From 8cc61a1d0d331e453d91e9655b654f64100d332f Mon Sep 17 00:00:00 2001
From: Kevin Howe <klh@ebi.ac.uk>
Date: Mon, 20 Aug 2012 14:45:57 +0000
Subject: [PATCH] Override set_methods for WormBase species to allow non-exact
matching to Uniprot records
---
.../xref_mapping/XrefMapper/wormbase.pm | 19 +++++++++++++++++--
1 file changed, 17 insertions(+), 2 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/wormbase.pm b/misc-scripts/xref_mapping/XrefMapper/wormbase.pm
index 33c91c34f4..7c228c6fbc 100644
--- a/misc-scripts/xref_mapping/XrefMapper/wormbase.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/wormbase.pm
@@ -7,8 +7,23 @@ use vars qw(@ISA);
@ISA = qw(XrefMapper::BasicMapper);
-# Abstact superclass, not intended to be created directly. Contains
-# common methods for the "tierII" nematodes in WormBase
+# This module is activated by specifying "taxon=wormbase" in the mapping input file
+# It contains some common config for worms maintained by WormBase (i.e. having genes
+# with WBGene ids etc)
+
+sub set_methods{
+
+ my $default_method = 'ExonerateGappedBest1';
+ my %override_method_for_source = (
+ ExonerateGappedBest5 => ['RefSeq_mRNA',
+ 'RefSeq_mRNA_predicted',
+ 'RefSeq_ncRNA',
+ 'RefSeq_ncRNA_predicted' ],
+ );
+
+ return $default_method, \%override_method_for_source;
+}
+
sub set_display_xrefs {
--
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