removed as never used and just confusing

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()){
-    push @arr, $hgnc_source_id;
-  }
-  $sth->finish;
-  
-  $sql = "select accession, label, version,  description from xref where source_id in (".join(", ",@arr).")";
-  print "$sql\n";;
-  $sth = $dbi->prepare($sql);
-  $sth->execute();
-  my ($acc, $lab, $ver);
-  my $hgnc_loaded_count = 0;
-  $sth->bind_columns(\$acc, \$lab, \$ver, \$desc);
-  while (my @row = $sth->fetchrow_array()) {
-    $label{$acc} = $lab;
-    $version{$acc} = $ver;
-    $description{$acc} = $desc;
-    $hgnc_loaded_count++;
-  }
-  $sth->finish;
-  if($hgnc_loaded_count == 0){
-    die "No point continuing no hgncs there\n";
-  }
-
-  print "$hgnc_loaded_count HGNC's to be used as labels\n";
-
-  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, "DIRECT");
-      $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;