added GKB mapping

misc-scripts/protein_match/get_Xmapping.pl

@@ -26,7 +26,8 @@ my $refseq_gnp = $conf{'refseq_gnp'};
 my $ens1       = $conf{'ens1'};
 my $ens4       = $conf{'ens4'};
 my $refseq_pred = $conf{'refseq_pred_gnp'};
-my $go           = $conf{'go'}; 
+my $go          = $conf{'go'}; 
+my $gkb         = $conf{'gkb'}; 
 
 #Get specific options for the mouse
 my $mgi_sp     = $conf{'mgi_sp'};
@@ -159,7 +160,19 @@ if ($organism eq "human") {
 	$array[9] =~ s/\'/\\\'/g;
 	print OUT "$array[1]\tSPTR\t$array[4]\tGO\t$array[4]\t$array[9]\tXREF\n";	
 	}
+    
+    close (GO);
+
+#Get the GKB (Genome Knowledge Database) mapping
+#Contacts: Imre Vastrik <vastrik@ebi.ac.uk>, Hester <eschmidt@ebi.ac.uk>
 
+    open (GKB,"$gkb") || die "Can't open GKB data: $gkb";
+
+    while (<GKB>) {
+	chomp;
+	my ($sp,$id) = split;
+	print OUT "$sp\tSPTR\t$id\tGKB\t$id\t\tXREF\n";
+    }
 }
 
 #Get Xref mapping specifically for mouse.
@@ -302,6 +315,7 @@ if($organism eq 'briggsae'){
 close(OUT);
 print STDERR "The output has been written there: $out\n";
 
+
 sub parse_sp_file{
   my ($file) = @_;
   #print STDERR "opening file ".$file."\n";
@@ -473,3 +487,4 @@ sub process_parsed_sp{
     }
   }
 }
+

misc-scripts/protein_match/mapping_conf.pl

@@ -104,6 +104,11 @@ package main;
                   #ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz
                   #'go' => '',
                   'go' => '',
+
+                  #Location of the file for GKB (Genome Knowledge Base) mapping.
+                  #Contacts: Imre Vastrik <vastrik@ebi.ac.uk>, Hester <eschmidt@ebi.ac.uk>
+ 
+                  'gkb' => '',
                   
                   #######
                   #Mouse#

misc-scripts/protein_match/maps2db.pl

@@ -355,13 +355,7 @@ if ($organism eq "drosophila") {
 
 }
 
-if ($organism eq "drosophila") {
-    my $query = "select distinct(stable_id) from gene_stable_id";
-    my $sth = $db->prepare($query);
 
-    
-    
-}
 
 if ($organism eq "elegans") {
   #print STDERR " parsing wormbase information\n";