From 155c3273723b45542d79456f770d502cc5766ec1 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Fri, 10 Dec 2010 14:20:36 +0000
Subject: [PATCH] Add projected xrefs to genes rather than transcripts by
default if there is no equivalent type in the target database.
---
misc-scripts/xref_projection/project_display_xrefs.pl | 7 +++----
1 file changed, 3 insertions(+), 4 deletions(-)
diff --git a/misc-scripts/xref_projection/project_display_xrefs.pl b/misc-scripts/xref_projection/project_display_xrefs.pl
index 450640859e..3419f612d5 100644
--- a/misc-scripts/xref_projection/project_display_xrefs.pl
+++ b/misc-scripts/xref_projection/project_display_xrefs.pl
@@ -312,8 +312,7 @@ sub project_display_names {
# other xrefs from this dbname as assigned to (see build_db_to_type)
# Note that if type is not found, it means that we're dealing with a db that has no
# xrefs in the target database, e.g. MarkerSymbol in mouse -> rat
- # In this case just assign to transcripts, except for special cases (e.g.
- # HGNC_curated_gene should always go to genes
+ # In this case just assign to genes
my @to_transcripts = @{$to_gene->get_all_Transcripts};
my $to_transcript = $to_transcripts[0];
@@ -322,12 +321,12 @@ sub project_display_names {
my $type = $db_to_type{$dbname};
- if ($type eq "Gene" || $dbname eq 'HGNC') {
+ if ($type eq "Gene" || $dbname eq 'HGNC' || !$type) {
$to_gene->add_DBEntry($dbEntry);
$to_dbea->store($dbEntry, $to_gene->dbID(), 'Gene', 1) if (!$print);
- } elsif ($type eq "Transcript" || $dbname eq 'HGNC_transcript_name' || !$type) {
+ } elsif ($type eq "Transcript" || $dbname eq 'HGNC_transcript_name') {
$to_transcript->add_DBEntry($dbEntry);
$to_dbea->store($dbEntry, $to_transcript->dbID(), 'Transcript', 1) if (!$print);
--
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