custom download for HGNC

misc-scripts/xref_mapping/XrefParser/HGNCParser.pm

@@ -142,14 +142,11 @@ sub run_script {
     my $acc              = $array[0];
     my $symbol           = $array[1];
     my $name             = $array[2];
-    my $status           = $array[5];
-    my $previous_symbols = $array[8];
-    my $synonyms         = $array[10];
-
-    if ($status ne 'Approved') { next; }
+    my $previous_symbols = $array[3];
+    my $synonyms         = $array[4];
 
     my $type = 'lrg';
-    my $id = $array[29];
+    my $id = $array[9];
     my $source_id = $name_to_source_id->{$type};
     if($id and $id =~ m/http:\/\/www.lrg-sequence.org\/LRG\/(LRG_\d+)/x){
       my $lrg_stable_id = $1;
@@ -178,9 +175,9 @@ sub run_script {
     $type = 'ccds';
     $source_id = $name_to_source_id->{$type};
 
-    my $ccds = $array[24];
+    my $ccds = $array[8];
     $ccds =~ s/"//g if defined $ccds;
-    my @ccds_list = split(/\|/,$ccds) if defined $ccds;
+    my @ccds_list = split(/,\s/,$ccds) if defined $ccds;
 
     foreach my $ccds (@ccds_list) {
       $id = $ccds_to_ens{$ccds};
@@ -208,7 +205,7 @@ sub run_script {
     # Direct Ensembl mappings
     #
     $type = 'ensembl_manual';
-    $id = $array[19];
+    $id = $array[6];
     $source_id = $name_to_source_id->{$type};
     if ($id){              # Ensembl direct xref
       $seen = 1;
@@ -232,7 +229,7 @@ sub run_script {
     }
 
     $type = 'refseq_manual';
-    $id = $array[23];
+    $id = $array[7];
     $source_id = $name_to_source_id->{$type};
     if ($id) {
       if(defined $refseq{$id} ){
@@ -260,7 +257,7 @@ sub run_script {
     # EntrezGene
     #
     $type = 'entrezgene_manual';
-    $id = $array[18];
+    $id = $array[5];
     $source_id = $name_to_source_id->{$type};
     if(defined $id ){
       if(defined $entrezgene{$id} ){
@@ -353,7 +350,7 @@ sub add_synonyms_for_hgnc{
   my $dbi        = $ref_arg->{dbi};
 
   if (defined $dead_name ) {     # dead name, add to synonym
-    my @array2 = split '\|', $dead_name ;
+    my @array2 = split ',\s', $dead_name ;
     foreach my $arr (@array2){
       $arr =~ s/"//g;
       $self->add_to_syn($name, $source_id, $arr, $species_id, $dbi);
@@ -361,7 +358,7 @@ sub add_synonyms_for_hgnc{
   }
 
   if (defined $alias ) {     # alias, add to synonym
-    my @array2 = split '\|', $alias;
+    my @array2 = split ',\s', $alias;
     foreach my $arr (@array2){
       $arr =~ s/"//g;
       $self->add_to_syn($name, $source_id, $arr, $species_id, $dbi);

misc-scripts/xref_mapping/xref_config.ini

@@ -1196,7 +1196,7 @@ prio_descr      = entrezgene_manual
 parser          = HGNCParser
 dependent_on    = EntrezGene,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
 release_uri     =
-data_uri        = script:wget=>ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt,host=>mysql-ens-core-prod-1,dbname=>homo_sapiens_ccds_91_38,port=>4524,
+data_uri        = script:wget=>https://www.genenames.org/cgi-bin/download?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_ensembl_id&col=gd_pub_refseq_ids&col=gd_ccds_ids&col=gd_lsdb_links&status=Approved&status_opt=2&where=&order_by=gd_app_sym_sort&format=text&limit=&hgnc_dbtag=on&submit=submit,host=>mysql-ens-core-prod-1,dbname=>homo_sapiens_ccds_91_38,port=>4524,
 
 
 [source HGNC::homo_sapiens#03]