fixed the various methods routines. this was not working at all but no one...

fixed the various methods routines. this was not working at all but no one ever used it so was never noticed. Needed now for uniprot swissport having a different percentage cutoff

misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm

@@ -148,14 +148,76 @@ sub dump_xref{
   }
 
   my @method=();
-  my @lists =@{$self->get_set_lists()};
+  my @species=();
+  my @sources=();
 
-  my $k = 0;
+
+  my @lists;
+
+  if($self->mapper->can('get_set_lists')){
+   @lists =@{$self->mapper->get_set_lists()};  }
+  else {
+    @lists =@{$self->get_set_lists()};
+  }
+
+  my $k = -1;
+  my $all = -1;
+  my $exception = 0;
   foreach my $list (@lists){
-    $method[$k++] = shift @$list;
+    $k++;
+    $method[$k] = shift @$list;
+    my $rest = shift @$list;
+    $species[$k] = $$rest[0];
+    $sources[$k] = $$rest[1];
+    if($sources[$k] eq "*"){
+      $all = $k;
+    }	
+    else{
+      $exception  = 1;
+    }	
+  }
+
+
+
+  my $number_of_sets = $k;
+
+  my @exception_sql = ();
+  if($exception){
+    my $source_sth = $xref->dbc->prepare("select s.source_id from source s, species sp, source_url u where  u.source_id = s.source_id and u.species_id = sp.species_id and sp.name like ? and s.name like ?");    
+    $k = 0;
+    my @exception_list =();
+    while($k <= $number_of_sets){
+      my @tmp=();
+      if($k != $all){
+	$source_sth->execute($species[$k], $sources[$k]);
+	while(my @row = $source_sth->fetchrow_array()){
+#	  print $row[0]."\t".$species[$k]."\t".$sources[$k]."\n";
+	  push @tmp, $row[0];
+	  push @exception_list, $row[0]
+	}	
+	$exception_sql[$k] .= " AND x.source_id in (".join(', ',@tmp).") ";
+	
+      }
+      $k++;
+    }
+    if($all != -1){
+      $exception_sql[$all] = " AND x.source_id not in (".join(', ', @exception_list).")";
+    }
+
   }
+  else{
+    $exception_sql[0] = "";
+  }
+
   $self->method(\@method);
-  
+
+#  $k = 0;
+#  while($k <= $number_of_sets){
+#    print $method[$k]."\t".$species[$k]."\t".$sources[$k]."\n";
+#    print $exception_sql[$k]."\n";
+#    $k++;
+#  }
+
   my $i=0;
   if(defined($self->mapper->dumpcheck())){
     my $skip = 1;
@@ -175,28 +237,33 @@ sub dump_xref{
   }
 
   print "Dumping Xref fasta files\n" if($self->verbose());
-  for my $sequence_type ('dna', 'peptide') {
+  $i = 0;
+  while($i <= $number_of_sets){
+    for my $sequence_type ('dna', 'peptide') {
+
+      my $filename = $xref->dir() . "/xref_".$i."_" . $sequence_type . ".fasta";
+      open(XREF_DUMP,">$filename") || die "Could not open $filename";
+
+      my $sql = "SELECT p.xref_id, p.sequence, x.species_id , x.source_id ";
+      $sql   .= "  FROM primary_xref p, xref x ";
+      $sql   .= "  WHERE p.xref_id = x.xref_id AND ";
+      $sql   .= "        p.sequence_type ='$sequence_type' ";
+      $sql   .= $exception_sql[$i];
+
+      my $sth = $xref->dbc->prepare($sql);
+      $sth->execute();
+      while(my @row = $sth->fetchrow_array()){
+	
+	$row[1] =~ s/(.{60})/$1\n/g;
+	print XREF_DUMP ">".$row[0]."\n".$row[1]."\n";
+	
+      }
+
+      close(XREF_DUMP);
+      $sth->finish();
 
-    my $filename = $xref->dir() . "/xref_0_" . $sequence_type . ".fasta";
-    open(XREF_DUMP,">$filename") || die "Could not open $filename";
-    
-    my $sql = "SELECT p.xref_id, p.sequence, x.species_id , x.source_id ";
-    $sql   .= "  FROM primary_xref p, xref x ";
-    $sql   .= "  WHERE p.xref_id = x.xref_id AND ";
-    $sql   .= "        p.sequence_type ='$sequence_type' ";
-    
-    my $sth = $xref->dbc->prepare($sql);
-    $sth->execute();
-    while(my @row = $sth->fetchrow_array()){
-      
-      $row[1] =~ s/(.{60})/$1\n/g;
-      print XREF_DUMP ">".$row[0]."\n".$row[1]."\n";
-      
     }
-    
-    close(XREF_DUMP);
-    $sth->finish();
-    
+    $i++;
   }
   my $sth = $xref->dbc->prepare("insert into process_status (status, date) values('xref_fasta_dumped',now())");
   $sth->execute();