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Commit b3861b19 authored by Arne Stabenau's avatar Arne Stabenau
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added biotype, source, confidence removed description as separate table

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modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+ 49
− 41
View file @ b3861b19
......@@ -71,7 +71,6 @@ sub _tables {
my $self = shift;
return ([ 'gene', 'g' ],
[ 'gene_description', 'gd' ],
[ 'gene_stable_id', 'gsi' ],
[ 'xref', 'x' ],
[ 'external_db' , 'exdb' ]);
......@@ -91,8 +90,9 @@ sub _columns {
my $self = shift;
return qw( g.gene_id g.seq_region_id g.seq_region_start g.seq_region_end
g.seq_region_strand g.analysis_id g.type g.display_xref_id
gd.description gsi.stable_id gsi.version UNIX_TIMESTAMP(gsi.created_date)
g.seq_region_strand g.analysis_id g.biotype g.display_xref_id
g.description g.confidence g.source
gsi.stable_id gsi.version UNIX_TIMESTAMP(gsi.created_date)
UNIX_TIMESTAMP(gsi.modified_date)
x.display_label x.dbprimary_acc x.description x.version
exdb.db_name exdb.status exdb.release );
......@@ -100,8 +100,7 @@ sub _columns {
sub _left_join {
return ( [ 'gene_description', "gd.gene_id = g.gene_id" ],
[ 'gene_stable_id', "gsi.gene_id = g.gene_id" ],
return ( [ 'gene_stable_id', "gsi.gene_id = g.gene_id" ],
[ 'xref', "x.xref_id = g.display_xref_id" ],
[ 'external_db', "exdb.external_db_id = x.external_db_id" ] );
}
......@@ -535,9 +534,15 @@ sub fetch_all_by_external_name {
my $entryAdaptor = $self->db->get_DBEntryAdaptor();
my @ids = $entryAdaptor->list_gene_ids_by_extids( $external_id );
my ( @ids, @result );
@ids = $entryAdaptor->list_gene_ids_by_extids( $external_id );
return $self->fetch_all_by_dbID_list(\@ids);
my $genes = $self->fetch_all_by_dbID_list(\@ids);
my %genes_by_dbIDs = map { $_->dbID(),$_ } @$genes;
@result = map { $genes_by_dbIDs{ $_ } } @ids;
return \@result;
}
......@@ -742,7 +747,7 @@ sub store {
$analysis_id = $db->get_AnalysisAdaptor->store($analysis);
}
my $type = $gene->type || "";
my $type = $gene->biotype || "";
my $original = $gene;
my $original_transcripts = $gene->get_all_Transcripts();
......@@ -751,22 +756,28 @@ sub store {
my $store_gene_sql =
"INSERT INTO gene " .
"SET type = ?, " .
"SET biotype = ?, " .
"analysis_id = ?, " .
"seq_region_id = ?, " .
"seq_region_start = ?, " .
"seq_region_end = ?, " .
"seq_region_strand = ?";
"seq_region_strand = ?, ".
"description = ?, " .
"source = ?, ".
"confidence = ? ";
my $sth = $self->prepare( $store_gene_sql );
$sth->execute(
"$type",
$analysis_id,
$seq_region_id,
$gene->start(),
$gene->end(),
$gene->strand()
);
$type,
$analysis_id,
$seq_region_id,
$gene->start(),
$gene->end(),
$gene->strand(),
$gene->description(),
$gene->source(),
$gene->confidence()
);
$sth->finish();
my $gene_dbID = $sth->{'mysql_insertid'};
......@@ -796,16 +807,6 @@ sub store {
}
# store the gene description associated with this gene if there is
# one
my $desc = $gene->description();
if(defined($desc)) {
$sth = $self->prepare("INSERT INTO gene_description " .
" SET gene_id = ?, " .
" description = ?" );
$sth->execute($gene_dbID, $desc);
$sth->finish();
}
# store the dbentries associated with this gene
my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
......@@ -945,12 +946,6 @@ sub remove {
$sth->execute( $gene->dbID );
$sth->finish();
# remove this genes description
$sth = $self->prepare( "delete from gene_description where gene_id = ?" );
$sth->execute( $gene->dbID() );
$sth->finish();
# remove this gene from the database
$sth = $self->prepare( "delete from gene where gene_id = ? " );
......@@ -1041,9 +1036,10 @@ sub update {
my $update_gene_sql = "
UPDATE gene
SET type = ?,
SET biotype = ?,
analysis_id = ?,
display_xref_id = ?
display_xref_id = ?,
confidence = ?
WHERE gene_id = ?";
my $display_xref = $gene->display_xref();
......@@ -1059,6 +1055,7 @@ sub update {
$sth->execute($gene->type(),
$gene->analysis->dbID(),
$display_xref_id,
$gene->confidence(),
$gene->dbID()
);
......@@ -1096,15 +1093,16 @@ sub _objs_from_sth {
my %sr_cs_hash;
my ( $gene_id, $seq_region_id, $seq_region_start, $seq_region_end,
$seq_region_strand, $analysis_id, $type, $display_xref_id,
$seq_region_strand, $analysis_id, $biotype, $display_xref_id,
$gene_description, $stable_id, $version, $created_date,
$modified_date, $xref_display_id,
$modified_date, $xref_display_id, $confidence, $source,
$xref_primary_acc, $xref_desc, $xref_version, $external_name,
$external_db, $external_status, $external_release );
$sth->bind_columns( \$gene_id, \$seq_region_id, \$seq_region_start,
\$seq_region_end, \$seq_region_strand, \$analysis_id, \$type,
\$display_xref_id, \$gene_description, \$stable_id, \$version,
\$seq_region_end, \$seq_region_strand, \$analysis_id, \$biotype,
\$display_xref_id, \$gene_description, \$confidence, \$source,
\$stable_id, \$version,
\$created_date, \$modified_date,
\$xref_display_id, \$xref_primary_acc, \$xref_desc, \$xref_version,
\$external_db, \$external_status,
......@@ -1222,7 +1220,7 @@ sub _objs_from_sth {
#finally, create the new gene
push @genes, Bio::EnsEMBL::Gene->new
( '-analysis' => $analysis,
'-type' => $type,
'-biotype' => $biotype,
'-start' => $seq_region_start,
'-end' => $seq_region_end,
'-strand' => $seq_region_strand,
......@@ -1237,13 +1235,21 @@ sub _objs_from_sth {
'-external_name' => $external_name,
'-external_db' => $external_db,
'-external_status' => $external_status,
'-display_xref' => $display_xref );
'-display_xref' => $display_xref,
'-confidence' => $confidence,
'-source' => $source );
}
return \@genes;
}
##########################
# #
# DEPRECATED METHODS #
# #
##########################
=head2 fetch_by_maximum_DBLink
......@@ -1255,6 +1261,8 @@ sub _objs_from_sth {
sub fetch_by_maximum_DBLink {
my ( $self, $external_id ) = @_;
deprecate( "use fetch_all_by_external_name instead" );
my $genes=$self->fetch_all_by_external_name( $external_id);
my $biggest;
......
modules/Bio/EnsEMBL/Gene.pm
+ 150
− 114
View file @ b3861b19
......@@ -60,10 +60,11 @@ sub new {
my ( $stable_id, $version, $external_name, $type, $external_db,
$external_status, $display_xref, $description, $transcripts,
$created_date, $modified_date ) =
$created_date, $modified_date, $confidence, $biotype, $source ) =
rearrange( [ 'STABLE_ID', 'VERSION', 'EXTERNAL_NAME', 'TYPE',
'EXTERNAL_DB', 'EXTERNAL_STATUS', 'DISPLAY_XREF', 'DESCRIPTION',
'TRANSCRIPTS', 'CREATED_DATE', 'MODIFIED_DATE'], @_ );
'TRANSCRIPTS', 'CREATED_DATE', 'MODIFIED_DATE',
'CONFIDENCE', 'BIOTYPE', 'SOURCE'], @_ );
if ($transcripts) {
$self->{'_transcript_array'} = $transcripts;
......@@ -79,9 +80,11 @@ sub new {
$self->external_db( $external_db ) if( defined $external_db );
$self->external_status( $external_status ) if( defined $external_status );
$self->display_xref( $display_xref ) if( defined $display_xref );
$self->type( $type ) if( defined $type );
$self->biotype( $type ) if( defined $type );
$self->biotype( $biotype ) if( defined $biotype );
$self->description($description);
$self->confidence( $confidence );
$self->source( $source );
return $self;
}
......@@ -101,7 +104,7 @@ sub new {
sub is_known{
my $self = shift;
return ($self->{'display_xref'}) ? 1 : 0;
return ( $self->{'confidence'} eq "KNOWN" );
}
......@@ -135,6 +138,44 @@ sub external_name {
}
=head2 confidence
Arg [1] : string $confidence
Example : none
Description: get/set for attribute confidence
Returntype : string
Exceptions : none
Caller : general
=cut
sub confidence {
my $self = shift;
$self->{'confidence'} = shift if( @_ );
return $self->{'confidence'};
}
=head2 source
Arg [1] : string $source
Example : none
Description: get/set for attribute source
Returntype : string
Exceptions : none
Caller : general
=cut
sub source {
my $self = shift;
$self->{'source'} = shift if( @_ );
return ( $self->{'source'} || "ensembl" );
}
=head2 external_db
Arg [1] : string $external_db
......@@ -178,9 +219,9 @@ sub external_db {
=cut
sub external_status {
my ( $self, $ext_status ) = @_;
my $self = shift;
return $self->{'_ext_status'} = $ext_status if defined $ext_status;
$self->{'_ext_status'} = shift if ( @_ );
return $self->{'_ext_status'} if exists $self->{'_ext_status'};
my $display_xref = $self->display_xref();
......@@ -342,6 +383,7 @@ sub get_all_Exons {
Arg [1] : string $type
Example : none
Description: get/set for attribute type
This function is going to be deprecated soon, use biotype instead
Returntype : string
Exceptions : none
Caller : general
......@@ -351,10 +393,30 @@ sub get_all_Exons {
sub type {
my $self = shift;
$self->{'biotype'} = shift if( @_ );
return ( $self->{'biotype'} || "protein_coding" );
}
=head2 biotype
Arg [1] : string $biotype
Example : $gene->biotype( "protein_coding" );
Description: get/set for the biotype attribute
Returntype : string
Exceptions : none
Caller : general
=cut
$self->{'type'} = shift if( @_ );
sub biotype {
my $self = shift;
return $self->{'type'};
$self->{'biotype'} = shift if( @_ );
return ( $self->{'biotype'} || "protein_coding" );
}
......@@ -556,7 +618,6 @@ sub transfer {
}
=head2 display_xref
Arg [1] : Bio::EnsEMBL::DBEntry $display_xref
......@@ -651,110 +712,6 @@ sub display_id {
###########################
# DEPRECATED METHODS FOLLOW
###########################
=head2 DEPRECATED add_DBLink
Description: DEPRECATED This method has been deprecated in favor of the
add_DBEntry method. Objects are responible for holding only
xrefs directly associated with themselves now.
=cut
sub add_DBLink{
my ($self,$value) = @_;
throw("add_DBLink is deprecated. You probably want add_DBEntry.");
# unless(defined $value && ref $value
# && $value->isa('Bio::Annotation::DBLink') ) {
# throw("This [$value] is not a DBLink");
# }
# if( !defined $self->{'_db_link'} ) {
# $self->{'_db_link'} = [];
# }
# push(@{$self->{'_db_link'}},$value);
}
=head2 temporary_id
Function: DEPRECATED: Use dbID or stable_id or something else instead
=cut
sub temporary_id {
my ($obj,$value) = @_;
deprecate( "I cant see what a temporary_id is good for, please use " .
"dbID or stableID or\n try without an id." );
if( defined $value) {
$obj->{'temporary_id'} = $value;
}
return $obj->{'temporary_id'};
}
=head2 created
Description: DEPRECATED - Transcripts no longer have a created attribute
=cut
sub created{
my ($self,$value) = @_;
deprecate( "The created attribute isnt available any more" );
if(defined $value ) {
$self->{'created'} = $value;
}
return $self->{'created'};
}
=head2 modified
Description: DEPRECATED - Transcripts no longer have a modified attribute
=cut
sub modified {
my ($self,$value) = @_;
deprecate( "The modified item isnt available any more" );
if( defined $value ) {
$self->{'modified'} = $value;
}
return $self->{'modified'};
}
=head2 chr_name
Description: DEPRECATED. Use project, tranform, or transfer to obtain this
gene in another coord system. Use $gene->slice->seq_region_name
to get the name of the underlying coord system. Or
$gene->slice->name().
=cut
sub chr_name {
my $self = shift;
deprecate( "Use project() to obtain other coordinate systems" );
my $gene_slice = $self->slice();
if( $gene_slice->coord_system()->name eq "chromosome" ) {
return $gene_slice->seq_region_name();
}
my $coords = $self->project( "toplevel" );
if( @$coords ) {
return $coords->[0]->[2]->seq_region_name();
}
}
=head2 get_all_DASFactories
......@@ -837,6 +794,8 @@ sub get_all_DASFeatures_by_slice{
}
return \%das_features;
}
=head2 get_all_DAS_Features
Arg [1] : none
......@@ -905,4 +864,81 @@ sub get_all_regulatory_features {
}
###########################
# DEPRECATED METHODS FOLLOW
###########################
=head2 DEPRECATED add_DBLink
Description: DEPRECATED This method has been deprecated in favor of the
add_DBEntry method. Objects are responible for holding only
xrefs directly associated with themselves now.
=cut
sub add_DBLink{
my ($self,$value) = @_;
throw("add_DBLink is deprecated. You probably want add_DBEntry.");
# unless(defined $value && ref $value
# && $value->isa('Bio::Annotation::DBLink') ) {
# throw("This [$value] is not a DBLink");
# }
# if( !defined $self->{'_db_link'} ) {
# $self->{'_db_link'} = [];
# }
# push(@{$self->{'_db_link'}},$value);
}
=head2 temporary_id
Function: DEPRECATED: Use dbID or stable_id or something else instead
=cut
sub temporary_id {
my ($obj,$value) = @_;
deprecate( "I cant see what a temporary_id is good for, please use " .
"dbID or stableID or\n try without an id." );
if( defined $value) {
$obj->{'temporary_id'} = $value;
}
return $obj->{'temporary_id'};
}
=head2 chr_name
Description: DEPRECATED. Use project, tranform, or transfer to obtain this
gene in another coord system. Use $gene->slice->seq_region_name
to get the name of the underlying coord system. Or
$gene->slice->name().
=cut
sub chr_name {
my $self = shift;
deprecate( "Use project() to obtain other coordinate systems" );
my $gene_slice = $self->slice();
if( $gene_slice->coord_system()->name eq "chromosome" ) {
return $gene_slice->seq_region_name();
}
my $coords = $self->project( "toplevel" );
if( @$coords ) {
return $coords->[0]->[2]->seq_region_name();
}
}
1;
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