Uniprot_genename source added

misc-scripts/xref_mapping/XrefParser/UniProtParser.pm

@@ -35,6 +35,7 @@ if (!defined(caller())) {
 
 # --------------------------------------------------------------------------------
 
+
 sub run {
 
   my $self = shift if (defined(caller(1)));
@@ -167,11 +168,7 @@ sub create_xrefs {
   my $num_sptr_pred = 0;
 
   my %dependent_sources = $self->get_dependent_xref_sources(); # name-id hash
-
-# get from HGNC file
-#  if(defined($dependent_sources{'HGNC'})){
-#    $dependent_sources{'HGNC'} = XrefParser::BaseParser->get_source_id_for_source_name("HGNC","uniprot");
-#  }	
+  my %GeneNameSynonym;
 
   if(defined($dependent_sources{'MGI'})){
     $dependent_sources{'MGI'} = XrefParser::BaseParser->get_source_id_for_source_name("MGI","uniprot");
@@ -293,8 +290,11 @@ sub create_xrefs {
     foreach my $line (@all_lines) {
       my ($accessions_only) = $line =~ /^AC\s+(.+)/;
       push(@accessions, (split /;\s*/, $accessions_only)) if ($accessions_only);
+
     }
 
+
+
     $xref->{INFO_TYPE} = "SEQUENCE_MATCH";
     $xref->{ACCESSION} = $accessions[0];
     for (my $a=1; $a <= $#accessions; $a++) {
@@ -393,6 +393,40 @@ sub create_xrefs {
     $xref->{SEQUENCE} = $parsed_seq;
     #print "Adding " . $xref->{ACCESSION} . " " . $xref->{LABEL} ."\n";
 
+    
+    my ($gns) = $_ =~ /(GN\s+Name.+)/; # /s allows . to match newline
+    my @gn_lines = ();
+    if ( defined $gns ) { @gn_lines = split /\n/, $gns }
+  
+    foreach my $gn (@gn_lines){
+      my $gene_name = undef;
+      my %depe;
+      
+      if($gn =~ /Name=(\S+);/){
+	$depe{ACCESSION} = uc($1);
+	$gene_name = $depe{ACCESSION};
+	$depe{SOURCE_NAME} = "Uniprot_genename";
+	$depe{SOURCE_ID} = $dependent_sources{"Uniprot_genename"};
+	$depe{LINKAGE_SOURCE_ID} = $xref->{SOURCE_ID};
+	push @{$xref->{DEPENDENT_XREFS}}, \%depe;
+	$dependent_xrefs{"Uniprot_genename"}++;
+	my @syn;
+	if($gn =~ /Synonyms=([^;]+);/){
+	  my $syn = $1;
+	  $syn =~ s/\s+//g;
+	  @syn= split(/,/,$syn);
+	  foreach my $ent (@syn){
+	    $GeneNameSynonym{$gene_name}{uc($ent)} = 1;
+#	    print "$gene_name\t$ent\n";
+	  }
+	}
+      }
+    }	
+
+    my ($deps) = $_ =~ /(DR\s+.+)/s; # /s allows . to match newline
+    my @dep_lines = ();
+    if ( defined $deps ) { @dep_lines = split /\n/, $deps }
+
     # dependent xrefs - only store those that are from sources listed in the source table
     my ($deps) = $_ =~ /(DR\s+.+)/s; # /s allows . to match newline
 
@@ -535,11 +569,31 @@ sub create_xrefs {
   print "Read $num_sp SwissProt xrefs and $num_sptr SPTrEMBL xrefs from $file\n" if($verbose);
   print "Found $num_sp_pred predicted SwissProt xrefs and $num_sptr_pred predicted SPTrEMBL xrefs\n" if (($num_sp_pred > 0 || $num_sptr_pred > 0) and $verbose);
 
+
+#  my $kount=0;
+  my $genename_source_id =  $dependent_sources{"Uniprot_genename"};
+  foreach my $namekey (keys %GeneNameSynonym){
+    #add xref
+    my $xref_id = $self->add_xref($namekey,"",$namekey, "", $genename_source_id, $species_id,"DEPENDENT");
+#    $kount++;
+#    print $namekey."\t";
+    foreach my $synkey (keys %{$GeneNameSynonym{$namekey}}){
+      #add synonyms for xref
+      $self->add_synonym($xref_id, $synkey);
+#      print "$synkey, ";
+    }
+#    print "\n";
+  }
+
+
+#  print "$kount gene anmes added\n";
+
   print "Added the following dependent xrefs:-\n" if($verbose);
   foreach my $key (keys %dependent_xrefs){
     print $key."\t".$dependent_xrefs{$key}."\n" if($verbose);
   }
 
+
   return \@xrefs;
 
   #TODO - currently include records from other species - filter on OX line??

misc-scripts/xref_mapping/xref_config.ini

@@ -2373,6 +2373,17 @@ prio_descr      =
 parser          = UniProtParser
 release_uri     =
 
+[source Uniprot_genename]
+# Special source used in UniProtParser foir gene names..
+name            = Uniprot_genename
+download        = N
+order           = 20
+priority        = 1
+prio_descr      =
+parser          = UniProtParser
+release_uri     =
+data_uri        = 
+
 [source Uniprot/SWISSPROT::drosophila_melanogaster]
 # Used by drosophila_melanogaster
 name            = Uniprot/SWISSPROT