Genes must have dbIDs in order to construct alternate alleles.");
}
my $sth = $self->prepare("INSERT INTO alt_allele (gene_id) VALUES (?)");
- $sth->bind_param(1,$gene->dbID,SQL_INTEGER);
+ $sth->bind_param(1, $gene->dbID, SQL_INTEGER);
$sth->execute();
my $alt_allele_id = $sth->{'mysql_insertid'};
@@ -705,37 +716,37 @@ sub store_alt_alleles {
$sth = $self->prepare("INSERT INTO alt_allele (alt_allele_id, gene_id) " .
"VALUES (?,?)");
- for(my $i = 1; $i < $num_genes; $i++) {
+ for (my $i = 1; $i < $num_genes; $i++) {
my $gene = $genes->[$i];
- if(!ref($gene) || !$gene->isa('Bio::EnsEMBL::Gene')) {
+ if (!ref($gene) || !$gene->isa('Bio::EnsEMBL::Gene')) {
throw("List reference of Bio::EnsEMBL::Gene argument expected");
}
$gene_id = $gene->dbID();
- if(!$gene_id) {
- #This is an error but we have already inserted into the database
- #delete the already inserted entries to restore the state of the
- #database
+ if (!$gene_id) {
+ # This is an error but we have already inserted into the database
+ # delete the already inserted entries to restore the state of the
+ # database
$sth->finish();
$sth->prepare("DELETE FROM alt_allele WHERE alt_allele_id = ?");
- $sth->bind_param(1,$alt_allele_id,SQL_INTEGER);
+ $sth->bind_param(1, $alt_allele_id, SQL_INTEGER);
$sth->execute();
$sth->finish();
throw('Genes must have dbIDs in order to construct alternate alleles.');
}
- $sth->bind_param(1,$alt_allele_id,SQL_INTEGER);
- $sth->bind_param(2,$gene_id,SQL_INTEGER);
+ $sth->bind_param(1, $alt_allele_id, SQL_INTEGER);
+ $sth->bind_param(2, $gene_id, SQL_INTEGER);
eval {
$sth->execute();
};
- if($@) {
- #an error occured, revert the db to the previous state
+ if ($@) {
+ # an error occured, revert the db to the previous state
$sth = $self->prepare("DELETE FROM alt_allele WHERE alt_allele_id = ?");
- $sth->bind_param(1,$alt_allele_id,SQL_INTEGER);
+ $sth->bind_param(1, $alt_allele_id, SQL_INTEGER);
$sth->execute();
$sth->finish();
throw("An SQL error occured inserting alternate alleles:\n$@");
@@ -750,10 +761,11 @@ sub store_alt_alleles {
=head2 store
- Arg [1] : Bio::EnsEMBL::Gene
+ Arg [1] : Bio::EnsEMBL::Gene $gene
+ The gene to store in the database
Example : $gene_adaptor->store($gene);
- Description: Stores a gene in the database
- Returntype : the database identifier of the newly stored gene
+ Description: Stores a gene in the database.
+ Returntype : the database identifier (dbID) of the newly stored gene
Exceptions : thrown if the $gene is not a Bio::EnsEMBL::Gene or if
$gene does not have an analysis object
Caller : general
@@ -762,15 +774,15 @@ sub store_alt_alleles {
=cut
sub store {
- my ( $self, $gene ) = @_;
+ my ($self, $gene) = @_;
- if(!ref $gene || !$gene->isa('Bio::EnsEMBL::Gene') ) {
+ if (!ref $gene || !$gene->isa('Bio::EnsEMBL::Gene') ) {
throw("Must store a gene object, not a $gene");
}
my $db = $self->db();
- if($gene->is_stored($db)) {
+ if ($gene->is_stored($db)) {
return $gene->dbID();
}
@@ -781,7 +793,7 @@ sub store {
throw("Genes must have an analysis object.") if(!defined($analysis));
my $analysis_id;
- if($analysis->is_stored($db)) {
+ if ($analysis->is_stored($db)) {
$analysis_id = $analysis->dbID();
} else {
$analysis_id = $db->get_AnalysisAdaptor->store($analysis);
@@ -789,34 +801,42 @@ sub store {
my $type = $gene->biotype || "";
+ # default to is_current = 1 if this attribute is not set
+ my $is_current = $gene->is_current;
+ $is_current = 1 unless (defined($is_current));
+
my $original = $gene;
my $original_transcripts = $gene->get_all_Transcripts();
my $seq_region_id;
($gene, $seq_region_id) = $self->_pre_store($gene);
- my $store_gene_sql =
- "INSERT INTO gene " .
- "SET biotype = ?, " .
- "analysis_id = ?, " .
- "seq_region_id = ?, " .
- "seq_region_start = ?, " .
- "seq_region_end = ?, " .
- "seq_region_strand = ?, ".
- "description = ?, " .
- "source = ?, ".
- "status = ? ";
- # colum status is used from schema version 34 onwards ( before it was confidence)
+ my $store_gene_sql = qq(
+ INSERT INTO gene
+ SET biotype = ?,
+ analysis_id = ?,
+ seq_region_id = ?,
+ seq_region_start = ?,
+ seq_region_end = ?,
+ seq_region_strand = ?,
+ description = ?,
+ source = ?,
+ status = ?,
+ is_current = ?
+ );
+ # colum status is used from schema version 34 onwards (before it was
+ # confidence)
my $sth = $self->prepare( $store_gene_sql );
- $sth->bind_param(1,$type,SQL_VARCHAR);
- $sth->bind_param(2,$analysis_id,SQL_INTEGER);
- $sth->bind_param(3,$seq_region_id,SQL_INTEGER);
- $sth->bind_param(4,$gene->start,SQL_INTEGER);
- $sth->bind_param(5,$gene->end,SQL_INTEGER);
- $sth->bind_param(6,$gene->strand,SQL_TINYINT);
- $sth->bind_param(7,$gene->description,SQL_LONGVARCHAR);
- $sth->bind_param(8,$gene->source,SQL_VARCHAR);
- $sth->bind_param(9,$gene->status,SQL_VARCHAR);
+ $sth->bind_param(1, $type, SQL_VARCHAR);
+ $sth->bind_param(2, $analysis_id, SQL_INTEGER);
+ $sth->bind_param(3, $seq_region_id, SQL_INTEGER);
+ $sth->bind_param(4, $gene->start, SQL_INTEGER);
+ $sth->bind_param(5, $gene->end, SQL_INTEGER);
+ $sth->bind_param(6, $gene->strand, SQL_TINYINT);
+ $sth->bind_param(7, $gene->description, SQL_LONGVARCHAR);
+ $sth->bind_param(8, $gene->source, SQL_VARCHAR);
+ $sth->bind_param(9, $gene->status, SQL_VARCHAR);
+ $sth->bind_param(10, $is_current, SQL_TINYINT);
$sth->execute();
$sth->finish();
@@ -836,9 +856,9 @@ sub store {
$self->db->dbc->from_seconds_to_date($gene->modified_date());
$sth = $self->prepare($statement);
- $sth->bind_param(1,$gene_dbID,SQL_INTEGER);
- $sth->bind_param(2,$gene->stable_id,SQL_VARCHAR);
- $sth->bind_param(3,$gene->version,SQL_INTEGER);
+ $sth->bind_param(1, $gene_dbID, SQL_INTEGER);
+ $sth->bind_param(2, $gene->stable_id, SQL_VARCHAR);
+ $sth->bind_param(3, $gene->version, SQL_INTEGER);
$sth->execute();
$sth->finish();
}
@@ -899,8 +919,8 @@ sub store {
if(defined($dxref_id)) {
$sth = $self->prepare
("UPDATE gene SET display_xref_id = ? WHERE gene_id = ?");
- $sth->bind_param(1,$dxref_id,SQL_INTEGER);
- $sth->bind_param(2,$gene_dbID,SQL_INTEGER);
+ $sth->bind_param(1, $dxref_id, SQL_INTEGER);
+ $sth->bind_param(2, $gene_dbID, SQL_INTEGER);
$sth->execute();
$sth->finish();
$display_xref->dbID($dxref_id);
@@ -929,14 +949,12 @@ sub store {
}
-
-
=head2 remove
Arg [1] : Bio::EnsEMBL::Gene $gene
the gene to remove from the database
Example : $gene_adaptor->remove($gene);
- Description: Removes a gene completely from the database. All associated
+ Description: Removes a gene completely from the database. All associated
transcripts, exons, stable_identifiers, descriptions, etc.
are removed as well. Use with caution!
Returntype : none
@@ -951,11 +969,11 @@ sub remove {
my $self = shift;
my $gene = shift;
- if(!ref($gene) || !$gene->isa('Bio::EnsEMBL::Gene')) {
+ if (!ref($gene) || !$gene->isa('Bio::EnsEMBL::Gene')) {
throw("Bio::EnsEMBL::Gene argument expected.");
}
- if( !$gene->is_stored($self->db()) ) {
+ if ( !$gene->is_stored($self->db()) ) {
warning("Cannot remove gene " . $gene->dbID() . ". Is not stored in " .
"this database.");
return;
@@ -970,7 +988,7 @@ sub remove {
# remove all alternative allele entries associated with this gene
my $sth = $self->prepare("delete from alt_allele where gene_id = ?");
- $sth->bind_param(1,$gene->dbID,SQL_INTEGER);
+ $sth->bind_param(1, $gene->dbID, SQL_INTEGER);
$sth->execute();
$sth->finish();
@@ -988,14 +1006,14 @@ sub remove {
# remove the gene stable identifier
$sth = $self->prepare( "delete from gene_stable_id where gene_id = ? " );
- $sth->bind_param(1,$gene->dbID,SQL_INTEGER);
+ $sth->bind_param(1, $gene->dbID, SQL_INTEGER);
$sth->execute();
$sth->finish();
# remove this gene from the database
$sth = $self->prepare( "delete from gene where gene_id = ? " );
- $sth->bind_param(1,$gene->dbID,SQL_INTEGER);
+ $sth->bind_param(1, $gene->dbID, SQL_INTEGER);
$sth->execute();
$sth->finish();
@@ -1008,66 +1026,64 @@ sub remove {
}
-
=head2 get_Interpro_by_geneid
- Arg [1] : string $gene
- the stable if of the gene to obtain
+ Arg [1] : String $gene_stable_id
+ The stable ID of the gene to obtain
Example : @i = $gene_adaptor->get_Interpro_by_geneid($gene->stable_id());
- Description: gets interpro accession numbers by gene stable id.
- A hack really - we should have a much more structured
- system than this
- Returntype : listref of strings
+ Description: Gets interpro accession numbers by gene stable id. A hack really
+ - we should have a much more structured system than this.
+ Returntype : listref of strings (Interpro_acc:description)
Exceptions : none
- Caller : domainview?
+ Caller : domainview
Status : Stable
=cut
sub get_Interpro_by_geneid {
- my ($self,$gene) = @_;
- my $sql="
+ my ($self, $gene_stable_id) = @_;
+
+ my $sql = qq(
SELECT i.interpro_ac,
x.description
- FROM transcript t,
- translation tl,
+ FROM transcript t,
+ translation tl,
protein_feature pf,
interpro i,
- xref x,
+ xref x,
gene_stable_id gsi
- WHERE gsi.stable_id = '$gene'
- AND t.gene_id = gsi.gene_id
- AND tl.transcript_id = t.transcript_id
- AND tl.translation_id = pf.translation_id
- AND i.id = pf.hit_id
- AND i.interpro_ac = x.dbprimary_acc";
+ WHERE gsi.stable_id = '$gene_stable_id'
+ AND t.gene_id = gsi.gene_id
+ AND t.is_current = 1
+ AND tl.transcript_id = t.transcript_id
+ AND tl.translation_id = pf.translation_id
+ AND i.id = pf.hit_id
+ AND i.interpro_ac = x.dbprimary_acc
+ );
- my $sth = $self->prepare($sql);
- $sth->execute;
-
- my @out;
- my %h;
- while( (my $arr = $sth->fetchrow_arrayref()) ) {
- if( $h{$arr->[0]} ) { next; }
- $h{$arr->[0]}=1;
- my $string = $arr->[0] .":".$arr->[1];
-
- push(@out,$string);
- }
-
+ my $sth = $self->prepare($sql);
+ $sth->execute;
+
+ my @out;
+ my %h;
+ while( (my $arr = $sth->fetchrow_arrayref()) ) {
+ if( $h{$arr->[0]} ) { next; }
+ $h{$arr->[0]}=1;
+ my $string = $arr->[0] .":".$arr->[1];
+ push(@out,$string);
+ }
- return \@out;
+ return \@out;
}
-
-
=head2 update
- Arg [1] : Bio::EnsEMBL::Gene
+ Arg [1] : Bio::EnsEMBL::Gene $gene
+ The gene to update
Example : $gene_adaptor->update($gene);
- Description: Updates the type, analysis and display_xref of a gene in the
- database.
+ Description: Updates the type, analysis, display_xref, status, is_current and
+ description of a gene in the database.
Returntype : None
Exceptions : thrown if the $gene is not a Bio::EnsEMBL::Gene
Caller : general
@@ -1076,50 +1092,54 @@ sub get_Interpro_by_geneid {
=cut
sub update {
- my ($self,$gene) = @_;
- my $update = 0;
-
- if( !defined $gene || !ref $gene || !$gene->isa('Bio::EnsEMBL::Gene') ) {
- throw("Must update a gene object, not a $gene");
- }
+ my ($self, $gene) = @_;
+ my $update = 0;
- my $update_gene_sql = "
- UPDATE gene
- SET biotype = ?,
- analysis_id = ?,
- display_xref_id = ?,
- status = ?,
- description = ?
- WHERE gene_id = ?";
-
- my $display_xref = $gene->display_xref();
- my $display_xref_id;
+ if ( !defined $gene || !ref $gene || !$gene->isa('Bio::EnsEMBL::Gene') ) {
+ throw("Must update a gene object, not a $gene");
+ }
- if( $display_xref && $display_xref->dbID() ) {
- $display_xref_id = $display_xref->dbID();
- } else {
- $display_xref_id = undef;
- }
+ my $update_gene_sql = qq(
+ UPDATE gene
+ SET biotype = ?,
+ analysis_id = ?,
+ display_xref_id = ?,
+ status = ?,
+ description = ?,
+ is_current = ?
+ WHERE gene_id = ?
+ );
+
+ my $display_xref = $gene->display_xref();
+ my $display_xref_id;
+
+ if ( $display_xref && $display_xref->dbID() ) {
+ $display_xref_id = $display_xref->dbID();
+ } else {
+ $display_xref_id = undef;
+ }
- my $sth = $self->prepare( $update_gene_sql );
+ my $sth = $self->prepare( $update_gene_sql );
- $sth->bind_param(1,$gene->biotype,SQL_VARCHAR);
- $sth->bind_param(2,$gene->analysis->dbID,SQL_INTEGER);
- $sth->bind_param(3,$display_xref_id,SQL_INTEGER);
- $sth->bind_param(4,$gene->status,SQL_VARCHAR);
- $sth->bind_param(5,$gene->description,SQL_VARCHAR);
- $sth->bind_param(6,$gene->dbID,SQL_INTEGER);
+ $sth->bind_param(1, $gene->biotype, SQL_VARCHAR);
+ $sth->bind_param(2, $gene->analysis->dbID, SQL_INTEGER);
+ $sth->bind_param(3, $display_xref_id, SQL_INTEGER);
+ $sth->bind_param(4, $gene->status, SQL_VARCHAR);
+ $sth->bind_param(5, $gene->description, SQL_VARCHAR);
+ $sth->bind_param(6, $gene->is_current, SQL_TINYINT);
+ $sth->bind_param(7, $gene->dbID, SQL_INTEGER);
- $sth->execute();
+ $sth->execute();
- # maybe should update stable id ???
+ # maybe should update stable id ???
}
# _objs_from_sth
# Arg [1] : StatementHandle $sth
-# Example : none
+# Arg [2] : Bio::EnsEMBL::AssemblyMapper $mapper
+# Arg [3] : Bio::EnsEMBL::Slice $dest_slice
# Description: PROTECTED implementation of abstract superclass method.
# responsible for the creation of Genes
# Returntype : listref of Bio::EnsEMBL::Genes in target coordinate system
@@ -1149,17 +1169,19 @@ sub _objs_from_sth {
my ( $gene_id, $seq_region_id, $seq_region_start, $seq_region_end,
$seq_region_strand, $analysis_id, $biotype, $display_xref_id,
$gene_description, $stable_id, $version, $created_date,
- $modified_date, $xref_display_id, $status, $source,
+ $modified_date, $xref_display_id, $status, $source, $is_current,
$xref_primary_acc, $xref_desc, $xref_version, $external_name,
$external_db, $external_status, $external_release, $external_db_name,
$info_type, $info_text);
$sth->bind_columns( \$gene_id, \$seq_region_id, \$seq_region_start,
- \$seq_region_end, \$seq_region_strand, \$analysis_id, \$biotype,
- \$display_xref_id, \$gene_description, \$status, \$source,
+ \$seq_region_end, \$seq_region_strand, \$analysis_id,
+ \$biotype, \$display_xref_id, \$gene_description,
+ \$status, \$source, \$is_current,
\$stable_id, \$version,
\$created_date, \$modified_date,
- \$xref_display_id, \$xref_primary_acc, \$xref_desc, \$xref_version,
+ \$xref_display_id, \$xref_primary_acc, \$xref_desc,
+ \$xref_version,
\$external_db, \$external_status,
\$external_release, \$external_db_name,
\$info_type, \$info_text);
@@ -1282,8 +1304,8 @@ sub _objs_from_sth {
}
#finally, create the new gene
- push @genes, Bio::EnsEMBL::Gene->new
- ( '-analysis' => $analysis,
+ push @genes, Bio::EnsEMBL::Gene->new(
+ '-analysis' => $analysis,
'-biotype' => $biotype,
'-start' => $seq_region_start,
'-end' => $seq_region_end,
@@ -1299,9 +1321,11 @@ sub _objs_from_sth {
'-external_name' => $external_name,
'-external_db' => $external_db,
'-external_status' => $external_status,
- '-display_xref' => $display_xref,
- '-status' => $status,
- '-source' => $source );
+ '-display_xref' => $display_xref,
+ '-status' => $status,
+ '-source' => $source,
+ '-is_current' => $is_current
+ );
}
return \@genes;
@@ -1310,27 +1334,27 @@ sub _objs_from_sth {
=head2 cache_gene_seq_mappings
- Args : none
Example : $gene_adaptor->cache_gene_seq_mappings();
Description: caches all the assembly mappings needed for genes
Returntype : None
Exceptions : None
Caller : general
Status : At Risk
- : New experimental code.
+ : New experimental code
=cut
sub cache_gene_seq_mappings{
my ($self) = @_;
- #get the sequence level to map too
+ # get the sequence level to map too
- my $sql = (<<SSQL);
- SELECT name
- FROM coord_system
+ my $sql = qq(
+ SELECT name
+ FROM coord_system
WHERE attrib like "%sequence_level%"
-SSQL
+ );
+
my $sth = $self->prepare($sql);
$sth->execute();
@@ -1342,144 +1366,148 @@ SSQL
my $ama = $self->db->get_AssemblyMapperAdaptor();
my $cs1 = $csa->fetch_by_name($sequence_level);
-
- #get level to map to two
+ # get level to map to two
my $mcc = $self->db->get_MetaCoordContainerAdaptor();
my $csnew = $mcc->fetch_all_CoordSystems_by_feature_type('gene');
- foreach my $cs2 (@$csnew){
- my $am = $ama->fetch_by_CoordSystems($cs1,$cs2);
+ foreach my $cs2 (@$csnew) {
+ my $am = $ama->fetch_by_CoordSystems($cs1, $cs2);
$am->register_all();
- };
+ }
}
=head2 fetch_all_by_exon_supporting_evidence
- Arg [1] : string hit_name
- Arg [2] : string feature type
- (one of "dna_align_feature" or "protein_align_feature")
+ Arg [1] : String $hit_name
+ Name of supporting feature
+ Arg [2] : String $feature_type
+ one of "dna_align_feature" or "protein_align_feature"
Arg [3] : (optional) Bio::Ensembl::Analysis
- Example : $genes = $gene_adaptor->fetch_all_by_exon_supporting_evidence();
- Description: Gets all the genes with transcripts with exons which have a specified hit on a particular
- type of feature. Optionally filter by analysis.
+ Example : $genes = $gene_adaptor->fetch_all_by_exon_supporting_evidence(
+ 'XYZ', 'dna_align_feature');
+ Description: Gets all the genes with transcripts with exons which have a
+ specified hit on a particular type of feature. Optionally filter
+ by analysis.
Returntype : Listref of Bio::EnsEMBL::Gene
Exceptions : If feature_type is not of correct type.
- Caller : ?
+ Caller : general
Status : At Risk
=cut
sub fetch_all_by_exon_supporting_evidence {
+ my ($self, $hit_name, $feature_type, $analysis) = @_;
- my ($self, $hit_name, $feature_type, $analysis) = @_;
-
- if($feature_type !~ /(dna)|(protein)_align_feature/) {
- throw("feature type must be dna_align_feature or protein_align_feature");
- }
-
- my $anal_from = ", analysis a " if ($analysis);
- my $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? " if ($analysis);
-
- my $sql = "SELECT DISTINCT(g.gene_id)
- FROM gene g,
- transcript t,
- exon_transcript et,
- supporting_feature sf,
- $feature_type f
- $anal_from
- WHERE g.gene_id=t.gene_id
- AND t.transcript_id = et.transcript_id
- AND et.exon_id = sf.exon_id
- AND sf.feature_id = f.${feature_type}_id
- AND sf.feature_type = ?
- AND f.hit_name=?
- $anal_where";
+ if ($feature_type !~ /(dna)|(protein)_align_feature/) {
+ throw("feature type must be dna_align_feature or protein_align_feature");
+ }
- my $sth = $self->prepare($sql);
+ my $anal_from = ", analysis a " if ($analysis);
+ my $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? " if ($analysis);
+
+ my $sql = qq(
+ SELECT DISTINCT(g.gene_id)
+ FROM gene g,
+ transcript t,
+ exon_transcript et,
+ supporting_feature sf,
+ $feature_type f
+ $anal_from
+ WHERE g.gene_id = t.gene_id
+ AND g.is_current = 1
+ AND t.transcript_id = et.transcript_id
+ AND et.exon_id = sf.exon_id
+ AND sf.feature_id = f.${feature_type}_id
+ AND sf.feature_type = ?
+ AND f.hit_name=?
+ $anal_where
+ );
- $sth->bind_param(1, $feature_type, SQL_VARCHAR);
- $sth->bind_param(2, $hit_name, SQL_VARCHAR);
- $sth->bind_param(3, $analysis->dbID(), SQL_INTEGER) if ($analysis);
+ my $sth = $self->prepare($sql);
- $sth->execute();
+ $sth->bind_param(1, $feature_type, SQL_VARCHAR);
+ $sth->bind_param(2, $hit_name, SQL_VARCHAR);
+ $sth->bind_param(3, $analysis->dbID(), SQL_INTEGER) if ($analysis);
- my @genes;
+ $sth->execute();
- while( my $id = $sth->fetchrow_array ) {
- my $gene = $self->fetch_by_dbID( $id );
- push(@genes, $gene) if $gene;
- }
+ my @genes;
- return \@genes;
+ while ( my $id = $sth->fetchrow_array ) {
+ my $gene = $self->fetch_by_dbID($id);
+ push(@genes, $gene) if $gene;
+ }
+ return \@genes;
}
=head2 fetch_all_by_transcript_supporting_evidence
- Arg [1] : string hit_name
- Arg [2] : string feature type
- (one of "dna_align_feature" or "protein_align_feature")
+ Arg [1] : String $hit_name
+ Name of supporting feature
+ Arg [2] : String $feature_type
+ one of "dna_align_feature" or "protein_align_feature"
Arg [3] : (optional) Bio::Ensembl::Analysis
- Example : $genes = $gene_adaptor->fetch_all_by_transcript_supporting_evidence();
- Description: Gets all the genes with transcripts with evidence for a specified hit on a particular
- type of feature. Optionally filter by analysis.
+ Example : $genes = $gene_adaptor->fetch_all_by_transcript_supporting_evidence('XYZ', 'dna_align_feature');
+ Description: Gets all the genes with transcripts with evidence for a
+ specified hit on a particular type of feature. Optionally filter
+ by analysis.
Returntype : Listref of Bio::EnsEMBL::Gene
Exceptions : If feature_type is not of correct type.
- Caller : ?
+ Caller : general
Status : At Risk
=cut
sub fetch_all_by_transcript_supporting_evidence {
+ my ($self, $hit_name, $feature_type, $analysis) = @_;
- my ($self, $hit_name, $feature_type, $analysis) = @_;
-
- if($feature_type !~ /(dna)|(protein)_align_feature/) {
- throw("feature type must be dna_align_feature or protein_align_feature");
- }
-
- my $anal_from = ", analysis a " if ($analysis);
- my $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? " if ($analysis);
-
- my $sql = "SELECT DISTINCT(g.gene_id)
- FROM gene g,
- transcript t,
- transcript_supporting_feature sf,
- $feature_type f
- $anal_from
- WHERE g.gene_id = t.gene_id
- AND t.transcript_id = sf.transcript_id
- AND sf.feature_id = f.${feature_type}_id
- AND sf.feature_type = ?
- AND f.hit_name=?
- $anal_where";
+ if($feature_type !~ /(dna)|(protein)_align_feature/) {
+ throw("feature type must be dna_align_feature or protein_align_feature");
+ }
- my $sth = $self->prepare($sql);
+ my $anal_from = ", analysis a " if ($analysis);
+ my $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? " if ($analysis);
+
+ my $sql = qq(
+ SELECT DISTINCT(g.gene_id)
+ FROM gene g,
+ transcript t,
+ transcript_supporting_feature sf,
+ $feature_type f
+ $anal_from
+ WHERE g.gene_id = t.gene_id
+ AND g.is_current = 1
+ AND t.transcript_id = sf.transcript_id
+ AND sf.feature_id = f.${feature_type}_id
+ AND sf.feature_type = ?
+ AND f.hit_name=?
+ $anal_where
+ );
- $sth->bind_param(1, $feature_type, SQL_VARCHAR);
- $sth->bind_param(2, $hit_name, SQL_VARCHAR);
- $sth->bind_param(3, $analysis->dbID(), SQL_INTEGER) if ($analysis);
+ my $sth = $self->prepare($sql);
- $sth->execute();
+ $sth->bind_param(1, $feature_type, SQL_VARCHAR);
+ $sth->bind_param(2, $hit_name, SQL_VARCHAR);
+ $sth->bind_param(3, $analysis->dbID(), SQL_INTEGER) if ($analysis);
- my @genes;
+ $sth->execute();
- while( my $id = $sth->fetchrow_array ) {
- my $gene = $self->fetch_by_dbID($id);
- push(@genes, $gene) if $gene;
- }
+ my @genes;
- return \@genes;
+ while( my $id = $sth->fetchrow_array ) {
+ my $gene = $self->fetch_by_dbID($id);
+ push(@genes, $gene) if $gene;
+ }
+ return \@genes;
}
-
-
##########################
# #
# DEPRECATED METHODS #
@@ -1491,25 +1519,24 @@ sub fetch_all_by_transcript_supporting_evidence {
Description: DEPRECATED - use fetch_all_by_external_name instead
-
=cut
sub fetch_by_maximum_DBLink {
- my ( $self, $external_id ) = @_;
+ my ($self, $external_id) = @_;
deprecate( "use fetch_all_by_external_name instead" );
- my $genes=$self->fetch_all_by_external_name( $external_id);
+ my $genes=$self->fetch_all_by_external_name($external_id);
my $biggest;
- my $max=0;
- my $size=scalar(@$genes);
+ my $max = 0;
+ my $size = scalar(@$genes);
if ($size > 0) {
foreach my $gene (@$genes) {
my $size = scalar(@{$gene->get_all_Exons});
if ($size > $max) {
$biggest = $gene;
- $max=$size;
+ $max = $size;
}
}
return $biggest;
@@ -1518,7 +1545,6 @@ sub fetch_by_maximum_DBLink {
}
-
=head2 get_display_xref
Description: DEPRECATED use $gene->display_xref
@@ -1526,39 +1552,40 @@ sub fetch_by_maximum_DBLink {
=cut
sub get_display_xref {
- my ($self, $gene ) = @_;
+ my ($self, $gene) = @_;
deprecate( "display xref should retrieved from Gene object directly" );
- if( !defined $gene ) {
- throw("Must call with a Gene object");
+ if ( !defined $gene ) {
+ throw("Must call with a Gene object");
}
- my $sth = $self->prepare("SELECT e.db_name,
- x.display_label,
- x.xref_id
- FROM gene g,
- xref x,
- external_db e
- WHERE g.gene_id = ?
- AND g.display_xref_id = x.xref_id
- AND x.external_db_id = e.external_db_id
- ");
- $sth->bind_param(1,$gene->dbID,SQL_INTEGER);
+ my $sth = $self->prepare(qq(
+ SELECT e.db_name,
+ x.display_label,
+ x.xref_id
+ FROM gene g,
+ xref x,
+ external_db e
+ WHERE g.gene_id = ?
+ AND g.display_xref_id = x.xref_id
+ AND x.external_db_id = e.external_db_id
+ ));
+
+ $sth->bind_param(1, $gene->dbID, SQL_INTEGER);
$sth->execute();
-
- my ($db_name, $display_label, $xref_id ) = $sth->fetchrow_array();
- if( !defined $xref_id ) {
+ my ($db_name, $display_label, $xref_id) = $sth->fetchrow_array();
+ if ( !defined $xref_id ) {
return undef;
}
- my $db_entry = Bio::EnsEMBL::DBEntry->new
- (
+
+ my $db_entry = Bio::EnsEMBL::DBEntry->new(
-dbid => $xref_id,
-adaptor => $self->db->get_DBEntryAdaptor(),
-dbname => $db_name,
-display_id => $display_label
- );
+ );
return $db_entry;
}
@@ -1575,23 +1602,22 @@ sub get_description {
deprecate( "Gene description should be loaded on gene retrieval. Use gene->get_description()" );
- if( !defined $dbID ) {
- throw("must call with dbID");
+ if ( !defined $dbID ) {
+ throw("must call with dbID");
}
my $sth = $self->prepare("SELECT description
FROM gene_description
WHERE gene_id = ?");
- $sth->bind_param(1,$dbID,SQL_INTEGER);
-
+
+ $sth->bind_param(1, $dbID, SQL_INTEGER);
$sth->execute();
+
my @array = $sth->fetchrow_array();
return $array[0];
}
-
-
=head2 fetch_by_Peptide_id
Description: DEPRECATED, use fetch_by_translation_stable_id()
@@ -1599,11 +1625,12 @@ sub get_description {
=cut
sub fetch_by_Peptide_id {
- my ( $self, $translation_stable_id) = @_;
+ my ( $self, $translation_stable_id) = @_;
- deprecate( "Please use better named fetch_by_translation_stable_id \n".caller(2) );
+ deprecate( "Please use better named fetch_by_translation_stable_id \n".
+ caller(2) );
- $self->fetch_by_translation_stable_id($translation_stable_id);
+ $self->fetch_by_translation_stable_id($translation_stable_id);
}
@@ -1616,10 +1643,10 @@ sub fetch_by_Peptide_id {
sub get_stable_entry_info {
my ($self,$gene) = @_;
- deprecated( "stable id info is loaded on default, no lazy loading necessary" );
+ deprecated("stable id info is loaded on default, no lazy loading necessary");
- if( !defined $gene || !ref $gene || !$gene->isa('Bio::EnsEMBL::Gene') ) {
- throw("Needs a gene object, not a $gene");
+ if ( !defined $gene || !ref $gene || !$gene->isa('Bio::EnsEMBL::Gene') ) {
+ throw("Needs a gene object, not a $gene");
}
my $created_date = $self->db->dbc->from_date_to_seconds("created_date");
@@ -1630,7 +1657,7 @@ sub get_stable_entry_info {
FROM gene_stable_id
WHERE gene_id = ?");
- $sth->bind_param(1,$gene->dbID,SQL_INTEGER);
+ $sth->bind_param(1, $gene->dbID, SQL_INTEGER);
$sth->execute();
my @array = $sth->fetchrow_array();
@@ -1643,7 +1670,6 @@ sub get_stable_entry_info {
}
-
=head2 fetch_all_by_DBEntry
Description: DEPRECATED - Use fetch_all_by_external_name instead
@@ -1652,13 +1678,12 @@ sub get_stable_entry_info {
sub fetch_all_by_DBEntry {
my $self = shift;
- deprecate('This method has been deprecated because there was another.' .
- "Method which did exactly the same thing.\n" .
- 'Use fetch_all_by_external_name instead.');
+
+ deprecate('Use fetch_all_by_external_name instead.');
+
return $self->fetch_all_by_external_name(@_);
}
-
1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index 307074c427..665f9831d7 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -1,26 +1,10 @@
-# EnsEMBL Transcript reading writing adaptor for mySQL
-#
-# Copyright EMBL-EBI 2001
-#
-# Author: Arne Stabenau
-# based on
-# Elia Stupkas Gene_Obj
-#
-# Date : 20.02.2001
-#
+package Bio::EnsEMBL::DBSQL::TranscriptAdaptor;
=head1 NAME
Bio::EnsEMBL::DBSQL::TranscriptAdaptor - An adaptor which performs database
interaction relating to the storage and retrieval of Transcripts
-=head1 DESCRIPTION
-
-This adaptor provides a means to retrieve and store information related to
-Transcripts. Primarily this involves the retrieval or storage of
-Bio::EnsEMBL::Transcript objects from a database.
-See Bio::EnsEMBL::Transcript for details of the Transcript class.
-
=head1 SYNOPSIS
$db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
@@ -37,19 +21,31 @@ See Bio::EnsEMBL::Transcript for details of the Transcript class.
($transcript) = @{$transcript_adaptor->fetch_all_by_external_name('BRCA2')};
+=head1 DESCRIPTION
-=head1 CONTACT
+This adaptor provides a means to retrieve and store information related to
+Transcripts. Primarily this involves the retrieval or storage of
+Bio::EnsEMBL::Transcript objects from a database.
- Post questions/comments to the EnsEMBL development list:
- ensembl-dev@ebi.ac.uk
+See Bio::EnsEMBL::Transcript for details of the Transcript class.
-=head1 METHODS
+=head1 LICENCE
-=cut
+This code is distributed under an Apache style licence. Please see
+http://www.ensembl.org/info/about/code_licence.html for details.
-package Bio::EnsEMBL::DBSQL::TranscriptAdaptor;
+=head1 AUTHOR
+
+Arne Stabenau <stabenau@ebi.ac.uk>, Ensembl core API team
+Based on Elia Stupkas Gene_Obj
+
+=head1 CONTACT
+
+Please post comments/questions to the Ensembl development list
+<ensembl-dev@ebi.ac.uk>
+
+=cut
-use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
@@ -57,20 +53,16 @@ use Bio::EnsEMBL::Gene;
use Bio::EnsEMBL::Exon;
use Bio::EnsEMBL::Transcript;
use Bio::EnsEMBL::Translation;
-
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
+use vars qw(@ISA);
@ISA = qw( Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor );
-
-
# _tables
#
-# Arg [1] : none
-# Example : none
-# Description: PROTECTED implementation of superclass abstract method
-# returns the names, aliases of the tables to use for queries
+# Description: PROTECTED implementation of superclass abstract method.
+# Returns the names, aliases of the tables to use for queries.
# Returntype : list of listrefs of strings
# Exceptions : none
# Caller : internal
@@ -86,10 +78,8 @@ sub _tables {
#_columns
#
-# Arg [1] : none
-# Example : none
-# Description: PROTECTED implementation of superclass abstract method
-# returns a list of columns to use for queries
+# Description: PROTECTED implementation of superclass abstract method.
+# Returns a list of columns to use for queries.
# Returntype : list of strings
# Exceptions : none
# Caller : internal
@@ -101,11 +91,13 @@ sub _columns {
my $created_date = $self->db->dbc->from_date_to_seconds("created_date");
my $modified_date = $self->db->dbc->from_date_to_seconds("modified_date");
- return ( 't.transcript_id', 't.seq_region_id', 't.seq_region_start', 't.seq_region_end',
- 't.seq_region_strand', 't.analysis_id', 't.gene_id',
+ return ( 't.transcript_id', 't.seq_region_id', 't.seq_region_start',
+ 't.seq_region_end', 't.seq_region_strand', 't.analysis_id',
+ 't.gene_id', 't.is_current',
't.display_xref_id', 'tsi.stable_id','tsi.version', $created_date,
$modified_date, 't.description', 't.biotype', 't.status',
- 'x.display_label', 'exdb.db_name' ,'exdb.status', 'exdb.db_display_name',
+ 'x.display_label', 'exdb.db_name' ,'exdb.status',
+ 'exdb.db_display_name',
'x.info_type', 'x.info_text');
}
@@ -117,13 +109,12 @@ sub _left_join {
}
-
=head2 fetch_by_stable_id
- Arg [1] : string $stable_id
+ Arg [1] : String $stable_id
The stable id of the transcript to retrieve
- Example : $trans = $trans_adptr->fetch_by_stable_id('ENST00000309301');
- Description: Retrieves a transcript via its stable id
+ Example : my $tr = $tr_adaptor->fetch_by_stable_id('ENST00000309301');
+ Description: Retrieves a transcript via its stable id.
Returntype : Bio::EnsEMBL::Transcript
Exceptions : none
Caller : general
@@ -131,33 +122,47 @@ sub _left_join {
=cut
-sub fetch_by_stable_id{
- my ($self,$id) = @_;
+sub fetch_by_stable_id {
+ my ($self, $stable_id) = @_;
- # because of the way this query is constructed (with a left join to the
- # transcript_stable_id table), it is faster to do 2 queries, getting the
- # transcript_id in the first query
- my $sth = $self->prepare("SELECT transcript_id from transcript_stable_id ".
- "WHERE stable_id = ?");
- $sth->bind_param(1,$id,SQL_VARCHAR);
- $sth->execute();
+ my $constraint = "tsi.stable_id = '$stable_id' AND t.is_current = 1";
+ my ($transcript) = @{ $self->generic_fetch($constraint) };
- my ($dbID) = $sth->fetchrow_array();
+ return $transcript;
+}
- return undef if(!$dbID);
- return $self->fetch_by_dbID($dbID);
+=head2 fetch_all_versions_by_stable_id
-}
+ Arg [1] : String $stable_id
+ The stable ID of the transcript to retrieve
+ Example : my $tr = $tr_adaptor->fetch_all_version_by_stable_id
+ ('ENST00000309301');
+ Description : Similar to fetch_by_stable_id, but retrieves all versions of a
+ transcript stored in the database.
+ Returntype : listref of Bio::EnsEMBL::Transcript objects
+ Exceptions : if we cant get the gene in given coord system
+ Caller : general
+ Status : At Risk
+=cut
+
+sub fetch_all_versions_by_stable_id {
+ my ($self, $stable_id) = @_;
+
+ my $constraint = "tsi.stable_id = '$stable_id'";
+
+ return $self->generic_fetch($constraint);
+}
=head2 fetch_by_translation_stable_id
- Arg [1] : string $transl_stable_id
+ Arg [1] : String $transl_stable_id
The stable identifier of the translation of the transcript to
retrieve
- Example : $t = $tadptr->fetch_by_translation_stable_id('ENSP00000311007');
+ Example : my $tr = $tr_adaptor->fetch_by_translation_stable_id
+ ('ENSP00000311007');
Description: Retrieves a Transcript object using the stable identifier of
its translation.
Returntype : Bio::EnsEMBL::Transcript
@@ -170,12 +175,18 @@ sub fetch_by_stable_id{
sub fetch_by_translation_stable_id {
my ($self, $transl_stable_id ) = @_;
- my $sth = $self->prepare( "SELECT t.transcript_id " .
- "FROM translation_stable_id tsi, translation t ".
- "WHERE tsi.stable_id = ? " .
- "AND t.translation_id = tsi.translation_id");
+ my $sth = $self->prepare(qq(
+ SELECT t.transcript_id
+ FROM translation_stable_id tsi,
+ transcript t,
+ translation tl
+ WHERE tsi.stable_id = ?
+ AND tl.translation_id = tsi.translation_id
+ AND tl.transcript_id = t.transcript_id
+ AND t.is_current = 1
+ ));
- $sth->bind_param(1,"$transl_stable_id",SQL_VARCHAR);
+ $sth->bind_param(1, $transl_stable_id, SQL_VARCHAR);
$sth->execute();
my ($id) = $sth->fetchrow_array;
@@ -190,10 +201,10 @@ sub fetch_by_translation_stable_id {
=head2 fetch_by_translation_id
- Arg [1] : int $id
+ Arg [1] : Int $id
The internal identifier of the translation whose transcript
- is to be retrieved.
- Example : $tr = $tr_adaptor->fetch_by_translation_id($transl->dbID());
+ is to be retrieved
+ Example : my $tr = $tr_adaptor->fetch_by_translation_id($transl->dbID);
Description: Given the internal identifier of a translation this method
retrieves the transcript associated with that translation.
If the transcript cannot be found undef is returned instead.
@@ -208,13 +219,13 @@ sub fetch_by_translation_id {
my $self = shift;
my $id = shift;
- throw("id argument is required.") if(!$id);
+ throw("id argument is required.") unless ($id);
my $sth = $self->prepare( "SELECT t.transcript_id " .
"FROM translation t ".
"WHERE t.translation_id = ?");
- $sth->bind_param(1,$id,SQL_INTEGER);
+ $sth->bind_param(1, $id, SQL_INTEGER);
$sth->execute();
my ($dbID) = $sth->fetchrow_array;
@@ -227,21 +238,21 @@ sub fetch_by_translation_id {
}
-
=head2 fetch_all_by_Gene
Arg [1] : Bio::EnsEMBL::Gene $gene
- Example : none
- Description: retrieves Transcript objects for given gene. Puts Genes slice
+ The gene to fetch transcripts of
+ Example : my $gene = $gene_adaptor->fetch_by_stable_id('ENSG0000123');
+ my @transcripts = $tr_adaptor->fetch_all_by_Gene($gene);
+ Description: Retrieves Transcript objects for given gene. Puts Genes slice
in each Transcript.
- Returntype : listref Bio::EnsEMBL::Transcript
+ Returntype : Listref of Bio::EnsEMBL::Transcript objects
Exceptions : none
Caller : Gene->get_all_Transcripts()
Status : Stable
=cut
-
sub fetch_all_by_Gene {
my $self = shift;
my $gene = shift;
@@ -259,19 +270,19 @@ sub fetch_all_by_Gene {
my $gslice = $gene->slice();
my $slice;
- if(!$gslice) {
+ if (!$gslice) {
throw("Gene must have attached slice to retrieve transcripts.");
}
- if($gene->start() < 1 || $gene->end() > $gslice->length()) {
+ if ($gene->start() < 1 || $gene->end() > $gslice->length()) {
$slice = $self->db->get_SliceAdaptor->fetch_by_Feature($gene);
} else {
$slice = $gslice;
}
- my $transcripts = $self->fetch_all_by_Slice_constraint($slice,$constraint);
+ my $transcripts = $self->fetch_all_by_Slice_constraint($slice, $constraint);
- if($slice != $gslice) {
+ if ($slice != $gslice) {
my @out;
foreach my $tr (@$transcripts) {
push @out, $tr->transfer($gslice);
@@ -279,27 +290,25 @@ sub fetch_all_by_Gene {
$transcripts = \@out;
}
-
return $transcripts;
}
-
=head2 fetch_all_by_Slice
Arg [1] : Bio::EnsEMBL::Slice $slice
- The slice to fetch transcripts on.
- Arg [2] : (optional) boolean $load_exons
- if true, exons will be loaded immediately rather than
- lazy loaded later.
- Arg [3] : (optional) string $logic_name
- the logic name of the type of features to obtain
- Example : @transcripts = @{ $tr_adaptor->fetch_all_by_Slice($slice) };
+ The slice to fetch transcripts on
+ Arg [2] : (optional) Boolean $load_exons
+ If true, exons will be loaded immediately rather than
+ lazy loaded later
+ Arg [3] : (optional) String $logic_name
+ The logic name of the type of features to obtain
+ Example : my @transcripts = @{ $tr_adaptor->fetch_all_by_Slice($slice) };
Description: Overrides superclass method to optionally load exons
- immediately rather than lazy-loading them later. This
+ immediately rather than lazy-loading them later. This
is more efficient when there are a lot of transcripts whose
exons are going to be used.
- Returntype : reference to list of transcripts
+ Returntype : Listref of Bio::EnsEMBL::Transcript objects
Exceptions : thrown if exon cannot be placed on transcript slice
Caller : Slice::get_all_Transcripts
Status : Stable
@@ -312,10 +321,11 @@ sub fetch_all_by_Slice {
my $load_exons = shift;
my $logic_name = shift;
- my $transcripts = $self->SUPER::fetch_all_by_Slice($slice, $logic_name);
+ my $transcripts = $self->SUPER::fetch_all_by_Slice_constraint($slice,
+ 't.is_current = 1', $logic_name);
# if there are 0 or 1 transcripts still do lazy-loading
- if(!$load_exons || @$transcripts < 2) {
+ if (!$load_exons || @$transcripts < 2) {
return $transcripts;
}
@@ -325,7 +335,6 @@ sub fetch_all_by_Slice {
# first check if the exons are already preloaded
return $transcripts if( exists $transcripts->[0]->{'_trans_exon_array'});
-
# get extent of region spanned by transcripts
my ($min_start, $max_end);
foreach my $tr (@$transcripts) {
@@ -379,9 +388,9 @@ sub fetch_all_by_Slice {
foreach my $ex (@$exons) {
my $new_ex;
- if($slice != $ext_slice) {
+ if ($slice != $ext_slice) {
$new_ex = $ex->transfer($slice) if($slice != $ext_slice);
- if(!$new_ex) {
+ if (!$new_ex) {
throw("Unexpected. Exon could not be transfered onto transcript slice.");
}
} else {
@@ -403,23 +412,23 @@ sub fetch_all_by_Slice {
}
-
=head2 fetch_all_by_external_name
- Arg [1] : string $external_id
+ Arg [1] : String $external_id
An external identifier of the transcript to be obtained
- Example : @trans = @{$tr_adaptor->fetch_all_by_external_name('ARSE')};
+ Example : my @transcripts = @{ $tr_adaptor->fetch_all_by_external_name
+ ('ARSE') };
Description: Retrieves all transcripts which are associated with an
external identifier such as a GO term, HUGO id, Swissprot
- identifer, etc. Usually there will only be a single transcript
- returned in the listref, but not always. Transcripts are
- returned in their native coordinate system. That is, the
+ identifer, etc. Usually there will only be a single transcript
+ returned in the listref, but not always. Transcripts are
+ returned in their native coordinate system. That is, the
coordinate system in which they are stored in the database. If
they are required in another coordinate system the
Transcript::transfer or Transcript::transform method can be
- used to convert them. If no transcripts with the external
+ used to convert them. If no transcripts with the external
identifier are found, a reference to an empty list is returned.
- Returntype : reference to a list of transcripts
+ Returntype : Listref of Bio::EnsEMBL::Transcript objects
Exceptions : none
Caller : general
Status : Stable
@@ -441,10 +450,11 @@ sub fetch_all_by_external_name {
=head2 fetch_by_display_label
- Arg [1] : string $label
- Example : my $transcript = $transcriptAdaptor->fetch_by_display_label( "BRCA2" );
- Description: returns the transcript which has the given display label or undef if
- there is none. If there are more than 1, only the first is reported.
+ Arg [1] : String $label - display label of transcript to fetch
+ Example : my $tr = $tr_adaptor->fetch_by_display_label("BRCA2");
+ Description: Returns the transcript which has the given display label or
+ undef if there is none. If there are more than 1, only the first
+ is reported.
Returntype : Bio::EnsEMBL::Transcript
Exceptions : none
Caller : general
@@ -456,18 +466,21 @@ sub fetch_by_display_label {
my $self = shift;
my $label = shift;
- my ( $transcript ) = @{$self->generic_fetch( "x.display_label = \"$label\"" )};
+ my $constraint = "x.display_label = '$label' AND t.is_current = 1";
+ my ($transcript) = @{ $self->generic_fetch($constraint) };
+
return $transcript;
}
=head2 fetch_all_by_exon_stable_id
- Arg [1] : string $stable_id
+ Arg [1] : String $stable_id
The stable id of an exon in a transcript
- Example : $trans = $trans_adptr->fetch_all_by_exon_stable_id('ENSE00000309301');
- Description: Retrieves a list of transcripts via an exon stable id
- Returntype : Bio::EnsEMBL::Transcript
+ Example : my $tr = $tr_adaptor->fetch_all_by_exon_stable_id
+ ('ENSE00000309301');
+ Description: Retrieves a list of transcripts via an exon stable id.
+ Returntype : Listref of Bio::EnsEMBL::Transcript objects
Exceptions : none
Caller : general
Status : Stable
@@ -475,18 +488,24 @@ sub fetch_by_display_label {
=cut
sub fetch_all_by_exon_stable_id {
- my ($self, $stable_id ) = @_;
+ my ($self, $stable_id) = @_;
+
my @trans ;
- my $sth = $self->prepare( qq( SELECT et.transcript_id
- FROM exon_transcript as et,
- exon_stable_id as esi
- WHERE esi.exon_id = et.exon_id and
- esi.stable_id = ? ));
- $sth->bind_param(1,"$stable_id",SQL_VARCHAR);
+
+ my $sth = $self->prepare(qq(
+ SELECT t.transcript_id
+ FROM exon_transcript et, exon_stable_id esi, transcript t
+ WHERE esi.exon_id = et.exon_id
+ AND et.transcript_id = t.transcript_id
+ AND esi.stable_id = ?
+ AND t.is_current = 1
+ ));
+
+ $sth->bind_param(1, $stable_id, SQL_VARCHAR);
$sth->execute();
while( my $id = $sth->fetchrow_array ) {
- my $transcript = $self->fetch_by_dbID( $id );
+ my $transcript = $self->fetch_by_dbID($id);
push(@trans, $transcript) if $transcript;
}
@@ -502,18 +521,18 @@ sub fetch_all_by_exon_stable_id {
Arg [1] : Bio::EnsEMBL::Transcript $transcript
The transcript to be written to the database
- Arg [2] : int $gene_dbID
+ Arg [2] : Int $gene_dbID
The identifier of the gene that this transcript is associated
with
- Arg [3] : (optional) int $analysis_id
+ Arg [3] : DEPRECATED (optional) Int $analysis_id
The analysis_id to use when storing this gene. This is for
backward compatibility only and used to fall back to the gene
analysis_id if no analysis object is attached to the transcript
(which you should do for new code).
- Example : $transID = $transcriptAdaptor->store($transcript, $gene->dbID);
+ Example : $transID = $tr_adaptor->store($transcript, $gene->dbID);
Description: Stores a transcript in the database and returns the new
internal identifier for the stored transcript.
- Returntype : int
+ Returntype : Int
Exceptions : none
Caller : general
Status : Stable
@@ -536,6 +555,10 @@ sub store {
#force lazy-loading of exons and ensure coords are correct
$transcript->recalculate_coordinates();
+ # default to is_current = 1 if this attribute is not set
+ my $is_current = $transcript->is_current;
+ $is_current = 1 unless (defined($is_current));
+
# store analysis
my $analysis = $transcript->analysis();
my $new_analysis_id;
@@ -565,7 +588,7 @@ sub store {
my $exons = $transcript->get_all_Exons();
my $exonAdaptor = $db->get_ExonAdaptor();
foreach my $exon ( @{$exons} ) {
- $exonAdaptor->store( $exon );
+ $exonAdaptor->store($exon);
}
my $original_translation = $transcript->translation();
@@ -585,19 +608,21 @@ sub store {
my $tst = $self->prepare(qq(
INSERT INTO transcript
(gene_id, analysis_id, seq_region_id, seq_region_start,
- seq_region_end, seq_region_strand, biotype, status, description)
- VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
+ seq_region_end, seq_region_strand, biotype, status, description,
+ is_current)
+ VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
));
- $tst->bind_param(1,$gene_dbID,SQL_INTEGER);
- $tst->bind_param(2,$new_analysis_id,SQL_INTEGER);
- $tst->bind_param(3,$seq_region_id,SQL_INTEGER);
- $tst->bind_param(4,$transcript->start,SQL_INTEGER);
- $tst->bind_param(5,$transcript->end,SQL_INTEGER);
- $tst->bind_param(6,$transcript->strand,SQL_TINYINT);
- $tst->bind_param(7,$transcript->biotype,SQL_VARCHAR);
- $tst->bind_param(8,$transcript->status,SQL_VARCHAR);
- $tst->bind_param(9,$transcript->description,SQL_LONGVARCHAR);
+ $tst->bind_param(1, $gene_dbID, SQL_INTEGER);
+ $tst->bind_param(2, $new_analysis_id, SQL_INTEGER);
+ $tst->bind_param(3, $seq_region_id, SQL_INTEGER);
+ $tst->bind_param(4, $transcript->start, SQL_INTEGER);
+ $tst->bind_param(5, $transcript->end, SQL_INTEGER);
+ $tst->bind_param(6, $transcript->strand, SQL_TINYINT);
+ $tst->bind_param(7, $transcript->biotype, SQL_VARCHAR);
+ $tst->bind_param(8, $transcript->status, SQL_VARCHAR);
+ $tst->bind_param(9, $transcript->description, SQL_LONGVARCHAR);
+ $tst->bind_param(10, $is_current, SQL_INTEGER);
$tst->execute();
$tst->finish();
@@ -679,8 +704,8 @@ sub store {
if(defined($dxref_id)) {
my $sth = $self->prepare( "update transcript set display_xref_id = ?".
" where transcript_id = ?");
- $sth->bind_param(1,$dxref_id,SQL_INTEGER);
- $sth->bind_param(2,$transc_dbID,SQL_INTEGER);
+ $sth->bind_param(1, $dxref_id, SQL_INTEGER);
+ $sth->bind_param(2, $transc_dbID, SQL_INTEGER);
$sth->execute();
$dxref->dbID($dxref_id);
$dxref->adaptor($dbEntryAdaptor);
@@ -702,9 +727,9 @@ sub store {
." values (?,?,?)");
my $rank = 1;
foreach my $exon ( @{$transcript->get_all_Exons} ) {
- $etst->bind_param(1,$exon->dbID,SQL_INTEGER);
- $etst->bind_param(2,$transc_dbID,SQL_INTEGER);
- $etst->bind_param(3,$rank,SQL_INTEGER);
+ $etst->bind_param(1, $exon->dbID, SQL_INTEGER);
+ $etst->bind_param(2, $transc_dbID, SQL_INTEGER);
+ $etst->bind_param(3, $rank, SQL_INTEGER);
$etst->execute();
$rank++;
}
@@ -726,20 +751,11 @@ sub store {
" stable_id = ?, ".
"version = ?, ";
- $statement .= "created_date = " . $self->db->dbc->from_seconds_to_date($transcript->created_date()) . ",";
-
-# if( $transcript->created_date() ) {
-# $statement .= "created_date = from_unixtime( ".$transcript->created_date()."),";
-# } else {
-# $statement .= "created_date = \"0000-00-00 00:00:00\",";
-# }
- $statement .= "modified_date = " . $self->db->dbc->from_seconds_to_date($transcript->modified_date()) ;
+ $statement .= "created_date = " .
+ $self->db->dbc->from_seconds_to_date($transcript->created_date()) . ",";
-# if( $transcript->modified_date() ) {
-# $statement .= "modified_date = from_unixtime( ".$transcript->modified_date().")";
-# } else {
-# $statement .= "modified_date = \"0000-00-00 00:00:00\"";
-# }
+ $statement .= "modified_date = " .
+ $self->db->dbc->from_seconds_to_date($transcript->modified_date()) ;
my $sth = $self->prepare($statement);
$sth->bind_param(1,$transc_dbID,SQL_INTEGER);
@@ -749,11 +765,10 @@ sub store {
$sth->finish();
}
-
-
# Now the supporting evidence
# should be stored from featureAdaptor
- my $sql = "insert into transcript_supporting_feature (transcript_id, feature_id, feature_type)
+ my $sql = "insert into transcript_supporting_feature
+ (transcript_id, feature_id, feature_type)
values(?, ?, ?)";
my $sf_sth = $self->prepare($sql);
@@ -780,9 +795,9 @@ sub store {
next;
}
- $sf_sth->bind_param(1,$transc_dbID,SQL_INTEGER);
- $sf_sth->bind_param(2,$sf->dbID,SQL_INTEGER);
- $sf_sth->bind_param(3,$type,SQL_VARCHAR);
+ $sf_sth->bind_param(1, $transc_dbID, SQL_INTEGER);
+ $sf_sth->bind_param(2, $sf->dbID, SQL_INTEGER);
+ $sf_sth->bind_param(3, $type, SQL_VARCHAR);
$sf_sth->execute();
}
@@ -802,13 +817,13 @@ sub store {
=head2 get_Interpro_by_transid
- Arg [1] : string $trans
- the stable if of the trans to obtain
- Example : @i = $trans_adaptor->get_Interpro_by_transid($trans->stable_id());
- Description: gets interpro accession numbers by transcript stable id.
+ Arg [1] : String $trans_stable_id
+ The stable if of the transcript to obtain
+ Example : @i = $tr_adaptor->get_Interpro_by_transid($trans->stable_id());
+ Description: Gets interpro accession numbers by transcript stable id.
A hack really - we should have a much more structured
- system than this
- Returntype : listref of strings
+ system than this.
+ Returntype : listref of strings (Interpro_acc:description)
Exceptions : none
Caller : domainview? , GeneView
Status : Stable
@@ -816,48 +831,51 @@ sub store {
=cut
sub get_Interpro_by_transid {
- my ($self,$transid) = @_;
-
- my $sth = $self->prepare
- ("SELECT STRAIGHT_JOIN i.interpro_ac, x.description " .
- "FROM transcript_stable_id tsi, ".
- "translation tl, ".
- "protein_feature pf, ".
- "interpro i, " .
- "xref x " .
- "WHERE tsi.stable_id = ? " .
- "AND tl.transcript_id = tsi.transcript_id " .
- "AND tl.translation_id = pf.translation_id " .
- "AND i.id = pf.hit_id " .
- "AND i.interpro_ac = x.dbprimary_acc");
-
- $sth->bind_param(1,$transid,SQL_VARCHAR);
- $sth->execute();
-
- my @out;
- my %h;
- while( (my $arr = $sth->fetchrow_arrayref()) ) {
- if( $h{$arr->[0]} ) { next; }
- $h{$arr->[0]}=1;
- my $string = $arr->[0] .":".$arr->[1];
- push(@out,$string);
- }
-
- return \@out;
-}
+ my ($self,$trans_stable_id) = @_;
+
+ my $sth = $self->prepare(qq(
+ SELECT STRAIGHT_JOIN i.interpro_ac, x.description
+ FROM transcript_stable_id tsi,
+ transcript t,
+ translation tl,
+ protein_feature pf,
+ interpro i,
+ xref x
+ WHERE tsi.stable_id = ?
+ AND tl.transcript_id = tsi.transcript_id
+ AND tl.translation_id = pf.translation_id
+ AND i.id = pf.hit_id
+ AND i.interpro_ac = x.dbprimary_acc
+ AND tsi.transcript_id = t.transcript_id
+ AND t.is_current = 1
+ ));
+ $sth->bind_param(1, $trans_stable_id, SQL_VARCHAR);
+ $sth->execute();
+ my @out;
+ my %h;
+ while( (my $arr = $sth->fetchrow_arrayref()) ) {
+ if( $h{$arr->[0]} ) { next; }
+ $h{$arr->[0]}=1;
+ my $string = $arr->[0] .":".$arr->[1];
+ push(@out,$string);
+ }
+
+ return \@out;
+}
=head2 remove
Arg [1] : Bio::EnsEMBL::Transcript $transcript
- Example : $transcript_adaptor->remove($transcript);
+ The transcript to remove from the database
+ Example : $tr_adaptor->remove($transcript);
Description: Removes a transcript completely from the database, and all
associated information.
This method is usually called by the GeneAdaptor::remove method
because this method will not preform the removal of genes
- which are associated with this transcript. Do not call this
+ which are associated with this transcript. Do not call this
method directly unless you know there are no genes associated
with the transcript!
Returntype : none
@@ -883,7 +901,7 @@ sub remove {
"not PredictionTranscripts");
}
- if( !$transcript->is_stored($self->db()) ) {
+ if ( !$transcript->is_stored($self->db()) ) {
warning("Cannot remove transcript ". $transcript->dbID .". Is not stored ".
"in this database.");
return;
@@ -897,7 +915,7 @@ sub remove {
my $sfsth = $self->prepare("SELECT feature_type, feature_id " .
"FROM transcript_supporting_feature " .
"WHERE transcript_id = ?");
- $sfsth->bind_param(1,$transcript->dbID,SQL_INTEGER);
+ $sfsth->bind_param(1, $transcript->dbID, SQL_INTEGER);
$sfsth->execute();
while(my ($type, $feature_id) = $sfsth->fetchrow()){
if($type eq 'protein_align_feature'){
@@ -917,7 +935,7 @@ sub remove {
# delete the association to supporting features
$sfsth = $self->prepare("DELETE FROM transcript_supporting_feature WHERE transcript_id = ?");
- $sfsth->bind_param(1,$transcript->dbID,SQL_INTEGER);
+ $sfsth->bind_param(1, $transcript->dbID, SQL_INTEGER);
$sfsth->execute();
$sfsth->finish();
@@ -950,7 +968,7 @@ sub remove {
my $sth = $self->prepare( "SELECT count(*)
FROM exon_transcript
WHERE exon_id = ?" );
- $sth->bind_param(1,$exon->dbID,SQL_INTEGER);
+ $sth->bind_param(1, $exon->dbID, SQL_INTEGER);
$sth->execute();
my ($count) = $sth->fetchrow_array();
$sth->finish();
@@ -962,18 +980,18 @@ sub remove {
my $sth = $self->prepare( "DELETE FROM exon_transcript
WHERE transcript_id = ?" );
- $sth->bind_param(1,$transcript->dbID,SQL_INTEGER);
+ $sth->bind_param(1, $transcript->dbID, SQL_INTEGER);
$sth->execute();
$sth = $self->prepare( "DELETE FROM transcript_stable_id
WHERE transcript_id = ?" );
- $sth->bind_param(1,$transcript->dbID,SQL_INTEGER);
+ $sth->bind_param(1, $transcript->dbID, SQL_INTEGER);
$sth->execute();
$sth->finish();
$sth = $self->prepare( "DELETE FROM transcript
WHERE transcript_id = ?" );
- $sth->bind_param(1,$transcript->dbID,SQL_INTEGER);
+ $sth->bind_param(1, $transcript->dbID, SQL_INTEGER);
$sth->execute();
$sth->finish();
@@ -984,18 +1002,18 @@ sub remove {
}
-
=head2 update
- Arg [1] : Bio::EnsEMBL::Transcript
- Example : $transcript_adaptor->update($transcript);
- Description: Updates a transcript in the database
+ Arg [1] : Bio::EnsEMBL::Transcript $transcript
+ The transcript to update
+ Example : $tr_adaptor->update($transcript);
+ Description: Updates a transcript in the database.
Returntype : None
- Exceptions : thrown if the $transcript is not a Bio::EnsEMBL::Transcript
- warn if trying to update the number of attached exons. This
- is a far more complex process and is not yet implemented.
+ Exceptions : thrown if the $transcript is not a Bio::EnsEMBL::Transcript.
warn if the method is called on a transcript that does not exist
in the database.
+ Should warn if trying to update the number of attached exons, but
+ this is a far more complex process and is not yet implemented.
Caller : general
Status : Stable
@@ -1003,6 +1021,7 @@ sub remove {
sub update {
my ($self, $transcript) = @_;
+
my $update = 0;
if( !defined $transcript || !ref $transcript ||
@@ -1016,7 +1035,8 @@ sub update {
display_xref_id = ?,
description = ?,
biotype = ?,
- status = ?
+ status = ?,
+ is_current = ?
WHERE transcript_id = ?
);
@@ -1031,24 +1051,25 @@ sub update {
my $sth = $self->prepare( $update_transcript_sql );
- $sth->bind_param(1,$transcript->analysis->dbID,SQL_INTEGER);
- $sth->bind_param(2,$display_xref_id,SQL_INTEGER);
- $sth->bind_param(3,$transcript->description,SQL_LONGVARCHAR);
- $sth->bind_param(4,$transcript->biotype,SQL_VARCHAR);
- $sth->bind_param(5,$transcript->status,SQL_VARCHAR);
- $sth->bind_param(6,$transcript->dbID,SQL_INTEGER);
+ $sth->bind_param(1, $transcript->analysis->dbID, SQL_INTEGER);
+ $sth->bind_param(2, $display_xref_id, SQL_INTEGER);
+ $sth->bind_param(3, $transcript->description, SQL_LONGVARCHAR);
+ $sth->bind_param(4, $transcript->biotype, SQL_VARCHAR);
+ $sth->bind_param(5, $transcript->status, SQL_VARCHAR);
+ $sth->bind_param(6, $transcript->is_current, SQL_INTEGER);
+ $sth->bind_param(7, $transcript->dbID, SQL_INTEGER);
$sth->execute();
}
+
=head2 list_dbIDs
- Arg [1] : none
- Example : @transcript_ids = @{$transcript_adaptor->list_dbIDs()};
- Description: Gets an array of internal ids for all transcripts in the current db
- Returntype : list of ints
+ Example : @transcript_ids = @{ $t_adaptor->list_dbIDs };
+ Description: Gets a list of internal ids for all transcripts in the db.
+ Returntype : Listref of Ints
Exceptions : none
- Caller : ?
+ Caller : general
Status : Stable
=cut
@@ -1059,15 +1080,15 @@ sub list_dbIDs {
return $self->_list_dbIDs("transcript");
}
-=head2 list_stable_dbIDs
- Arg [1] : none
- Example : @stable_trans_ids = @{$transcript_adaptor->list_stable_dbIDs()};
- Description: Gets an array of stable ids for all transcripts in the current
+=head2 list_stable_ids
+
+ Example : @stable_trans_ids = @{ $transcript_adaptor->list_stable_ids };
+ Description: Gets a list of stable ids for all transcripts in the current
database.
- Returntype : listref of ints
+ Returntype : Listref of Strings
Exceptions : none
- Caller : ?
+ Caller : general
Status : Stable
=cut
@@ -1082,10 +1103,11 @@ sub list_stable_ids {
#_objs_from_sth
# Arg [1] : StatementHandle $sth
-# Example : none
+# Arg [2] : Bio::EnsEMBL::AssemblyMapper $mapper
+# Arg [3] : Bio::EnsEMBL::Slice $dest_slice
# Description: PROTECTED implementation of abstract superclass method.
-# responsible for the creation of Transcripts
-# Returntype : listref of Bio::EnsEMBL::Transcripts in target coord system
+# Responsible for the creation of Transcripts.
+# Returntype : Listref of Bio::EnsEMBL::Transcripts in target coord system
# Exceptions : none
# Caller : internal
# Status : Stable
@@ -1110,7 +1132,7 @@ sub _objs_from_sth {
my %sr_cs_hash;
my ( $transcript_id, $seq_region_id, $seq_region_start, $seq_region_end,
- $seq_region_strand, $analysis_id, $gene_id,
+ $seq_region_strand, $analysis_id, $gene_id, $is_current,
$display_xref_id, $stable_id, $version, $created_date, $modified_date,
$description, $biotype, $status,
$external_name, $external_db, $external_status, $external_db_name,
@@ -1118,10 +1140,11 @@ sub _objs_from_sth {
$sth->bind_columns( \$transcript_id, \$seq_region_id, \$seq_region_start,
\$seq_region_end, \$seq_region_strand, \$analysis_id,
- \$gene_id, \$display_xref_id, \$stable_id, \$version,
- \$created_date, \$modified_date,
+ \$gene_id, \$is_current, \$display_xref_id, \$stable_id,
+ \$version, \$created_date, \$modified_date,
\$description, \$biotype, \$status,
- \$external_name, \$external_db, \$external_status, \$external_db_name,
+ \$external_name, \$external_db, \$external_status,
+ \$external_db_name,
\$info_type, \$info_text);
my $asm_cs;
@@ -1243,18 +1266,19 @@ sub _objs_from_sth {
my $display_xref;
if( $display_xref_id ) {
- $display_xref = Bio::EnsEMBL::DBEntry->new_fast
- ({ 'dbID' => $display_xref_id,
+ $display_xref = Bio::EnsEMBL::DBEntry->new_fast({
+ 'dbID' => $display_xref_id,
'adaptor' => $dbEntryAdaptor,
'display_id' => $external_name,
'db_display_name' => $external_db_name,
- 'dbname' => $external_db});
+ 'dbname' => $external_db
+ });
}
#finally, create the new transcript
- push @transcripts, Bio::EnsEMBL::Transcript->new
- ( '-analysis' => $analysis,
+ push @transcripts, Bio::EnsEMBL::Transcript->new(
+ '-analysis' => $analysis,
'-start' => $seq_region_start,
'-end' => $seq_region_end,
'-strand' => $seq_region_strand,
@@ -1272,7 +1296,9 @@ sub _objs_from_sth {
'-display_xref' => $display_xref,
'-description' => $description,
'-biotype' => $biotype,
- '-status' => $status );
+ '-status' => $status,
+ '-is_current' => $is_current
+ );
}
return \@transcripts;
@@ -1281,209 +1307,223 @@ sub _objs_from_sth {
=head2 fetch_all_by_exon_supporting_evidence
- Arg [1] : string hit_name
- Arg [2] : string feature type
- (one of "dna_align_feature" or "protein_align_feature")
+ Arg [1] : String $hit_name
+ Name of supporting feature
+ Arg [2] : String $feature_type
+ one of "dna_align_feature" or "protein_align_feature"
Arg [3] : (optional) Bio::Ensembl::Analysis
- Example : $transcripts = $transcript_adaptor->fetch_all_by_exon_supporting_evidence();
- Description: Gets all the transcripts with exons which have a specified hit on a particular
- type of feature. Optionally filter by analysis.
- Returntype : Listref of Bio::EnsEMBL::Transcript
+ Example : $tr = $tr_adaptor->fetch_all_by_exon_supporting_evidence
+ ('XYZ', 'dna_align_feature');
+ Description: Gets all the transcripts with exons which have a specified hit
+ on a particular type of feature. Optionally filter by analysis.
+ Returntype : Listref of Bio::EnsEMBL::Transcript objects
Exceptions : If feature_type is not of correct type.
- Caller : ?
+ Caller : general
Status : At Risk
=cut
sub fetch_all_by_exon_supporting_evidence {
+ my ($self, $hit_name, $feature_type, $analysis) = @_;
- my ($self, $hit_name, $feature_type, $analysis) = @_;
-
- if($feature_type !~ /(dna)|(protein)_align_feature/) {
- throw("feature type must be dna_align_feature or protein_align_feature");
- }
-
- my $anal_from = ", analysis a " if ($analysis);
- my $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? " if ($analysis);
-
- my $sql = "SELECT DISTINCT(t.transcript_id)
- FROM transcript t,
- exon_transcript et,
- supporting_feature sf,
- $feature_type f
- $anal_from
- WHERE t.transcript_id = et.transcript_id
- AND et.exon_id = sf.exon_id
- AND sf.feature_id = f.${feature_type}_id
- AND sf.feature_type = ?
- AND f.hit_name=?
- $anal_where";
+ if($feature_type !~ /(dna)|(protein)_align_feature/) {
+ throw("feature type must be dna_align_feature or protein_align_feature");
+ }
- my $sth = $self->prepare($sql);
+ my $anal_from = ", analysis a " if ($analysis);
+ my $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? "
+ if ($analysis);
+
+ my $sql = qq(
+ SELECT DISTINCT(t.transcript_id)
+ FROM transcript t,
+ exon_transcript et,
+ supporting_feature sf,
+ $feature_type f
+ $anal_from
+ WHERE t.transcript_id = et.transcript_id
+ AND t.is_current = 1
+ AND et.exon_id = sf.exon_id
+ AND sf.feature_id = f.${feature_type}_id
+ AND sf.feature_type = ?
+ AND f.hit_name=?
+ $anal_where
+ );
- $sth->bind_param(1, $feature_type, SQL_VARCHAR);
- $sth->bind_param(2, $hit_name, SQL_VARCHAR);
- $sth->bind_param(3, $analysis->dbID(), SQL_INTEGER) if ($analysis);
+ my $sth = $self->prepare($sql);
- $sth->execute();
+ $sth->bind_param(1, $feature_type, SQL_VARCHAR);
+ $sth->bind_param(2, $hit_name, SQL_VARCHAR);
+ $sth->bind_param(3, $analysis->dbID(), SQL_INTEGER) if ($analysis);
- my @transcripts;
+ $sth->execute();
- while( my $id = $sth->fetchrow_array ) {
- my $transcript = $self->fetch_by_dbID( $id );
- push(@transcripts, $transcript) if $transcript;
- }
+ my @transcripts;
- return \@transcripts;
+ while( my $id = $sth->fetchrow_array ) {
+ my $transcript = $self->fetch_by_dbID( $id );
+ push(@transcripts, $transcript) if $transcript;
+ }
+ return \@transcripts;
}
=head2 fetch_all_by_transcript_supporting_evidence
- Arg [1] : string hit_name
- Arg [2] : string feature type
- (one of "dna_align_feature" or "protein_align_feature")
+ Arg [1] : String $hit_name
+ Name of supporting feature
+ Arg [2] : String $feature_type
+ one of "dna_align_feature" or "protein_align_feature"
Arg [3] : (optional) Bio::Ensembl::Analysis
- Example : $transcripts = $transcript_adaptor->fetch_all_by_transcript_supporting_evidence();
- Description: Gets all the transcripts with evidence for a specified hit on a particular
- type of feature. Optionally filter by analysis.
- Returntype : Listref of Bio::EnsEMBL::Transcript
+ Example : $transcripts = $transcript_adaptor->fetch_all_by_transcript_supporting_evidence('XYZ', 'dna_align_feature');
+ Description: Gets all the transcripts with evidence for a specified hit on a
+ particular type of feature. Optionally filter by analysis.
+ Returntype : Listref of Bio::EnsEMBL::Transcript objects
Exceptions : If feature_type is not of correct type.
- Caller : ?
+ Caller : general
Status : At Risk
=cut
sub fetch_all_by_transcript_supporting_evidence {
+
+ my ($self, $hit_name, $feature_type, $analysis) = @_;
- my ($self, $hit_name, $feature_type, $analysis) = @_;
-
- if($feature_type !~ /(dna)|(protein)_align_feature/) {
- throw("feature type must be dna_align_feature or protein_align_feature");
- }
+ if($feature_type !~ /(dna)|(protein)_align_feature/) {
+ throw("feature type must be dna_align_feature or protein_align_feature");
+ }
- my $anal_from = ", analysis a " if ($analysis);
- my $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? " if ($analysis);
+ my $anal_from = ", analysis a " if ($analysis);
+ my $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? "
+ if ($analysis);
+
+ my $sql = qq(
+ SELECT DISTINCT(t.transcript_id)
+ FROM transcript t,
+ transcript_supporting_feature sf,
+ $feature_type f
+ $anal_from
+ WHERE t.transcript_id = sf.transcript_id
+ AND t.is_current = 1
+ AND sf.feature_id = f.${feature_type}_id
+ AND sf.feature_type = ?
+ AND f.hit_name=?
+ $anal_where
+ );
- my $sql = "SELECT DISTINCT(t.transcript_id)
- FROM transcript t,
- transcript_supporting_feature sf,
- $feature_type f
- $anal_from
- WHERE t.transcript_id = sf.transcript_id
- AND sf.feature_id = f.${feature_type}_id
- AND sf.feature_type = ?
- AND f.hit_name=?
- $anal_where";
+ my $sth = $self->prepare($sql);
- my $sth = $self->prepare($sql);
+ $sth->bind_param(1, $feature_type, SQL_VARCHAR);
+ $sth->bind_param(2, $hit_name, SQL_VARCHAR);
+ $sth->bind_param(3, $analysis->dbID(), SQL_INTEGER) if ($analysis);
- $sth->bind_param(1, $feature_type, SQL_VARCHAR);
- $sth->bind_param(2, $hit_name, SQL_VARCHAR);
- $sth->bind_param(3, $analysis->dbID(), SQL_INTEGER) if ($analysis);
+ $sth->execute();
- $sth->execute();
+ my @transcripts;
- my @transcripts;
+ while( my $id = $sth->fetchrow_array ) {
+ my $transcript = $self->fetch_by_dbID( $id );
+ push(@transcripts, $transcript) if $transcript;
+ }
- while( my $id = $sth->fetchrow_array ) {
- my $transcript = $self->fetch_by_dbID( $id );
- push(@transcripts, $transcript) if $transcript;
- }
+ return \@transcripts;
+}
- return \@transcripts;
-}
+##########################
+# #
+# DEPRECATED METHODS #
+# #
+##########################
=head2 get_display_xref
- Description: DEPRECATED use $transcript->display_xref()
+ Description: DEPRECATED. Use $transcript->display_xref() instead.
=cut
sub get_display_xref {
my ($self, $transcript) = @_;
- deprecate( "display_xref should be retreived from Transcript object directly." );
+ deprecate("display_xref should be retreived from Transcript object directly.");
- if( !defined $transcript ) {
- throw("Must call with a Transcript object");
+ if ( !defined $transcript ) {
+ throw("Must call with a Transcript object");
}
- my $sth = $self->prepare("SELECT e.db_name,
- x.display_label,
- e.db_external_name,
- x.xref_id
- FROM transcript t,
- xref x,
- external_db e
- WHERE t.transcript_id = ?
- AND t.display_xref_id = x.xref_id
- AND x.external_db_id = e.external_db_id
- ");
- $sth->bind_param(1,$transcript->dbID,SQL_INTEGER);
+ my $sth = $self->prepare(qq(
+ SELECT e.db_name,
+ x.display_label,
+ e.db_external_name,
+ x.xref_id
+ FROM transcript t,
+ xref x,
+ external_db e
+ WHERE t.transcript_id = ?
+ AND t.display_xref_id = x.xref_id
+ AND x.external_db_id = e.external_db_id
+ ));
+
+ $sth->bind_param(1, $transcript->dbID, SQL_INTEGER);
$sth->execute();
-
- my ($db_name, $display_label, $xref_id, $display_db_name ) = $sth->fetchrow_array();
- if( !defined $xref_id ) {
+ my ($db_name, $display_label, $xref_id, $display_db_name ) =
+ $sth->fetchrow_array();
+
+ if ( !defined $xref_id ) {
return undef;
}
- my $db_entry = Bio::EnsEMBL::DBEntry->new
- (
+ my $db_entry = Bio::EnsEMBL::DBEntry->new(
-dbid => $xref_id,
-adaptor => $self->db->get_DBEntryAdaptor(),
-dbname => $db_name,
-display_id => $display_label
-db_display_name => $display_db_name
- );
+ );
return $db_entry;
}
-
-
=head2 get_stable_entry_info
- Description: DEPRECATED Use $transcript->stable_id()
+ Description: DEPRECATED. Use $transcript->stable_id() instead.
=cut
sub get_stable_entry_info {
- my ($self,$transcript) = @_;
+ my ($self, $transcript) = @_;
- deprecate( "Stable ids should be loaded directly now" );
+ deprecate("Stable ids should be loaded directly now");
- unless( defined $transcript && ref $transcript &&
+ unless ( defined $transcript && ref $transcript &&
$transcript->isa('Bio::EnsEMBL::Transcript') ) {
throw("Needs a Transcript object, not a $transcript");
}
- my $sth = $self->prepare("SELECT stable_id, version
- FROM transcript_stable_id
- WHERE transcript_id = ?");
- $sth->bind_param(1,$transcript->dbID,SQL_INTEGER);
+ my $sth = $self->prepare(qq(
+ SELECT stable_id, version
+ FROM transcript_stable_id
+ WHERE transcript_id = ?
+ ));
+
+ $sth->bind_param(1, $transcript->dbID, SQL_INTEGER);
$sth->execute();
my @array = $sth->fetchrow_array();
$transcript->{'_stable_id'} = $array[0];
$transcript->{'_version'} = $array[1];
-
return 1;
}
-
-
=head2 fetch_all_b_DBEntry
- Description: DEPRECATED this method has been renamed
- fetch_all_by_external_name
+ Description: DEPRECATED. Use fetch_all_by_external_name() instead.
=cut
--
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