From a854ce954b74a701469b35679554996ba7268667 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Fri, 5 Dec 2014 16:27:50 +0000
Subject: [PATCH] ENSCORESW-1142: add source RefSeq_ncRNA for NR_ transcripts
---
.../xref_mapping/XrefParser/RefSeqCoordinateParser.pm | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
index 05d8bc57e8..fdee63dbc6 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
@@ -41,6 +41,7 @@ sub run_script {
my $peptide_source_id = $self->get_source_id_for_source_name('RefSeq_peptide', 'otherfeatures');
my $mrna_source_id = $self->get_source_id_for_source_name('RefSeq_mRNA', 'otherfeatures');
+ my $ncrna_source_id = $self->get_source_id_for_source_name('RefSeq_ncRNA', 'otherfeatures');
my $user = "ensro";
my $host;
@@ -339,11 +340,13 @@ sub run_script {
# If a best match was defined for the refseq transcript, store it as direct xref for ensembl transcript
if ($best_id) {
my ($acc, $version) = split(/\./, $id);
+ my $source_id = $mrna_source_id;
+ $source_id = $ncrna_source_id if $acc =~ /^NR_/;
my $xref_id = $self->add_xref({ acc => $acc,
version => $version,
label => $id,
desc => '',
- source_id => $mrna_source_id,
+ source_id => $source_id,
species_id => $species_id,
info_type => 'DIRECT' });
$self->add_direct_xref($xref_id, $best_id, "Transcript", "");
--
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