Few changes, added a script to load the mapping into the database

misc-scripts/protein_match/get_hugo_mapping.pl

@@ -92,14 +92,6 @@ while (<ENS2>) {
     $_ =~ s/\r//g;
     my ($hgnc1,$hugo) = split(/\t/,$_);
     
-#    if (!defined $hugo_sp{$hgnc1}) {
-#	print ERROR "Can't map back $hugo_sp{$hgnc} (ENS2)\n";
-#    }
-
-#    if (!defined $hugo_refseq{$hgnc1}) {
-#	print ERROR "Can't map back $hugo_refseq{$hgnc} (ENS2)\n";
-#    }
-
     if ($hugo_sp{$hgnc1}) {
 	print OUT "$map{$hugo_sp{$hgnc1}}\t$hugo_sp{$hgnc1}\tHUGOSYMBOL\t$hugo\n";
     }

misc-scripts/protein_match/get_xrefs.pl

@@ -39,6 +39,8 @@ my %embl_clone;
 	    'output:s'=>\$out
             );
 
+#perl ../../../src/ensembl-live/misc-scripts/protein_match/get_xrefs.pl -mapping ../map_outputs/totalmap.final -xrefs ../sec_outputs/xrefs.map -dbmap ../sec_outputs/mapdb.map -refseq ../primary/hs.gnp -output final.map 
+
 open (DBMAP,"$dbmap") || die "Can't open file $dbmap\n"; 
 open (XREF,"$xrefs") || die "Can't open file $xrefs\n";
 open (MAP,"$mapping") || die "Can't open file $mapping\n";

misc-scripts/protein_match/load_mapping.pl

+use strict;
+use DBI;
+use Getopt::Long;
+use Bio::EnsEMBL::DBSQL::DBEntryAdaptor;
+use Bio::EnsEMBL::DBEntry;
+
+my %hugosyn;
+my %hugosymbol;
+my %scopsyn;
+my %gene_map;
+my %transcript_map;
+my ($mapping, $hugosyn, $scopsyn, $out);
+
+
+
+&GetOptions(
+	    'mapping:s'=>\$mapping,
+	    'hugosyn:s'=>\$hugosyn,
+	    'scopsyn:s'=>\$scopsyn
+            );
+
+my $dsn = "DBI:mysql:database=ensembl090_tmp;host=ecs1c";    
+my $db = DBI->connect("$dsn",'ensadmin') || die ("Could not connect to db!");   
+
+my $adaptor =  Bio::EnsEMBL::DBSQL::DBEntryAdaptor->new($db);
+
+
+#open (MAPS, "$map");
+#while (<MAP>) {
+#    chomp;
+#    my ($transcript,$gen
+#Read Hugo file to get out synonyms
+
+open (HUGO, "$hugosyn") || die "Can't open file $mapping\n";
+while (<HUGO>) {
+    chomp;
+    my ($hgnc, $symbol, $alias, $withdrawn) = split (/\t/,$_);
+    
+    my @aliases = split (/, /,$alias);
+    my @withdrawns = split (/, /,$withdrawn);
+    
+    $hugosymbol{$symbol}=$hgnc;
+
+    foreach my $al(@aliases) {
+	push(@{$hugosyn{$symbol}},$al);
+    }
+
+    foreach my $wi(@withdrawns) {
+	push(@{$hugosyn{$symbol}},$wi);
+    }
+}
+close (HUGO);
+
+
+#Read SCOP file to get out synonyms
+open (SCOP, "$scopsyn") || die "Can't open file $scopsyn\n";
+while (<SCOP>) {
+    chomp;
+    my ($scopac, $pdb, $chain, $scopnb) = split(/\t/,$_);
+    
+    #my $uni = "$pdb||$chain";
+
+    push(@{$scopsyn{$scopac}},$pdb);
+    push(@{$scopsyn{$scopac}},$chain);
+    push(@{$scopsyn{$scopac}},$scopnb);
+}
+close (SCOP);
+
+#Read final mapping
+open (MAPPING, "$mapping") || die "Can't open file $mapping\n";
+while (<MAPPING>) {
+    chomp;
+    my ($ens, $db, $primary_ac) = split(/\t/,$_);
+
+#Get SP mapping
+    if (($db ne "HUGOSYMBOL") && ($db ne "SCOP") && ($db ne "SCOP1") && ($db ne "HUGOID") && ($db ne "HUGOALIAS") && ($db ne "HUGOWITHDRAWN")) {
+	my ($ac1) = $ens =~ /COBP(\d+)/;
+	$ens = "COBT"."$ac1";
+	my $dbentry = Bio::EnsEMBL::DBEntry->new
+	    ( -adaptor => $adaptor,
+	      -primary_id => $primary_ac,
+	      -display_id => $primary_ac,
+	      -version => 1,
+	      -release => 1,
+	      -dbname => $db );
+	$adaptor->store($dbentry,$ens,"Gene");
+    }
+
+    if ($db eq "HUGOSYMBOL") {
+	#print STDERR "HERE\n";
+	my ($ac1) = $ens =~ /COBP(\d+)/;
+	$ens = "COBT"."$ac1";
+	
+	my $dbentry = Bio::EnsEMBL::DBEntry->new
+	    ( -adaptor => $adaptor,
+	      -primary_id => $primary_ac,
+	      -display_id => $primary_ac,
+	      -version => 1,
+	      -release => 1,
+	      -dbname => $db );
+	if ($hugosyn{$primary_ac}) {
+	    my @synonyms = @{$hugosyn{$primary_ac}};
+	    #print STDERR "SYN: @synonyms\n";
+	    foreach my $syn (@synonyms) {
+		
+		if ($syn =~ /\S+/) {
+		    #print STDERR "$syn\n";
+		    $dbentry->add_synonym($syn);
+		   
+		}
+	    }
+	}
+	
+	
+	$adaptor->store($dbentry,$ens,"Gene");
+    }
+
+    if ($db eq "SCOP") {
+     	my ($ac1) = $ens =~ /COBP(\d+)/;
+	$ens = "COBT"."$ac1";
+	my $dbentry = Bio::EnsEMBL::DBEntry->new
+	    ( -adaptor => $adaptor,
+	      -primary_id => $primary_ac,
+	      -display_id => $primary_ac,
+	      -version => 1,
+	      -release => 1,
+	      -dbname => $db );
+	if ($scopsyn{$primary_ac}) {
+	my @synonyms = @{$scopsyn{$primary_ac}};
+	foreach my $syn (@synonyms) {
+	    if ($syn =~ /\S+/) {
+			$dbentry->add_synonym($syn);
+	    }
+	}
+    }
+	$adaptor->store($dbentry,$ens,"Gene");
+	
+    }
+
+}

misc-scripts/protein_match/process_pmach.pl

@@ -39,6 +39,8 @@ my ($ens,$sp,$refseq,$pdb);
 &finalprocess($refseq);
 &finalprocess($pdb);
 
+#perl ../../../src/ensembl-live/misc-scripts/protein_match/process_pmach.pl -ens ../primary/TGWpep -sp ../primary/SPTr.human.expanded -refseq ../primary/hs2.fsa -pdb ../primary/scop.fas
+
 sub runpmatch {
     print STDERR "Running pmatch\n";