From de1f6d9fd05945ed356c7ec3c036dcbefbe3f827 Mon Sep 17 00:00:00 2001
From: Web Admin <w3adm@sanger.ac.uk>
Date: Fri, 24 Jan 2003 17:26:39 +0000
Subject: [PATCH] added xref "status" stuff to chromosome summaries, genes and
transcripts
---
modules/Bio/EnsEMBL/Chromosome.pm | 27 +++++++++++++++-
modules/Bio/EnsEMBL/Gene.pm | 28 ++++++++++++++++
modules/Bio/EnsEMBL/Lite/ChromosomeAdaptor.pm | 21 ++++++------
modules/Bio/EnsEMBL/Lite/GeneAdaptor.pm | 32 +++++++++++++------
modules/Bio/EnsEMBL/Transcript.pm | 31 ++++++++++++++++++
5 files changed, 119 insertions(+), 20 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Chromosome.pm b/modules/Bio/EnsEMBL/Chromosome.pm
index 9363b55317..7a8e769989 100755
--- a/modules/Bio/EnsEMBL/Chromosome.pm
+++ b/modules/Bio/EnsEMBL/Chromosome.pm
@@ -53,6 +53,7 @@ use Bio::EnsEMBL::Root;
-adaptor => $adaptor,
-length => $length,
-known_genes => $known_genes,
+ -xref_genes => $xref_genes,
-unknown_genes => $unknown_genes,
-snps => $snps);
Description: Creates a new chromosome object
@@ -70,12 +71,13 @@ sub new {
bless($self, $class);
my ( $chr_name, $chromosome_id, $adaptor, $length,
- $known_genes, $unknown_genes, $snps) =
+ $known_genes, $xref_genes, $unknown_genes, $snps) =
$self->_rearrange([qw(CHR_NAME
DBID
ADAPTOR
LENGTH
KNOWN_GENES
+ XREF_GENES
UNKNOWN_GENES
SNPS)],
@args);
@@ -89,6 +91,7 @@ sub new {
$self->dbID($chromosome_id);
$self->unknown_genes($unknown_genes);
$self->length($length);
+ $self->xref_genes($xref_genes);
$self->known_genes($known_genes);
$self->snps($snps);
@@ -187,6 +190,28 @@ sub length {
+=head2 xref_genes
+
+ Arg [1] : int $number_of_xref_genes
+ Example : none
+ Description: get/set for the attribute xref_genes, the number of xref genes
+ on this chromosome
+ Returntype : int
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub xref_genes {
+ my ($self, $xref_genes) = @_;
+
+ if(defined $xref_genes) {
+ $self->{'xref_genes'} = $xref_genes;
+ }
+
+ return $self->{'xref_genes'};
+}
+
=head2 known_genes
Arg [1] : int $number_of_known_genes
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index a4501e917e..1c1adbc7c1 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -440,6 +440,34 @@ sub external_db {
}
}
+=head2 external_status
+
+ Arg [1] : string $external_status
+ Example : none
+ Description: get/set for attribute external_status. The status of
+ the external db of the one that belongs to the external_name.
+ Returntype : string
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub external_status {
+ my ( $self, $ext_status ) = @_;
+
+ return $self->{'_ext_status'} = $ext_status if defined $ext_status;
+ return $self->{'_ext_status'} if exists $self->{'_ext_status'};
+
+ my $display_xref = $self->display_xref();
+
+ if( defined $display_xref ) {
+ return $display_xref->status()
+ } else {
+ return undef;
+ }
+}
+
+
=head2 description
diff --git a/modules/Bio/EnsEMBL/Lite/ChromosomeAdaptor.pm b/modules/Bio/EnsEMBL/Lite/ChromosomeAdaptor.pm
index 40bd433e76..02884b2f06 100644
--- a/modules/Bio/EnsEMBL/Lite/ChromosomeAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Lite/ChromosomeAdaptor.pm
@@ -88,14 +88,14 @@ sub fetch_by_dbID {
# from the database and add it to the cache.
#
unless($chr = $self->{'_chr_cache'}->{$id}) {
- my $sth = $self->prepare( "SELECT name, known_genes, unknown_genes,
+ my $sth = $self->prepare( "SELECT name, known_genes, unknown_genes, xref_genes,
snps, length
FROM chromosome
WHERE chromosome_id = ?" );
$sth->execute( $id );
- my($name, $known_genes, $unknown_genes, $snps, $length);
- $sth->bind_columns(\$name,\$known_genes,\$unknown_genes,\$snps,\$length);
+ my($name, $known_genes, $unknown_genes, $snps, $length, $xref_genes);
+ $sth->bind_columns(\$name,\$known_genes,\$unknown_genes,\$xref_genes, \$snps,\$length);
$sth->fetch();
@@ -112,6 +112,7 @@ sub fetch_by_dbID {
-dbID => $id,
-chr_name => $name,
-known_genes => $known_genes,
+ -xref_genes => $xref_genes,
-unknown_genes => $unknown_genes,
-snps => $snps,
'-length' => $length );
@@ -156,14 +157,14 @@ sub fetch_by_chr_name{
# from the database and add it to the cache.
#
unless($chr = $self->{'_chr_name_cache'}->{$chr_name}) {
- my $sth = $self->prepare( "SELECT chromosome_id, known_genes, unknown_genes,
+ my $sth = $self->prepare( "SELECT chromosome_id, known_genes, unknown_genes, xref_genes,
snps, length
FROM chromosome
WHERE name = ?" );
$sth->execute( $chr_name );
- my($dbID, $known_genes, $unknown_genes, $snps, $length);
- $sth->bind_columns(\$dbID,\$known_genes,\$unknown_genes,\$snps,\$length);
+ my($name, $known_genes, $unknown_genes, $snps, $length, $xref_genes, $dbID);
+ $sth->bind_columns(\$dbID,\$known_genes,\$unknown_genes,\$xref_genes, \$snps,\$length);
if ($sth->rows > 0) {
$sth->fetch();
@@ -172,6 +173,7 @@ sub fetch_by_chr_name{
-dbID => $dbID,
-chr_name => $chr_name,
-known_genes => $known_genes,
+ -xref_genes => $xref_genes,
-unknown_genes => $unknown_genes,
-snps => $snps,
'-length' => $length );
@@ -201,13 +203,13 @@ sub fetch_all {
my @chrs = ();
- my $sth = $self->prepare( "SELECT chromosome_id, name, known_genes,
+ my $sth = $self->prepare( "SELECT chromosome_id, name, known_genes, xref_genes,
unknown_genes, snps, length
FROM chromosome" );
$sth->execute();
- my($chromosome_id, $name, $known_genes, $unknown_genes, $snps, $length);
- $sth->bind_columns(\$chromosome_id,\$name,\$known_genes,
+ my($chromosome_id, $name, $known_genes, $unknown_genes, $xref_genes, $snps, $length);
+ $sth->bind_columns(\$chromosome_id,\$name,\$known_genes,\$xref_genes,
\$unknown_genes,\$snps,\$length);
while($sth->fetch()) {
@@ -216,6 +218,7 @@ sub fetch_all {
-chr_name => $name,
-dbID => $chromosome_id,
-known_genes => $known_genes,
+ -xref_genes => $xref_genes,
-unknown_genes => $unknown_genes,
-snps => $snps,
'-length' => $length );
diff --git a/modules/Bio/EnsEMBL/Lite/GeneAdaptor.pm b/modules/Bio/EnsEMBL/Lite/GeneAdaptor.pm
index 327b1db98c..6e667562fa 100644
--- a/modules/Bio/EnsEMBL/Lite/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Lite/GeneAdaptor.pm
@@ -182,10 +182,12 @@ sub fetch_all_by_Slice {
my $sth = $self->prepare( "SELECT t.id, t.transcript_id, t.chr_name, t.chr_start, t.chr_end,
t.chr_strand, t.transcript_name, t.translation_id,
t.translation_name, t.gene_id, t.type, t.gene_name, t.db,
- t.exon_structure, t.external_name, t.exon_ids, t.external_db,
+ t.exon_structure, t.external_name, t.external_status, t.exon_ids, t.external_db,
t.coding_start, t.coding_end,
g.external_name as gene_external_name,
- g.external_db as gene_external_db, g.type as gene_type
+ g.external_db as gene_external_db,
+ g.external_status as gene_external_status,
+ g.type as gene_type
FROM transcript t
LEFT JOIN gene g
ON g.gene_id = t.gene_id
@@ -256,9 +258,10 @@ sub fetch_by_stable_id {
( "SELECT t.id, t.transcript_id, t.chr_name, t.chr_start, t.chr_end,
t.chr_strand, t.transcript_name, t.translation_id,
t.translation_name, t.gene_id, t.type, t.gene_name,
- t.db, t.exon_structure, t.external_name, t.exon_ids,
+ t.db, t.exon_structure, t.external_name, t.external_status, t.exon_ids,
t.external_db, t.coding_start, t.coding_end,
g.external_name as gene_external_name,
+ g.external_status as gene_external_status,
g.external_db as gene_external_db, g.type as gene_type
FROM transcript t
LEFT JOIN gene g
@@ -291,9 +294,10 @@ sub fetch_by_transcript_stable_id {
( "SELECT t.id, t.transcript_id, t.chr_name, t.chr_start, t.chr_end,
t.chr_strand, t.transcript_name, t.translation_id,
t.translation_name, t.gene_id, t.type, t.gene_name, t.db,
- t.exon_structure, t.external_name, t.exon_ids,
+ t.exon_structure, t.external_name, t.external_status, t.exon_ids,
t.external_db, t.coding_start, t.coding_end,
g.external_name as gene_external_name,
+ g.external_status as gene_external_status,
g.external_db as gene_external_db, g.type as gene_type
FROM transcript t
LEFT JOIN gene g
@@ -346,6 +350,7 @@ sub _objects_from_sth {
$gene->strand( $hr->{'chr_strand'} );
if( defined $hr->{'gene_type' } ) {
+ $gene->external_name( $hr->{'gene_external_status'} );
$gene->external_name( $hr->{'gene_external_name'} );
$gene->external_db( $hr->{'gene_external_db'} );
$gene->type( $hr->{'gene_type'} );
@@ -482,6 +487,7 @@ sub _objects_from_sth {
$transcript->coding_end( $coding_end );
$transcript->stable_id( $hr->{ 'transcript_name' });
$transcript->type( $hr->{ 'type' } );
+ $transcript->external_status( $hr->{'external_status'} );
$transcript->external_name( $hr->{'external_name'} );
$transcript->external_db( $hr->{'external_db' } );
@@ -550,7 +556,7 @@ sub _get_empty_Genes {
my $sth = $self->prepare
( "SELECT g.db, g.gene_id, g.gene_name, g.chr_name, g.chr_start,
- g.chr_end, g.chr_strand, g.type, g.external_name, g.external_db
+ g.chr_end, g.chr_strand, g.type, g.external_name, g.external_db, g.external_status
FROM gene g
WHERE g.chr_name = ? AND g.chr_start <= ? AND
g.chr_start >= ? AND g.chr_end >= ?" );
@@ -576,6 +582,7 @@ sub _get_empty_Genes {
$gene->strand( $hashref->{'chr_strand'} );
if( defined $hashref->{'type' } ) {
+ $gene->external_status( $hashref->{'external_status'} );
$gene->external_name( $hashref->{'external_name'} );
$gene->external_db( $hashref->{'external_db'} );
$gene->type( $hashref->{'type'} );
@@ -629,10 +636,11 @@ sub fetch_all_by_external_name {
my $sth = $self->prepare( "SELECT t.id, t.transcript_id, t.chr_name, t.chr_start, t.chr_end,
t.chr_strand, t.transcript_name, t.translation_id,
t.translation_name, t.gene_id, t.type, t.gene_name, t.db,
- t.exon_structure, t.external_name, t.exon_ids, t.external_db,
+ t.exon_structure, t.external_name, t.exon_ids, t.external_db, t.external_status,
t.coding_start, t.coding_end,
g.external_name as gene_external_name,
- g.external_db as gene_external_db, g.type as gene_type
+ g.external_db as gene_external_db, g.external_status as gene_external_status,
+ g.type as gene_type
FROM transcript t, gene_xref as gx, gene as g
where g.gene_id = t.gene_id AND g.db = t.db and t.db = ? and gx.external_name = ? and gx.gene_id = g.gene_id
order by g.gene_name, t.gene_name"
@@ -656,7 +664,7 @@ sub _get_empty_Genes_by_external_name {
my $sth = $self->prepare(
"SELECT distinct g.db, g.gene_id, g.gene_name, g.chr_name, g.chr_start,
- g.chr_end, g.chr_strand, g.type, g.external_name, g.external_db
+ g.chr_end, g.chr_strand, g.type, g.external_name, g.external_db, g.external_status
FROM gene g, gene_xref as gx
WHERE g.gene_id = gx.gene_id and g.db = ? and gx.external_name = ?" );
@@ -678,6 +686,7 @@ sub _get_empty_Genes_by_external_name {
$gene->strand( $hashref->{'chr_strand'} );
if( defined $hashref->{'type' } ) {
+ $gene->external_status( $hashref->{'external_status'} );
$gene->external_name( $hashref->{'external_name'} );
$gene->external_db( $hashref->{'external_db'} );
$gene->type( $hashref->{'type'} );
@@ -726,6 +735,7 @@ sub store {
chr_strand = ?,
description = ?,
external_db = ?,
+ external_status = ?,
external_name = ? "
);
@@ -733,6 +743,7 @@ sub store {
$gene->type(), $gene->dbID(), $gene->stable_id(),
$gene->chr_name(), $gene->start(), $gene->end(),
$gene->strand(), $gene->description(), $gene->external_db(),
+ $gene->external_status(),
$gene->external_name() );
# now store transcripts
@@ -757,7 +768,8 @@ sub store {
gene_name = ?,
exon_structure = ?,
exon_ids = ?,
- external_db = ?,
+ external_db = ?,
+ external_status = ?,
external_name = ? "
);
@@ -791,7 +803,7 @@ sub store {
$tr->start(), $tr->end(), $gene->strand(), $tr->coding_start(),
$tr->coding_end(), $tr->translation->dbID(),
$tr->translation->stable_id(), $gene->dbID(), $gene->stable_id(),
- $exon_structure, $exon_ids, $tr->external_db(),
+ $exon_structure, $exon_ids, $tr->external_db(), $tr->external_status(),
$tr->external_name() );
}
}
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 7c37d21bc2..a41fb37123 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -182,6 +182,37 @@ sub external_db {
}
}
+=head2 external_status
+
+ Title : external_status
+ Usage : $ext_db = $obj->external_status();
+ Function: external_name if available
+ Returns : the external db link for this transcript
+ Args : new external db (optional)
+
+=cut
+
+sub external_status {
+ my ( $self, $ext_status ) = @_;
+
+ if(defined $ext_status) {
+ return ( $self->{'_ext_status'} = $ext_status );
+ }
+
+ if( exists $self->{'_ext_status'} ) {
+ return $self->{'_ext_status'};
+ }
+
+ my $display_xref = $self->display_xref();
+
+ if( defined $display_xref ) {
+ return $display_xref->status()
+ } else {
+ return undef;
+ }
+}
+
+
=head2 external_name
--
GitLab