From d8fd649be4d28036f22d6a66db160af4e43b4ec3 Mon Sep 17 00:00:00 2001
From: Javier Herrero <jh7@sanger.ac.uk>
Date: Wed, 20 Apr 2005 11:57:12 +0000
Subject: [PATCH] Fix the length of the RepeatConsensus when the sequence is
like "xxx(N)"
---
modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm
index 11ca0faf0f..881b80492e 100644
--- a/modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm
@@ -174,8 +174,7 @@ sub _generic_fetch {
SELECT repeat_consensus_id
, repeat_name
, repeat_class
- , repeat_type
- , LENGTH(repeat_consensus)
+ , repeat_type
, repeat_consensus
FROM repeat_consensus
WHERE }. $where_clause);
@@ -185,11 +184,16 @@ sub _generic_fetch {
\$repeat_consensus_id,
\$repeat_name,
\$repeat_class,
- \$repeat_type,
- \$repeat_length,
+ \$repeat_type,
\$repeat_consensus
);
+
+ if ($repeat_consensus =~ /^(\d+)\(N\)$/) {
+ $repeat_length = $1;
+ } else {
+ $repeat_length = CORE::length($repeat_consensus);
+ }
my @consensi;
while ($sth->fetch) {
push @consensi, Bio::EnsEMBL::RepeatConsensus->new
--
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