From 01224e7f1910fe3f3aac9a234a147e8985826aa5 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Fri, 23 Sep 2005 08:56:56 +0000
Subject: [PATCH] Added coding_gene() and coding_transcript() methods to pull
data from regulatory_factor_coding table.
---
modules/Bio/EnsEMBL/RegulatoryFactor.pm | 82 +++++++++++++++++++++++--
1 file changed, 78 insertions(+), 4 deletions(-)
diff --git a/modules/Bio/EnsEMBL/RegulatoryFactor.pm b/modules/Bio/EnsEMBL/RegulatoryFactor.pm
index f8edfee8f5..7f19d40bef 100644
--- a/modules/Bio/EnsEMBL/RegulatoryFactor.pm
+++ b/modules/Bio/EnsEMBL/RegulatoryFactor.pm
@@ -57,9 +57,10 @@ sub new_fast {
=head2 name
- Arg [1] : string $name (optional)
- Example : $name = $regulatory_factor->name()
- Description: Getter/Setter for the name of this regulatory factor
+ Arg [1] : none
+ Example : $trans = $regulatory_factor->get_coding_transcript()
+ Description: Returns the transcript that codes for this regulatory factor,
+ if it is defined.
Returntype : string
Exceptions : none
Caller : general
@@ -75,11 +76,84 @@ sub name {
}
+=head2 coding_transcript
+
+ Arg [1] : none
+ Example : $transcript = $regulatory_factor->coding_transcript()
+ Description: Get the transcript which codes for this regulatory factor.
+ Returntype : Bio::EnsEMBL::Transcript, or undef
+ Exceptions : none
+ Caller : general
+ Status : At Risk
+ : under development
+
+=cut
+
+sub coding_transcript {
+
+ my $self = shift;
+
+ my ($transcript_id);
+
+ my $sth = $self->adaptor()->db()->dbc()->prepare("SELECT transcript_id
+ FROM regulatory_factor_coding
+ WHERE regulatory_factor_id=?");
+
+ $sth->execute($self->dbID());
+ $sth->bind_columns(\$transcript_id);
+
+ my $transcript_adaptor = $self->adaptor()->db()->get_TranscriptAdaptor();
+ my $transcript;
+ if ($sth->fetch) {
+ $transcript = $transcript_adaptor->fetch_by_dbID($transcript_id);
+ }
+
+ return $transcript;
+}
+
+
+=head2 coding_gene
+
+ Arg [1] : none
+ Example : $gene = $regulatory_factor->coding_gene()
+ Description: Get the gene which codes for this regulatory factor.
+ Returntype : Bio::EnsEMBL::Gene, or undef
+ Exceptions : none
+ Caller : general
+ Status : At Risk
+ : under development
+
+=cut
+
+sub coding_gene {
+
+ my $self = shift;
+
+ my ($gene_id);
+
+ my $sth = $self->adaptor()->db()->dbc()->prepare("SELECT gene_id
+ FROM regulatory_factor_coding
+ WHERE regulatory_factor_id=?");
+
+ $sth->execute($self->dbID());
+ $sth->bind_columns(\$gene_id);
+
+ my $gene_adaptor = $self->adaptor()->db()->get_GeneAdaptor();
+ my $gene;
+ if ($sth->fetch) {
+ $gene = $gene_adaptor->fetch_by_dbID($gene_id);
+ }
+
+ return $gene;
+}
+
+
+
=head2 type
Arg [1] : string $type
Example : $type = $regulatory_factor->type()
- Description: Getter/Setter for the length of this regulatory factor
+ Description: Getter/Setter for the type of this regulatory factor
Returntype : int
Exceptions : none
Caller : general
--
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