Add PRINTS back as it is needed for the protein alignments but store the...

Add PRINTS back as it is needed for the protein alignments but store the source in the  interpro table as this is usefull information, that allows us to ignore PRINTS later.

misc-scripts/xref_mapping/XrefParser/InterproParser.pm

@@ -46,7 +46,7 @@ sub run {
 
   my $add_interpro_sth =
     $self->dbi()
-    ->prepare("INSERT INTO interpro (interpro, pfam) VALUES(?,?)");
+    ->prepare("INSERT INTO interpro (interpro, pfam, dbtype ) VALUES(?,?,?)");
 
   my $get_interpro_sth =
     $self->dbi()
@@ -59,11 +59,6 @@ sub run {
         . "(accession,version,label,description,source_id,species_id, info_type) "
         . "VALUES(?,?,?,?,?,?,?)" );
 
-#  my $get_xref_sth =
-#    $self->dbi()
-#    ->prepare( "SELECT xref_id FROM xref "
-#        . "WHERE accession = ? AND source_id = ?" );
-
   my $dir = dirname($file);
 
   my %short_name;
@@ -112,16 +107,16 @@ sub run {
         my ($members) = $_ =~ /<member_list>(.+)<\/member_list>/s;
 
         while ( $members =~
-/db="(PROSITE|PFAM|PREFILE|PROFILE|TIGRFAMs|PIRSF|SMART|SSF)"\s+dbkey="(\S+)"/cgm
+/db="(PROSITE|PFAM|PREFILE|PROFILE|TIGRFAMs|PRINTS|PIRSF|SMART|SSF)"\s+dbkey="(\S+)"/cgm
           )
         {
             my ( $db_type, $id ) = ( $1, $2 );
             if( $db_type eq 'SSF' ){ $id =~ s/^SSF// } # Strip SSF prefix
 
-            if ( !$self->get_xref( $interpro, $id, $species_id ) ) {
-                $add_interpro_sth->execute( $interpro, $id );
-                $count{$db_type}++;
-            }
+#            if ( !$self->get_xref( $interpro, $id, $species_id ) ) {#no idea why if was checking for something with source of the name it would never work
+	    $add_interpro_sth->execute( $interpro, $id, $db_type );
+	    $count{$db_type}++;
+#            }
         }
     }
   }
@@ -158,14 +153,4 @@ sub run {
     return 0;
 }
 
-#sub get_xref{
-#  my ($get_xref_sth, $acc, $source) = @_;
-#
-#  $get_xref_sth->execute($acc, $source) || die "FAILED $acc  $source\n";
-#  if(my @row = $get_xref_sth->fetchrow_array()) {
-#    return $row[0];
-#  }   
-#  return 0;
-#}
-
 1;