Added GO mapping

misc-scripts/protein_match/get_Xmapping.pl

@@ -25,7 +25,8 @@ my $refseq_gnp = $conf{'refseq_gnp'};
 #Get specific options for human
 my $ens1       = $conf{'ens1'};
 my $ens4       = $conf{'ens4'};
-my $refeseq_pred =$conf{'refseq_pred'};
+my $refeseq_pred = $conf{'refseq_pred'};
+my $go           = $conf{'go'}; 
 
 #Get specific options for the mouse
 my $mgi_sp     = $conf{'mgi_sp'};
@@ -189,6 +190,8 @@ if ($organism eq "human") {
 #Read the file containing the NCBI prediction in gnp format
     open (REFSEQ,"$refseq_pred") || die "Can't open $refseq_pred\n";
     
+    print STDERR "Reading Refseq file with NCBI predictions\n";
+
     $/ = "\/\/\n";
     
     while (<REFSEQ>) {
@@ -197,8 +200,8 @@ if ($organism eq "human") {
 	
 	$refseq_map{$dna_ac} = $prot_ac; 
 	
-#Its a curated Refseq, flag it as known
-	print OUT "$prot_ac\tRefSeq_pred\t$prot_ac\tRefSeq\t$prot_ac\t\tPRED\n";
+#Its a curated Refseq, flag it as predicted
+	print OUT "$prot_ac\tRefSeq_pred\t$prot_ac\tRefSeq_pred\t$prot_ac\t\tPRED\n";
        
 	my ($mim) = $_ =~ /\/db_xref=\"MIM:(\d+)/;
 	my ($locus) = $_ =~ /\/db_xref=\"LocusID:(\d*)/;
@@ -207,6 +210,17 @@ if ($organism eq "human") {
     
     $/ = "\n";
 
+    open (GO,"$go") || die "Can't open $go\n";
+
+    print STDERR "Reading GO file\n";
+
+    while (<GO>) {
+	chomp;
+	my @array = split (/\t/,$_);
+	
+	print OUT "$array[1]\tSPTR\t$array[3]\tGO\t$array[3]\t\tXREF"
+	}
+
 }
 
 #Get Xref mapping specifically for mouse.

misc-scripts/protein_match/mapping_conf.pl

@@ -101,6 +101,10 @@ package main;
                   #Location of the file in .gnp format for the NCBI prediction
                   #'refseq_pred' => '',
                   'refseq_pred' => '',
+
+                  #Location of the file for GO mapping (gene_association.goa)
+                  #'go' => '',
+                  'go' => '',
                   
                   #######
                   #Mouse#

misc-scripts/protein_match/maps2db.pl

@@ -80,7 +80,7 @@ print STDERR "Reading X_map ($xmap)\n";
 while (<XMAP>) {
     
     chomp;
-    my ($targetid,$targetdb,$xac,$xdb,$xid,$xsyn) = split (/\t/,$_);
+    my ($targetid,$targetdb,$xac,$xdb,$xid,$xsyn,$status) = split (/\t/,$_);
 
     if ($check eq "yes") {
 #Get the all of the EMBL accessions for a given SP
@@ -117,6 +117,7 @@ while (<XMAP>) {
     $p->xDB($xdb);
     $p->xID($xid);
     $p->xSYN($xsyn);
+    $p->stat($status);
 
     push(@{$map{$targetid}},$p);
 }
@@ -177,6 +178,8 @@ MAPPING: while (<MAP>) {
 		      -release => 1,
 		      -dbname => $a->xDB);
 
+		$dbentry->status($a->stat);
+
 		if (($check eq "yes") && (($a->xDB eq "SPTREMBL") || ($a->xDB eq "SWISS-PROT"))) {
 
 		    if (($sp2embl{$a->xAC}) && ($ens2embl{$queryid})) {