diff --git a/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm b/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm index 8f0d7895ce48ba337cbdbe124e7381c7f02f56fa..aab30cc91a8ef894776071fe30c3b5f57406d993 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}); - } - }