From 24e3477dc719a9ee517620b278661814de7e65fa Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Wed, 3 Aug 2016 10:29:20 +0100
Subject: [PATCH] skip HGNC mappings via refseq or entrezgene
---
.../xref_mapping/XrefParser/HGNCParser.pm | 41 ++-----------------
1 file changed, 4 insertions(+), 37 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm b/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm
index 8f0d7895ce..aab30cc91a 100644
--- a/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm
@@ -129,29 +129,10 @@ sub run {
#
# RefSeq
+ # Skip, these are not curated
#
$type = 'refseq_mapped';
$id = $array[8];
- $source_id = $name_to_source_id->{$type};
- if ($id) {
- if(defined $refseq{$id} ){
- $seen = 1;
- foreach my $xref_id (@{$refseq{$id}}){
- $name_count{$type}++;
- $self->add_dependent_xref({ master_xref_id => $xref_id,
- acc => $acc,
- label => $symbol,
- desc => $name || '',
- source_id => $source_id,
- species_id => $species_id} );
- }
- $self->add_synonyms_for_hgnc( {source_id => $source_id,
- name => $acc,
- species_id => $species_id,
- dead => $previous_symbols,
- alias => $synonyms});
- }
- }
$type = 'refseq_manual';
$id = $array[6];
@@ -206,25 +187,11 @@ sub run {
}
}
+ # Skip entrezgene mapped
+ # these are NCBI provided mapping, not HGNC
+
$type = 'entrezgene_mapped';
$id = $array[7];
- if(defined $id ){
- if(defined $entrezgene{$id} ){
- $seen = 1;
- $self->add_dependent_xref({ master_xref_id => $entrezgene{$id},
- acc => $acc,
- label => $symbol,
- desc => $name || '',
- source_id => $source_id,
- species_id => $species_id} );
- $name_count{$type}++;
- $self->add_synonyms_for_hgnc( {source_id => $source_id,
- name => $acc,
- species_id => $species_id,
- dead => $previous_symbols,
- alias => $synonyms});
- }
- }
--
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