Mapping getting bigger and bigger, added a script which

prepare the data for scop mapping.

E.

misc-scripts/protein_match/get_embl_mim_mapping.pl

@@ -2,6 +2,8 @@ use strict;
 
 #Some doc will come ...
 
+#perl ../../../src/ensembl-live/misc-scripts/protein_match/get_embl_mim_mapping.pl -sp ../primary/hum_sp_sptrembl.pep -dbmap mapdb.map -output sp_embl_mim.map
+
 use Getopt::Long;
 use Bio::SeqIO;
 

misc-scripts/protein_match/get_scops.pl

+use strict;
+
+#Some doc will come
+#The scop mapping which should be used here can be found at:
+#http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.dom.scop.txt_1.53  (for the 1.53 release)
+
+#perl ../../../src/ensembl-live/misc-scripts/protein_match/get_scops.pl -scop ../secondary/dir.dom.scop.txt_1.53 -dbmap mapdb.map -out scops.map
+
+use Getopt::Long;
+
+my ($scop,$dbmap,$out);
+
+my %map;
+
+
+&GetOptions(
+	    'scop:s'=>\$scop,
+	    'out:s'=>\$out,
+	    'dbmap:s'=>\$dbmap
+            );
+
+open (DBMAP,"$dbmap") || die "Can't open file $dbmap\n"; 
+open (SCOP,"$scop") || die "Can't open file $scop\n";
+open (OUT,">$out") || die "Can't open file $out\n";
+    open (ERROR, ">scop.err") || die "Can't open file scop.err\n";
+
+print STDERR "Reading dbmap\n";
+
+while (<DBMAP>) {
+    chomp;
+    my ($mapac,$mapdb) = split(/\t/,$_);
+    
+    $map{$mapac} = $mapdb;
+}
+
+print STDERR "Reading Scop file\n";
+
+while (<SCOP>) {
+    chomp;
+    my ($scopac, $pdb, $chain, $scopnb) = split(/\t/,$_);
+    
+	if (!defined $map{$scopac}) {
+	    print ERROR "can't map $scopac\n";
+	}
+
+    print OUT "$map{$scopac}\t$scopac\tSCOP1\t$pdb\|\|$chain\n";
+    print OUT "$map{$scopac}\t$scopac\tSCOP1\t$scopnb\n";
+}