From 87179b2134a6ef2702f9917a18a2ac69d3c5eb86 Mon Sep 17 00:00:00 2001
From: juguang <juguang@sanger.ac.uk>
Date: Wed, 5 Nov 2003 12:54:40 +0000
Subject: [PATCH] add fetch_by_transcript_id
---
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm | 16 +++++++++++++++-
modules/Bio/EnsEMBL/Utils/Converter.pm | 2 +-
.../Utils/Converter/bio_ens_featurePair.pm | 2 +-
3 files changed, 17 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index d4bfb4bd61..bdd5e79467 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -152,7 +152,21 @@ sub fetch_by_translation_stable_id {
return undef;
}
}
-
+=head2 fetch_by_translation_id
+
+=cut
+
+sub fetch_by_translation_id {
+ my ($self, $transl_id) = @_;
+ my $sth = $self->prepare(
+ "SELECT transcript_id
+ FROM transcript
+ WHERE translation_id = ?");
+ $sth->execute($transl_id);
+ my ($id) = $sth->fetchrow_array;
+ return $id? $self->fetch_by_dbID($id) : undef;
+}
+
=head2 fetch_all_by_DBEntry
Arg [1] : in $external_id
diff --git a/modules/Bio/EnsEMBL/Utils/Converter.pm b/modules/Bio/EnsEMBL/Utils/Converter.pm
index e17464b039..6ac9fe96f0 100644
--- a/modules/Bio/EnsEMBL/Utils/Converter.pm
+++ b/modules/Bio/EnsEMBL/Utils/Converter.pm
@@ -161,7 +161,7 @@ sub convert{
return \@output;
}
-sub _converter_single{
+sub _convert_single{
my ($self, $input) = @_;
$self->throw("Not implemented. Please check the instance subclass");
}
diff --git a/modules/Bio/EnsEMBL/Utils/Converter/bio_ens_featurePair.pm b/modules/Bio/EnsEMBL/Utils/Converter/bio_ens_featurePair.pm
index ad424257e8..7b521a7be6 100644
--- a/modules/Bio/EnsEMBL/Utils/Converter/bio_ens_featurePair.pm
+++ b/modules/Bio/EnsEMBL/Utils/Converter/bio_ens_featurePair.pm
@@ -30,7 +30,7 @@ Bio::EnsEMBL::Utils::Converter::bio_ens_featurePair
=head1 AUTHOR Juguang Xiao
-Juguang Xiao <juguang@fugu-sg.org>
+Juguang Xiao <juguang@tll.org.sg>
=head1 APPENDIX
--
GitLab