Mapping devellopemments

misc-scripts/protein_match/get_ens2embl.pl

 use strict;
+
+=head1 Get_ens2ensembl.pl
+
+=head1 Description
+
+=head2 Aims
+The aim of thi script is to get from the database the corresponding clones for each Ensembl peptides. This will be then used to postprocess pmatch and get a more sensible mapping.
+
+=cut
+
+
 use Bio::SeqIO;
 use Bio::EnsEMBL::DBSQL::Obj;
 use Bio::EnsEMBL::DBLoader;

misc-scripts/protein_match/get_xrefs.pl

@@ -28,7 +28,7 @@ my %hash;
 my %ref_map;
 my %ens2embl;
 my %sp2embl;
-
+my %embl_clone;
 
 &GetOptions(
             
@@ -47,6 +47,17 @@ if ($refseq) {
 }
 open (OUT,">$out") || die "Can't open file $out\n";
 
+open (CLONE,"clones.txt") || die "Can't open file\n";
+
+#Put in a hash all of the embl clones used by Ensembl
+while (<CLONE>) {
+    chomp;
+    my ($embl_ac,$id) = split(/\t/,$_);
+    print "$embl_ac\n";
+    $embl_clone{$embl_ac}=1;
+}
+
+
 while (<DBMAP>) {
     chomp;
 #Get put in a hash the corresponding database for an external accession number. Get the infos from a file already processed following this format:
@@ -82,13 +93,21 @@ while (<XREF>) {
     
 	push(@{$hash{$xrac}},$both);
     }
-    if ($xrdb eq "ENSEMBL") {
+
+#Get the embl clone corresponding for each Ensembl peptides
+    if (($xrdb eq "ENSEMBL")) {
+	
 	push(@{$ens2embl{$xrac}},$id);
     }
-    if (($xrdb eq "SP") && ($db eq "EMBL")) {
-	push(@{$sp2embl{$xrac}},$id);
-    }
 
+#Get the embl ACs for each SP and SPTREMBL proteins
+    if ((($xrdb eq "SP") || ($xrdb eq "SPTREMBL")) && ($db eq "EMBL")) {
+	 #print "$id\n";
+	if ($embl_clone{$id}) {
+	    
+	    push(@{$sp2embl{$xrac}},$id);
+	}
+    }
 }
 
 while (<MAP>) {
@@ -96,35 +115,50 @@ while (<MAP>) {
 
 #P01111  COBP00000000001 100     PRIMARY  
     my ($xr,$ens,$perc,$tag) = split (/\t/,$_);
-    if (($tag eq "PRIMARY") || ($tag eq "DUPLICATE")) {
 
+#Hack to be taken away
+    my ($en1,$en2) = $ens =~ /(\w{3})P(\d+)/;
+    my $enst = $en1."T".$en2;
+
+#For now take primary or duplicates and only matches which correspond to more than 25% of the external peptide. These criteria will have to be lowered up.
+    if ((($tag eq "PRIMARY") || ($tag eq "DUPLICATE")) && ($perc >= 25)) {
+	
 #Its a hack an another solution will have to be found, if the external known gene is a refseq protein accession number get back the equivalent refseq DNA accession number 
 	if ($xr =~ /^NP_\d+/) {
 	    $xr = $ref_map{$xr};
 	}
 
+#If the external peptide correspond to an embl clone, we will take the match only if the Ensembl peptide correspond to the same clone (at least one exon)
 	if ($sp2embl{$xr}) {
+	    print "$xr\t".@{$sp2embl{$xr}}."\n";
 	    my $tot_sp_embl;
 	    my $tot_ens_embl;
 	    my @sp_embl = @{$sp2embl{$xr}};
 	    
 	    foreach my $sing1 (@sp_embl) {
+		#print "$sing1\n";
 		$tot_sp_embl .= $sing1;
-	    }
-	    
 
-	    my @ens_embl = @{$ens2embl{$xr}};
-	    
-	    foreach my $sing2 (@sp_embl) {
-		$tot_ens_embl .= $sing2;
 	    }
-	    if ($tot_ens_embl =~ $tot_sp_embl) {
-		print OUT "$ens\t$map{$xr}\t$xr\n";
+	  	  	    
+	    if ($ens2embl{$enst}) {
+		my @ens_embl = @{$ens2embl{$enst}};
+	    
+		foreach my $sing2 (@sp_embl) {
+		    $tot_ens_embl .= $sing2;
+		}
+		if ($tot_ens_embl =~ $tot_sp_embl) {
+		    print  OUT "$ens\t$map{$xr}\t$xr\n";
+		}
+		else {
+		    #print "no\n";
+		}
 	    }
 	}
-	
+	else {
 #Print the know gene AC and its database
 	print OUT "$ens\t$map{$xr}\t$xr\n";
+    }
 
 #Print all of the external database it links to (eg: HUGO)
 	foreach my $both (@{$hash{$xr}}){

misc-scripts/protein_match/print_ens2embl.pl

+use strict;
+use Bio::SeqIO;
+use Bio::EnsEMBL::DBSQL::Obj;
+use Bio::EnsEMBL::DBLoader;
+use Getopt::Long;
+use Bio::SeqIO;
+
+
+my $dbpass = undef;
+my $dbuser = 'ensro';
+my $ensdbname = 'ensembl080';
+my $host = 'ecs1c.sanger.ac.uk';
+my $output;
+
+
+&GetOptions(
+	    'db:s' => \$ensdbname,
+	    'host:s'=> \$host,
+	    'dbuser:s'=> \$dbuser,
+	    'output:s' => \$output
+	    );
+
+
+my $enslocator = "Bio::EnsEMBL::DBSQL::Obj/host=$host;dbname=$ensdbname;user=$dbuser;pass=$dbpass;perlonlyfeatures=1";
+my $ensdb =  Bio::EnsEMBL::DBLoader->new($enslocator);
+
+
+my $sth = $ensdb->prepare ("select t.id,cl.embl_id from transcript as t, exon_transcript as et, clone as cl, contig as c, exon as e where t.id=et.transcript and et.exon = e.id and e.contig = c.internal_id and c.clone = cl.internal_id");
+
+$sth->execute;
+
+my %hash;
+my %seen;
+
+print STDERR "Getting data\n";
+while (my @row = $sth->fetchrow) {
+    if (! defined $seen{$row[1]}) {
+	push(@{$hash{$row[0]}},$row[1]);
+	$seen{$row[1]} = 1;
+    }
+}
+    
+print STDERR "Writing out\n";
+open (OUT,">$output");
+
+foreach my $keys (keys %hash) {
+    my @array = @{$hash{$keys}};
+    
+    foreach my $arr (@array) {
+	print OUT "ENSEMBL\t$keys\tEMBL\t$arr\n";
+    }
+}
+
+
+
+
+
+

misc-scripts/protein_match/process_pmach.pl

@@ -32,9 +32,9 @@ my ($ens,$sp,$refseq);
 
 &runpmatch();
 &postprocesspmatch($sp);
-#&postprocesspmatch($refseq);
+&postprocesspmatch($refseq);
 &finalprocess($sp);
-#&finalprocess($refseq);
+&finalprocess($refseq);
 
 sub runpmatch {
     print STDERR "Running pmatch\n";
@@ -87,7 +87,7 @@ sub postprocesspmatch {
 
 #Write out the processed data
     foreach my $key ( keys %hash1 ) {
-	if ($hashlength{$key} >= 20) {
+	if (($hashlength{$key} >= 20)) {
 	    ($a,$b) = split(/:/,$key);
 	    print OUT "$a\t$b\t$hash1{$key}\n";
 	}