HUGO -> HGNC

misc-scripts/xref_mapping/XrefParser/HGNCParser.pm

+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 "\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 $file = shift;
+
+  print STDERR "source = $source_id\tspecies = $species_id\n";
+  if(!defined($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 (%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 $swiss_count = 0;
+  my $refseq_count = 0;
+  my $entrezgene_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 ( $_ = $hugo_io->getline() ) {
+
+    chomp;
+
+    # 0 HGNC ID	           # primary accession
+    # 1 Approved Symbol    # label
+    # 2 Approved Name      # description
+    # 3 Previous Symbols   # synonyms
+    # 4 Aliases            # aliases
+    # 5 entrezgene ID   manually curated
+    # 6 RefSeq ID       manually curated
+    # 7 entrezgene ID   mapped
+    # 8 RefSeq ID       mapped
+
+    my @array = split(/\t/,$_);
+
+    # Use the RefSeq if available as this is manually curated
+    # If no RefSeq, use the Swissprot instead
+
+    my $seen = 0;
+    if ($array[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, $arr);
+	  }
+	}
+
+	if (defined($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, $arr);
+	  }
+	}
+      }
+    }
+    if ($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, $arr);
+	  }
+	}
+
+	if (defined($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, $arr);
+	  }
+	}
+      }
+    }
+
+    if(defined($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, $arr);
+	  }
+	}
+	
+	if (defined($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, $arr);
+	  }
+	}
+      }    
+    }
+
+    if(defined($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, $arr);
+	  }
+	}
+	
+	if (defined($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, $arr);
+	  }
+	}
+      }    
+    }
+    if(!$seen){ # Store to keep descriptions etc
+      $self->add_xref($array[0], "", $array[1], $array[2], $source_id, $species_id);      
+    }
+
+
+  } # while HGNC
+
+  $hugo_io->getline();
+
+  print "Loaded a total of " . ($refseq_count + $entrezgene_count) . " HGNC xrefs, $refseq_count from RefSeq curated mappings and $entrezgene_count from EntrezGene mappings\n";
+
+  print "$mismatch xrefs could not be associated via RefSeq or EntrezGene\n";
+
+  return 0; # successful
+
+}
+
+sub rename_url_file{
+  return "hugo.txt";
+}
+
+1;
+    
+

misc-scripts/xref_mapping/XrefParser/HGNC_CCDSParser.pm

+package XrefParser::HGNC_CCDSParser;
+
+use strict;
+
+use DBI;
+
+use base qw( XrefParser::BaseParser );
+
+# Parse file of HGNC records and assign direct xrefs
+# All assumed to be linked to genes
+
+sub run {
+
+  my ($self, $source_id, $species_id, $file) = @_;
+
+  my $hugo_io = $self->get_filehandle($file);
+
+  if ( !defined $hugo_io ) {
+    print "Could not open $file\n";
+    return 1;
+  }
+
+
+
+  # becouse the direct mapping have no descriptions etc
+  # we have to steal these fromt he previous HGNC parser.
+  # This is why the order states this is after the other one.
+  # maybe 1091,1092 is not right maybe should use name = HGNC and priority = 30r4 ??
+
+  my %label;
+  my %version;
+  my %description;
+
+  my $dbi = $self->dbi();  
+  my $sql = "select accession, label, version,  description from xref where source_id in (1091, 1092, 1094)";
+  my $sth = $dbi->prepare($sql);
+  $sth->execute();
+  my ($acc, $lab, $ver, $desc);
+  $sth->bind_columns(\$acc, \$lab, \$ver, \$desc);
+  while (my @row = $sth->fetchrow_array()) {
+    $label{$acc} = $lab;
+    $version{$acc} = $ver;
+    $description{$acc} = $desc;
+  }
+  $sth->finish;
+ 
+  $sql = 'select x.accession, d.ensembl_stable_id, d.type 
+            from xref x, direct_xref d, source s 
+             where s.source_id = x.source_id and 
+                   x.xref_id = d.general_xref_id and s.name like "CCDS"'; 
+ 
+  $sth = $dbi->prepare($sql);
+  $sth->execute();
+  my ($access, $stable_id, $type);
+  $sth->bind_columns(\$access, \$stable_id, \$type);
+  my %ensembl_stable_id;
+  my %ensembl_type;
+  while (my @row = $sth->fetchrow_array()) {
+    $ensembl_stable_id{$access} = $stable_id;
+    $ensembl_type{$access} = $type;
+  }
+  $sth->finish;
+  
+ 
+  my $line_count = 0;
+  my $xref_count = 0;
+  my %seen;
+  my $ignore_count = 0;
+  my $ignore_examples ="";
+
+  while( $_ = $hugo_io->getline() ) {
+    chomp;
+    my ($ccds,$hgnc) = split;
+    
+    $line_count++;
+    if(!defined($label{$hgnc})){
+      $ignore_count++;
+      if($ignore_count < 10){
+	$ignore_examples .= " ".$hgnc;
+      }
+      next;
+    }
+    if(!defined($seen{$hgnc})){
+      $seen{$hgnc} = 1;
+      my $key = "CCDS".$ccds;
+      if(defined($ensembl_stable_id{$key})){
+	my $xref_id = $self->add_xref($hgnc, $version{$hgnc} , $label{$hgnc}||$hgnc , 
+				      $description{$hgnc}, $source_id, $species_id);
+	$self->add_direct_xref($xref_id, $ensembl_stable_id{$key}, $ensembl_type{$key}, "");
+	$xref_count++;
+      }
+    }
+  }
+  print "Parsed $line_count HGNC identifiers from $file, added $xref_count xrefs and $xref_count direct_xrefs  from $line_count lines.\n";
+  if($ignore_count){
+    print $ignore_count." ignoreed due to numbers no identifiers being no longer valid :- $ignore_examples\n";
+  }
+
+  $hugo_io->close();
+
+  return 0;
+
+}
+
+1;

misc-scripts/xref_mapping/XrefParser/HGNC_ENSGParser.pm

+package XrefParser::HGNC_ENSGParser;
+
+use strict;
+
+use DBI;
+
+use base qw( XrefParser::BaseParser );
+
+# Parse file of HGNC records and assign direct xrefs
+# All assumed to be linked to genes
+
+sub run {
+
+  my ($self, $source_id, $species_id, $file) = @_;
+
+  my $hugo_io = $self->get_filehandle($file);
+
+  if ( !defined $hugo_io ) {
+    print "Could not open $file\n";
+    return 1;
+  }
+
+  my $line_count = 0;
+  my $xref_count = 0;
+
+  # becouse the direct mapping have no descriptions etc
+  # we have to steal these fromt he previous HGNC parser.
+  # This is why the order states this is after the other one.
+  # maybe 1091,1092 is not right maybe should use name = HGNC and priority = 30r4 ??
+
+  my %label;
+  my %version;
+  my %description;
+
+  my $dbi = $self->dbi();  
+
+  #get the source ids for HGNC refseq, entrezgene and unitprot
+  my $sql = 'select source_id, priority_description from source where name like "HGNC"';
+  my $sth = $dbi->prepare($sql);
+  
+  $sth->execute();
+  my ($hgnc_source_id, $desc);
+  $sth->bind_columns(\$hgnc_source_id, \$desc);
+  my @arr;
+  while($sth->fetch()){
+    if(lc($desc) eq "refseq" or lc($desc) eq "uniprot" or lc($desc) eq "entrezgene"){
+      push @arr, $hgnc_source_id;
+    }
+  }
+  $sth->finish;
+  
+  $sql = "select accession, label, version,  description from xref where source_id in (".join(", ",@arr).")";
+  $sth = $dbi->prepare($sql);
+  $sth->execute();
+  my ($acc, $lab, $ver);
+  $sth->bind_columns(\$acc, \$lab, \$ver, \$desc);
+  while (my @row = $sth->fetchrow_array()) {
+    $label{$acc} = $lab;
+    $version{$acc} = $ver;
+    $description{$acc} = $desc;
+  }
+  $sth->finish;
+
+
+  my $ignore_count = 0;
+  my $ignore_examples ="";
+  my %acc;
+
+  while ( $_ = $hugo_io->getline() ) {
+
+    my ($hgnc, $stable_id) = split;
+
+    if(!defined($label{$hgnc})){
+      $ignore_count++;
+      if($ignore_count < 10){
+	$ignore_examples .= " ".$hgnc;
+      }
+      next;
+    }
+    if(!defined($acc{$hgnc})){
+      $acc{$hgnc} = 1;
+      my $version ="";
+      $line_count++;
+      
+      my $xref_id = $self->add_xref($hgnc, $version{$hgnc} , $label{$hgnc}||$hgnc , $description{$hgnc}, $source_id, $species_id);
+      $xref_count++;
+      
+
+      $self->add_direct_xref($xref_id, $stable_id, "gene", "");
+    }
+  }
+
+  print "Parsed $line_count HGNC identifiers from $file, added $xref_count xrefs and $line_count direct_xrefs\n";
+  if($ignore_count){
+    print $ignore_count." ignoreed due to numbers no identifiers being no longer valid :- $ignore_examples\n";
+  }
+
+  $hugo_io->close();
+
+  return 0;
+}
+
+1;