From 75e5fd551d1a5f57ddc8f8d37fb13dba6217d900 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Wed, 31 Jan 2018 17:00:13 +0000
Subject: [PATCH] use correct field delimiter
---
misc-scripts/xref_mapping/XrefParser/HGNCParser.pm | 10 ++++++----
1 file changed, 6 insertions(+), 4 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm b/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm
index 3ec3d6be67..f77cb949d4 100644
--- a/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm
@@ -179,8 +179,8 @@ sub run_script {
$source_id = $name_to_source_id->{$type};
my $ccds = $array[24];
- $ccds =~ s/"//g;
- my @ccds_list = split(/\|/,$ccds);
+ $ccds =~ s/"//g if defined $ccds;
+ my @ccds_list = split(/\|/,$ccds) if defined $ccds;
foreach my $ccds (@ccds_list) {
$id = $ccds_to_ens{$ccds};
@@ -353,15 +353,17 @@ sub add_synonyms_for_hgnc{
my $dbi = $ref_arg->{dbi};
if (defined $dead_name ) { # dead name, add to synonym
- my @array2 = split ',\s*', $dead_name ;
+ my @array2 = split '\|', $dead_name ;
foreach my $arr (@array2){
+ $arr =~ s/"//g;
$self->add_to_syn($name, $source_id, $arr, $species_id, $dbi);
}
}
if (defined $alias ) { # alias, add to synonym
- my @array2 = split ',\s*', $alias;
+ my @array2 = split '\|', $alias;
foreach my $arr (@array2){
+ $arr =~ s/"//g;
$self->add_to_syn($name, $source_id, $arr, $species_id, $dbi);
}
}
--
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