Raw content of XrefParser::HGNC_ENSGParser
<![CDATA[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 ignoreed due to numbers no identifiers being no longer valid :- $ignore_examples\n";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;
]]>