From 07a96f2abb300a26a95b7415ea7d954303302095 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Wed, 15 Feb 2012 14:30:48 +0000
Subject: [PATCH] new parser for Orphanet xrefs dependent on HGNC identifiers
---
.../xref_mapping/XrefParser/OrphanetParser.pm | 131 ++++++++++++++++++
1 file changed, 131 insertions(+)
create mode 100644 misc-scripts/xref_mapping/XrefParser/OrphanetParser.pm
diff --git a/misc-scripts/xref_mapping/XrefParser/OrphanetParser.pm b/misc-scripts/xref_mapping/XrefParser/OrphanetParser.pm
new file mode 100644
index 0000000000..520961be38
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefParser/OrphanetParser.pm
@@ -0,0 +1,131 @@
+package XrefParser::OrphanetParser;
+
+use strict;
+use warnings;
+use Carp;
+use File::Basename;
+
+use XML::LibXML;
+
+use base qw( XrefParser::BaseParser );
+
+sub run {
+
+
+ my ($self, $ref_arg) = @_;
+ my $source_id = $ref_arg->{source_id};
+ my $species_id = $ref_arg->{species_id};
+ my $files = $ref_arg->{files};
+ my $verbose = $ref_arg->{verbose};
+
+ if((!defined $source_id) or (!defined $species_id) or (!defined $files) ){
+ croak "Need to pass source_id, species_id and file as pairs";
+ }
+ $verbose |=0;
+
+ my $xml_file = @{$files}[0];
+
+ print STDERR "Orphanet file to parse, $xml_file\n" if($verbose);
+
+ my %gene_disorders;
+
+ my $term = undef;
+ my $desc = undef;
+
+ my $xml_parser = XML::LibXML->new();
+ my $orphanet_doc = $xml_parser->parse_file($xml_file);
+
+ my ($jdbor_node) = $orphanet_doc->findnodes('JDBOR');
+ my $release = $jdbor_node->getAttribute('version');
+ # Set release
+ $self->set_release( $source_id,$release );
+
+
+ my $gene_disorder_count = 0;
+ my $disorder_count = 0;
+
+ foreach my $disorder ($orphanet_doc->findnodes('JDBOR/DisorderList/Disorder')) {
+ my ($orpha_number_node) = $disorder->findnodes('./OrphaNumber');
+ my $orpha_number = $orpha_number_node->to_literal;
+ my ($name_node) = $disorder->findnodes('./Name');
+ my $name = $name_node->to_literal;
+
+ my @genes = $disorder->findnodes('./GeneList/Gene');
+
+ if ( scalar(@genes) > 0) {
+
+ $disorder_count++;
+ }
+
+ foreach my $gene (@genes) {
+
+ my $ref;
+ #get the HGNC xref
+ foreach my $external_reference_node ($gene->findnodes('./ExternalReferenceList/ExternalReference')) {
+ my ($source_node) = $external_reference_node->findnodes('./Source');
+ if ($source_node->to_literal =~ /HGNC/) {
+ my ($ref_node) = $external_reference_node->findnodes('./Reference');
+ $ref = $ref_node->to_literal;
+ }
+ }
+ if (defined($ref)) {
+ $gene_disorders{$ref}{$orpha_number} = $name;
+ $gene_disorder_count++;
+ }
+ }
+
+ }
+
+ print "Parsed $disorder_count disorders\n";
+ print "Found $gene_disorder_count genes associated with disorders\n";
+
+
+ #get the mapping that are already there so that we don't get lots of duplicates.
+ # stored in the global hash xref_dependent_mapped.
+ $self->get_dependent_mappings($source_id);
+
+
+ my (%hgnc) = %{$self->get_valid_codes("HGNC", $species_id)};
+
+ print "got " . scalar(keys (%hgnc)) . " HGNC entries\n";
+
+ print "species_id, source_id: $species_id, $source_id\n";
+
+ my $added = 0;
+ my %Orphanet_xrefs;
+
+ foreach my $hgnc_acc (keys (%gene_disorders)) {
+
+ # Get the master_xref_id
+
+ if(!defined($hgnc{$hgnc_acc})){
+ print STDERR "failed to get the master_xref_if for HGNC, $hgnc_acc!\n";
+ }
+ else{
+ foreach my $master_xref_id (@{$hgnc{$hgnc_acc}}){
+
+ foreach my $orpha_number (keys %{$gene_disorders{$hgnc_acc}}) {
+
+ $self->add_dependent_xref({ master_xref_id => $master_xref_id,
+ acc => $orpha_number,
+ source_id => $source_id,
+ species_id => $species_id,
+ desc => $gene_disorders{$hgnc_acc}{$orpha_number} });
+ $Orphanet_xrefs{$orpha_number}++;
+ $added++;
+ }
+ }
+ }
+
+ }
+
+ print "Added " . scalar(keys %Orphanet_xrefs) . " Orphanet xrefs and " . $added . " dependent xrefs\n";
+ if ($added > 0) {
+ return 0;
+ } else {
+ return 1;
+ }
+
+}
+
+1;
--
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