general tidy

misc-scripts/xref_mapping/XrefMapper/Interpro.pm

 package XrefMapper::Interpro;
+use strict;
+use warnings;
 
 use vars '@ISA';
 @ISA = qw{ XrefMapper::BasicMapper };
 
-use strict;
-use warnings;
+
 use XrefMapper::BasicMapper;
 
 sub new {
@@ -34,18 +35,47 @@ sub process{
 
   $object_xref_id++;
 
-  my $add_object_xref_sth = $self->xref->dbc->prepare('insert into object_xref (object_xref_id, ensembl_id,ensembl_object_type, xref_id, linkage_type, ox_status, master_xref_id ) values (?, ?, ?, ?, ?, "DUMP_OUT", ?)');
 
+
+#
+# Get the sql and sths required.
+#
+
+  my $add_ox_sql = (<<"AOX");
+INSERT INTO object_xref
+       (object_xref_id, ensembl_id,ensembl_object_type, xref_id,
+        linkage_type, ox_status, master_xref_id )
+       VALUES (?, ?, ?, ?, ?, "DUMP_OUT", ?)
+AOX
+  my $add_object_xref_sth = $self->xref->dbc->prepare($add_ox_sql);
+
+
+  my $add_go_xref_sql = (<<"AGX");
+INSERT INTO go_xref (object_xref_id, linkage_type)
+  VALUES (?, ?)
+AGX
+  my $add_go_xref_sth = $self->xref->dbc->prepare($add_go_xref_sql);
+
+  my $ins_ix_sql = (<<"IXS");
+INSERT INTO identity_xref (object_xref_id, query_identity, target_identity)
+  VALUES (?, 100, 100)
+IXS
+  my $ins_ix_sth = $self->xref->dbc->prepare($ins_ix_sql);
+
+  my $dep_sql = (<<"DLS");
+SELECT dependent_xref_id, linkage_annotation
+  FROM dependent_xref
+   WHERE master_xref_id = ?
+DLS
+  my $dep_sth    = $self->xref->dbc->prepare($dep_sql);
+  
   local $add_object_xref_sth->{RaiseError}; #catch duplicates
   local $add_object_xref_sth->{PrintError}; # cut down on error messages
-  
-  my $add_go_xref_sth = $self->xref->dbc->prepare('insert into go_xref (object_xref_id, linkage_type) values (?, ?)'); 
 
-  my $ins_ix_sth = $self->xref->dbc->prepare("insert into identity_xref (object_xref_id, query_identity, target_identity) values(?, 100, 100)");
 
   # Get a mapping of protein domains to ensembl translations for
   # interpro dependent xrefs
-  my $core_sql = "SELECT hit_name, translation_id FROM protein_feature" ;
+  my $core_sql = 'SELECT hit_name, translation_id FROM protein_feature' ;
   my $core_sth = $self->core->dbc->prepare($core_sql);
   $core_sth->execute();
   my %domain_to_translation = ();
@@ -56,26 +86,35 @@ sub process{
     push @{$domain_to_translation{$domain}}, $translation;
   }
 
-  my $dep_sth    = $self->xref->dbc->prepare("select dependent_xref_id, linkage_annotation from dependent_xref where master_xref_id = ?");
-  
-  # Get a list of interpro data, including dependent xrefs if avail
-  $sth = $self->xref->dbc->prepare("
-    SELECT ip.interpro, ip.pfam, x2.xref_id, x2.source_id,
-           dx.linkage_annotation, dx.master_xref_id
-      FROM interpro ip, xref x
-        LEFT JOIN dependent_xref dx ON x.xref_id=dx.master_xref_id
-          LEFT JOIN xref x2 ON dx.dependent_xref_id=x2.xref_id
-            WHERE ip.interpro = x.accession and ip.dbtype != 'PRINTS'");
+
+  my $int_sql = (<<"ISQ");
+SELECT ip.interpro, ip.pfam, x2.xref_id, x2.source_id,
+       dx.linkage_annotation, dx.master_xref_id
+  FROM interpro ip, xref x
+    LEFT JOIN dependent_xref dx 
+         ON x.xref_id=dx.master_xref_id
+    LEFT JOIN xref x2 
+         ON dx.dependent_xref_id=x2.xref_id
+      WHERE ip.interpro = x.accession and ip.dbtype != 'PRINTS'
+ISQ
+  $sth = $self->xref->dbc->prepare($int_sql);
+
+
   my $rv = $sth->execute();
-#  my %interpro_cache;
-  my %added;
+
+#  my %added;
   my $dup=0;
   while( my $row = $sth->fetchrow_arrayref() ){
     my ( $interpro, $pfam, $dx_xref_id, $dx_source_id, $go_linkage, $master_id ) = @$row;
     if( $dx_xref_id ){
       foreach my $ensembl_id( @{$domain_to_translation{$pfam}||[]} ){
         #...And the interpro domain maps to a translation
-	$add_object_xref_sth->execute($object_xref_id, $ensembl_id, 'Translation', $dx_xref_id, 'DEPENDENT', $master_id);	  
+        $add_object_xref_sth->execute($object_xref_id,
+				      $ensembl_id,
+				      'Translation',
+				      $dx_xref_id,
+				      'DEPENDENT',
+				      $master_id);
 	if($add_object_xref_sth->err){
 	  my $err = $add_object_xref_sth->errstr;
 	  if($err =~ /Duplicate/){
@@ -87,7 +126,6 @@ sub process{
 	  }
 	}
 	$ins_ix_sth->execute($object_xref_id);
-	$added{$dx_source_id}++;
 	$oxref_count++;
 	if($go_linkage){
 	  $add_go_xref_sth->execute($object_xref_id, $go_linkage );
@@ -107,15 +145,20 @@ sub process{
 	  my $dep_xref_id;
 	  my $link;
 	  $dep_sth->bind_columns(\$dep_xref_id, \$link);
-	  while($dep_sth->fetch()){
-	    $add_object_xref_sth->execute($object_xref_id, $ensembl_id, 'Translation', $dep_xref_id, 'DEPENDENT', $new_master_id);	  
+          while($dep_sth->fetch()){
+	    $add_object_xref_sth->execute($object_xref_id,
+					  $ensembl_id,
+					  'Translation',
+					  $dep_xref_id,
+					  'DEPENDENT',
+					  $new_master_id);
 	    if(!$add_object_xref_sth->err){
 	      push @master_xref_ids, $dep_xref_id;
 	      if($link){
 		$add_go_xref_sth->execute($object_xref_id, $link );
 	      }
 	      $ins_ix_sth->execute($object_xref_id);
-	    }	    
+	    }
 	    $object_xref_id++;
 	  }
 	}
@@ -127,16 +170,15 @@ sub process{
     }
   }
   $sth->finish();
-  
-  
-  print "\n".$dup." already existed\n\n" if($self->verbose);
-
-  print("  Wrote $ipro_count interpro table entries\n") if($self->verbose);
-  print("    including $oxref_count object xrefs, \n") if($self->verbose);
-  print("    and $goxref_count go xrefs\n") if($self->verbose);
-#  foreach my $key (keys %added){
-#    print "id= $key has ".$added{$key}. " object xrefs added\n";
-#  }
+
+
+  if($self->verbose){
+    print "\n".$dup." already existed\n\n";
+    print "  Wrote $ipro_count interpro table entries\n";
+    print "    including $oxref_count object xrefs, \n";
+    print "    and $goxref_count go xrefs\n";
+  }
+  return;
 }
 
 1;