Raw content of XrefParser::HGNCParser
<![CDATA[package XrefParser::HGNCParser;
use strict;
use File::Basename;
use base qw( XrefParser::BaseParser );
my $xref_sth ;
my $dep_sth;
my $syn_sth;
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
if (!defined(caller())) {
if (scalar(@ARGV) != 1) {
print STDERR "\nUsage: HGNCParser.pm file <source_id> <species_id>\n\n";
exit(1);
}
run(@ARGV);
}
sub run {
my $self = shift if (defined(caller(1)));
my $source_id = shift;
my $species_id = shift;
my $files_ref = shift;
my $rel_file = shift;
my $verbose = shift;
my $file = @{$files_ref}[0];
if(!defined($source_id)){
$source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
}
if(!defined($species_id)){
$species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
}
my $hgnc_refseq_manual = XrefParser::BaseParser->get_source_id_for_source_name("HGNC","refseq_manual");
if(!defined($hgnc_refseq_manual)){
die "Could not get source id for HGNC with priority description of refseq_manual\n";
}
my $hgnc_refseq_mapped = XrefParser::BaseParser->get_source_id_for_source_name("HGNC","refseq_mapped");
if(!defined($hgnc_refseq_mapped)){
die "Could not get source id for HGNC with priority description of refseq_mapped\n";
}
my $hgnc_entrezgene_manual = XrefParser::BaseParser->get_source_id_for_source_name("HGNC","entrezgene_manual");
if(!defined($hgnc_entrezgene_manual)){
die "Could not get source id for HGNC with priority description of entrezgene_manual\n";
}
my $hgnc_entrezgene_mapped = XrefParser::BaseParser->get_source_id_for_source_name("HGNC","entrezgene_mapped");
if(!defined($hgnc_entrezgene_mapped)){
die "Could not get source id for HGNC with priority description of entrezgene_mapped\n";
}
my $hgnc_ensembl_mapped = XrefParser::BaseParser->get_source_id_for_source_name("HGNC","ensembl_mapped");
if(!defined($hgnc_ensembl_mapped)){
die "Could not get source id for HGNC with priority description of ensembl_mapped\n";
}
my $hgnc_desc_only = XrefParser::BaseParser->get_source_id_for_source_name("HGNC","desc_only");
if(!defined($hgnc_desc_only)){
die "Could not get source id for HGNC with priority description of desc_only\n";
}
# my (%swiss) = %{XrefParser::BaseParser->get_valid_codes("uniprot",$species_id)};
my (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};
my @list;
push @list, "refseq_peptide";
push @list, "refseq_dna";
my (%entrezgene) = %{XrefParser::BaseParser->get_valid_xrefs_for_dependencies("EntrezGene",@list)};
my $refseq_count = 0;
my $entrezgene_count = 0;
my $ensembl_count = 0;
my $mismatch = 0;
my $hugo_io = $self->get_filehandle($file);
if ( !defined $hugo_io ) {
print "ERROR: Can't open HGNC file $file\n";
return 1;
}
$_ = $hugo_io->getline();
while ( $_ = $hugo_io->getline() ) {
chomp;
# 0 HGNC ID # primary accession
# 1 Approved Symbol # label
# 2 Approved Name # description
# 3 Previous Symbols # synonyms
# 4 Aliases # aliases
# 5 entrezgene ID manually curated
# 6 RefSeq ID manually curated
# 7 entrezgene ID mapped
# 8 RefSeq ID mapped
# 9 Ensembl ID mapped
my @array = split(/\t/,$_);
# Use the RefSeq if available as this is manually curated
# If no RefSeq, use the Swissprot instead
my $seen = 0;
if ($array[9]){ # Ensembl direct xref
$seen =1;
$ensembl_count++;
XrefParser::BaseParser->add_to_direct_xrefs($array[9],'gene', $array[0], '', $array[1], $array[2], "", $hgnc_ensembl_mapped, $species_id);
if (defined($array[3])) { # dead name, add to synonym
my @array2 = split(',\s*', $array[3]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_ensembl_mapped, $arr, $species_id);
}
}
if (defined($array[4])) { # alias, add to synonym
my @array2 = split(',\s*', $array[4]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_ensembl_mapped, $arr, $species_id);
}
}
}
if ($array[6]) { # RefSeq
if(defined($refseq{$array[6]})){
$seen = 1;
$refseq_count++;
XrefParser::BaseParser->add_to_xrefs($refseq{$array[6]}, $array[0], '', $array[1], $array[2], "", $hgnc_refseq_manual, $species_id);
if (defined($array[3])) { # dead name, add to synonym
my @array2 = split(',\s*', $array[3]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_refseq_manual, $arr, $species_id);
}
}
if (defined($array[4])) { # alias, add to synonym
my @array2 = split(',\s*', $array[4]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_refseq_manual, $arr, $species_id);
}
}
}
}
if ($array[8]) { # RefSeq
if(defined($refseq{$array[8]})){
$seen = 1;
$refseq_count++;
XrefParser::BaseParser->add_to_xrefs($refseq{$array[8]}, $array[0], '', $array[1], $array[2], "", $hgnc_refseq_mapped, $species_id);
if (defined($array[3])) { # dead name, add to synonym
my @array2 = split(',\s*', $array[3]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_refseq_mapped, $arr, $species_id);
}
}
if (defined($array[4])) { # alias, add to synonym
my @array2 = split(',\s*', $array[4]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_refseq_mapped, $arr, $species_id);
}
}
}
}
if(defined($array[5])){
if(defined($entrezgene{$array[5]})){
$seen = 1;
XrefParser::BaseParser->add_to_xrefs($entrezgene{$array[5]}, $array[0], '',
$array[1], $array[2], "", $hgnc_entrezgene_manual, $species_id);
$entrezgene_count++;
if (defined($array[3])) { # dead name, add to synonym
my @array2 = split(',\s*', $array[3]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_entrezgene_manual, $arr, $species_id);
}
}
if (defined($array[4])) { # alias, add to synonym
my @array2 = split(',\s*', $array[4]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_entrezgene_manual, $arr, $species_id);
}
}
}
}
if(defined($array[7])){
if(defined($entrezgene{$array[7]})){
$seen = 1;
XrefParser::BaseParser->add_to_xrefs($entrezgene{$array[7]}, $array[0], '',
$array[1], $array[2], "", $hgnc_entrezgene_mapped, $species_id);
$entrezgene_count++;
if (defined($array[3])) { # dead name, add to synonym
my @array2 = split(',\s*', $array[3]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_entrezgene_mapped, $arr, $species_id);
}
}
if (defined($array[4])) { # alias, add to synonym
my @array2 = split(',\s*', $array[4]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_entrezgene_mapped, $arr, $species_id);
}
}
}
}
if(!$seen){ # Store to keep descriptions etc
$self->add_xref($array[0], "", $array[1], $array[2], $hgnc_desc_only, $species_id, "MISC");
if (defined($array[3])) { # dead name, add to synonym
my @array2 = split(',\s*', $array[3]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_desc_only, $arr, $species_id);
}
}
if (defined($array[4])) { # alias, add to synonym
my @array2 = split(',\s*', $array[4]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_desc_only, $arr, $species_id);
}
}
$mismatch++;
}
} # while HGNC
$hugo_io->close();
print "Loaded a total of " . ($refseq_count + $entrezgene_count) . " HGNC xrefs, $refseq_count from RefSeq curated mappings and $entrezgene_count from EntrezGene mappings and $ensembl_count from ensembl_mapping\n" if($verbose);
print "$mismatch xrefs could not be associated via RefSeq, EntrezGene or ensembl\n" if($verbose);
return 0; # successful
}
sub rename_url_file{
return "hugo.txt";
}
1;
]]>