Added a small script needed in the mapping process

misc-scripts/protein_match/get_dbmap.pl

+use strict;
+
+=head1 get_all_external
+
+=head2 Description
+
+This script will set up a mapping of each primary database (SP, SPTREMBL, Refseq and PDB) to their respective name. This mapping will be then used to give a database name to each ACs.
+
+=head2 Options
+
+-sp
+-sptrembl
+-refseq
+-pdb
+
+=head2 Contact
+
+mongin@ebi.ac.uk
+birney@ebi.ac.uk
+
+=cut
+
+#perl ../../../src/ensembl-live/misc-scripts/protein_match/get_dbmap.pl -sp ../primary/01_04_hum_sprot.txt -sptrembl ../primary/07_04_hum_sptrembl.txt -refseq ../primary/hs.gnp -scop ../primary/scop.fas
+
+use Getopt::Long;
+use Bio::SeqIO;
+
+my ($sp, $sptrembl, $refseq, $scop, $out);
+
+&GetOptions(
+	    'sp:s'=>\$sp,
+	    'sptrembl:s'=>\$sptrembl,
+	    'refseq:s'=>\$refseq,
+	    'scop:s'=>\$scop,
+	    'out:s'=>\$out
+	    );
+
+open (OUT,">mapdb.map");
+
+print STDERR "Getting SP mapping\n";
+
+my $in  = Bio::SeqIO->new(-file => $sp, '-format' =>'swiss');
+
+while ( my $seq = $in->next_seq() ) {
+    print OUT $seq->accession."\tSP\n";
+    
+    my @secs = $seq->get_secondary_accessions;
+    if (@secs) {
+	foreach my $sec (@secs) {
+	    print OUT "$sec\tSP\n";
+	}
+    }
+    
+}
+
+print STDERR "Getting SPTREMBL mapping\n";
+
+my $in1  = Bio::SeqIO->new(-file => $sptrembl, '-format' =>'swiss');
+
+while ( my $seq1 = $in1->next_seq() ) {
+    print OUT $seq1->accession."\tSPTREMBL\n";
+    
+    my @secs = $seq1->get_secondary_accessions;
+    if (@secs) {
+	foreach my $sec (@secs) {
+	    print OUT "$sec\tSPTREMBL\n";
+	}
+    }
+    
+}
+
+print "Getting refseq mapping\n";
+
+open (REFSEQ,"$refseq") || die "Can't open file\n";
+
+$/ = "\/\/\n";
+
+while (<REFSEQ>) {
+    my ($prot_ac) = $_ =~ /ACCESSION\s+(\S+)/;
+    my ($dna_ac) = $_ =~ /DBSOURCE    REFSEQ: accession\s+(\w+)/;
+    
+    if ($dna_ac) {
+	print OUT "$dna_ac\tREFSEQ\n";
+    }
+}
+close (REFSEQ);
+
+$/ = "\n";
+
+print "Getting Scop mapping\n";
+
+open (SCOP,"$scop") || die "Can't open file\n";
+
+while (<SCOP>) {
+    my ($scop_ac) = $_ =~ /^>(\S+)/;
+    if ($scop_ac) {
+	print OUT "$scop_ac\tSCOP\n";
+    }
+}
+close (SCOP);
+    
+close (OUT);
+
+
+
+
+
+
+
+
+

misc-scripts/protein_match/get_embl_mim_mapping.pl

@@ -37,7 +37,7 @@ while ( my $seq1 = $in1->next_seq() ) {
     
     
     foreach my $link(@dblink) {
-	if (($link->database eq "EMBL") || ($link->database eq "MIM") || ($link->database eq "PDB")) {
+	if (($link->database eq "EMBL") || ($link->database eq "MIM")) {
 	    
 	    if (!defined $map{$ac}) {
 		die "Can't map $ac\n";

misc-scripts/protein_match/process_pmach.pl

@@ -21,20 +21,23 @@ birney@ebi.ac.uk
 
 use Getopt::Long;
 
-my ($ens,$sp,$refseq);
+my ($ens,$sp,$refseq,$pdb);
 
 &GetOptions(
             
             'ens:s'=>\$ens,
             'sp:s'=>\$sp,
-            'refseq:s'=>\$refseq
+            'refseq:s'=>\$refseq,
+	    'pdb:s'=>\$pdb
             );
 
 &runpmatch();
 &postprocesspmatch($sp);
 &postprocesspmatch($refseq);
+&postprocesspmatch($pdb);
 &finalprocess($sp);
 &finalprocess($refseq);
+&finalprocess($pdb);
 
 sub runpmatch {
     print STDERR "Running pmatch\n";
@@ -42,9 +45,13 @@ sub runpmatch {
 #Run pmatch and store the data in files which will be kept for debugging
     my $pmatch1 = "/nfs/griffin2/rd/bin.ALPHA/pmatch -T 14 $sp $ens > ens_sp_rawpmatch";
     my $pmatch2 = "/nfs/griffin2/rd/bin.ALPHA/pmatch -T 14 $refseq $ens > ens_refseq_rawpmatch";
-    
+    my $pmatch3 = "/nfs/griffin2/rd/bin.ALPHA/pmatch -T 14 $pdb $ens > ens_pdb_rawpmatch";
+
+
     system($pmatch1); # == 0 or die "$0\Error running '$pmatch1' : $!";
     system($pmatch2); #== 0 or die "$0\Error running '$pmatch2' : $!";
+   system($pmatch3); #== 0 or die "$0\Error running '$pmatch2' : $!"; 
+
 }
 
 
@@ -61,11 +68,17 @@ sub postprocesspmatch {
 	open (PROC, "ens_sp_rawpmatch") || die "Can't open File\n";
     }
     
-    else {
+    elsif ($db eq $refseq) {
 	print STDERR "Postprocessing pmatch for REFSEQ mapping\n"; 
 	open (OUT, ">ens_refseq.processed") || die "Can't open File\n";;
 	open (PROC, "ens_refseq_rawpmatch") || die "Can't open file ens_refseq_rawpmatch\n";
     }
+
+    elsif ($db eq $pdb) {
+	print STDERR "Postprocessing pmatch for PDB mapping\n"; 
+	open (OUT, ">ens_pdb.processed") || die "Can't open File\n";;
+	open (PROC, "ens_pdb_rawpmatch") || die "Can't open file ens_refseq_rawpmatch\n";
+    }
     
     while (<PROC>) {
 #538     COBP00000033978 1       538     35.3    Q14146  1       538     35.3 
@@ -109,12 +122,19 @@ sub finalprocess {
 	open (OUT, ">ens_sp.final");
     }
 
-    else {
+    elsif ($db eq $refseq) {
 	print STDERR "Getting final mapping for REFSEQ mapping\n";
 	open (PROC, "ens_refseq.processed") || die "Can' open file ens_refseq.processed\n";
-	open (OUT, ">refseq.final");
+	open (OUT, ">ens_refseq.final");
     }
 
+    elsif ($db eq $pdb) {
+	print STDERR "Getting final mapping for PDB mapping\n";
+	open (PROC, "ens_refseq.processed") || die "Can' open file ens_refseq.processed\n";
+	open (OUT, ">ens_pdb.final");
+    }
+
+
     my %hash2;
     while (<PROC>) {
 	my ($ens,$known,$perc) = split;