From 791bb28a15e50421d781ae1e5a56245707707736 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Mon, 1 Nov 2010 15:37:06 +0000
Subject: [PATCH] Handle ASMPATCH and LRG genes.
---
.../StableIdGenerator/EnsemblGeneric.pm | 41 ++++++++++++++-----
1 file changed, 31 insertions(+), 10 deletions(-)
diff --git a/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm b/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
index cd358926ee..95769d6d21 100644
--- a/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
@@ -132,7 +132,12 @@ sub initial_stable_id {
my $s_dbh = $s_dba->dbc->db_handle;
# look in the ${type}_stable_id table first
- my $sql = qq(SELECT MAX(stable_id) FROM ${type}_stable_id);
+ my $sql = qq(
+ SELECT MAX(stable_id)
+ FROM ${type}_stable_id
+ WHERE stable_id LIKE "ENS%"
+ );
+
$init_stable_id = $self->fetch_value_from_db($s_dbh, $sql);
# also look in gene_archive to make sure there are no larger Ids there
@@ -178,16 +183,23 @@ sub initial_stable_id {
=cut
sub increment_stable_id {
- my $self = shift;
+ my $self = shift;
my $stable_id = shift;
- unless ($self->is_valid($stable_id)) {
- throw("Unknown or missing stable ID: $stable_id.");
+ if ( !$self->is_valid($stable_id) ) {
+ throw( sprintf( "Unknown or missing stable ID '%s'", $stable_id ) );
}
-
- $stable_id =~ /ENS([A-Z]{1,4})(\d{11})/;
- my $number = $2;
- my $new_stable_id = 'ENS'.$1.(++$number);
+
+ if ( $stable_id =~ /^LRG/ ) {
+ throw( sprintf( "We do not increment LRG genes... (got '%s'). "
+ . "Something's wrong.",
+ $stable_id ) );
+ }
+
+ $stable_id =~ /(ENS|ASMPATCH)([A-Z]{1,4})(\d{11})/;
+
+ my $number = $3;
+ my $new_stable_id = $1 . $2 . ( ++$number );
return $new_stable_id;
}
@@ -210,8 +222,17 @@ sub increment_stable_id {
=cut
sub is_valid {
- my ($self, $stable_id) = @_;
- return ($stable_id and ($stable_id =~ /ENS([A-Z]{1,4})(\d{11})/));
+ my ( $self, $stable_id ) = @_;
+
+ if ( defined($stable_id) ) {
+ if ( $stable_id =~ /^(ENS|ASMPATCH)([A-Z]{1,4})(\d{11})/
+ || $stable_id =~ /^LRG/ )
+ {
+ return 1;
+ }
+ }
+
+ return 0;
}
--
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