make get_valid_codes - return hashref

misc-scripts/xref_mapping/XrefParser/BaseParser.pm

@@ -270,7 +270,7 @@ sub get_valid_codes{
       $valid_codes{$row[0]} =$row[1];
     }
   }
-  return %valid_codes;
+  return \%valid_codes;
 }
 
 # --------------------------------------------------------------------------------

misc-scripts/xref_mapping/XrefParser/GOParser.pm

@@ -40,8 +40,8 @@ sub run {
   }
 
 
-  my (%swiss) = XrefParser::BaseParser->get_valid_codes("uniprot",$species_id);
-  my (%refseq) = XrefParser::BaseParser->get_valid_codes("refseq",$species_id);
+  my (%swiss) = %{XrefParser::BaseParser->get_valid_codes("uniprot",$species_id)};
+  my (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};
 
   my $count  = 0;
 

misc-scripts/xref_mapping/XrefParser/HUGOParser.pm

@@ -63,8 +63,8 @@ sub run {
   close ENS4;
 
   
-  my (%swiss)  =  XrefParser::BaseParser->get_valid_codes("uniprot",$species_id);
-  my (%refseq) =  XrefParser::BaseParser->get_valid_codes("refseq",$species_id);
+  my (%swiss)  =  %{XrefParser::BaseParser->get_valid_codes("uniprot",$species_id)};
+  my (%refseq) =  %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};
  
 
   my $count = 0;

misc-scripts/xref_mapping/XrefParser/MGDParser.pm

@@ -43,8 +43,8 @@ sub run {
     $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
   }                                                                                                                      
                                                                                                                       
-  my (%swiss) = XrefParser::BaseParser->get_valid_codes("uniprot",$species_id);
-  my (%refseq) = XrefParser::BaseParser->get_valid_codes("refseq",$species_id);
+  my (%swiss) = %{XrefParser::BaseParser->get_valid_codes("uniprot",$species_id)};
+  my (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};
 
 
   my $count = 0;

misc-scripts/xref_mapping/XrefParser/RGDParser.pm

@@ -44,8 +44,8 @@ sub run {
   }
 
 
-  my (%genbank) = XrefParser::BaseParser->get_valid_codes("EMBL",$species_id);
-  my (%refseq) = XrefParser::BaseParser->get_valid_codes("refseq",$species_id);
+  my (%genbank) = %{XrefParser::BaseParser->get_valid_codes("EMBL",$species_id)};
+  my (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};
 
   open(RGD,"<".$file) || die "Could not open $file\n";
 #Genbank_Nucleotide      Gene_Symbol     RGD_ID

misc-scripts/xref_mapping/XrefParser/ZFINParser.pm

@@ -42,8 +42,8 @@ sub run {
   my $dir = dirname($file);
   
 
-  my (%swiss) = XrefParser::BaseParser->get_valid_codes("uniprot",$species_id);
-  my (%refseq) = XrefParser::BaseParser->get_valid_codes("refseq",$species_id);
+  my (%swiss) = %{XrefParser::BaseParser->get_valid_codes("uniprot",$species_id)};
+  my (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};
 
   open(SWISSPROT,"<".$dir."/swissprot.txt") || die "Could not open $dir/swissprot.txt\n";
 #e.g.