standardise display xref assignment

misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm

@@ -44,16 +44,21 @@ my %transcript_length;
 
 sub gene_description_sources {
 
-  return ("RFAM",
+  return ("VGNC",
+          "HGNC",
+          "MGI",
+          "ZFIN_ID",
+          "Xenbase",
+          "RFAM",
+          "miRBase",
+          "EntrezGene",
+          "RefSeq_peptide",
+          "RefSeq_mRNA",
+          "Uniprot_gn",
+          "Uniprot/SWISSPROT",
           "RNAMMER",
           "TRNASCAN_SE",
-	  "miRBase",
-          "HGNC",
-          "VGNC",
-          "IMGT/GENE_DB",
-	  "Uniprot/SWISSPROT",
-	  "RefSeq_peptide",
-	  "RefSeq_mRNA");
+          "IMGT/GENE_DB");
 
 }
 
@@ -86,8 +91,8 @@ sub gene_display_xref_sources {
   my @list = qw(VGNC
                 RFAM
                 miRBase
-                Uniprot_gn
-                EntrezGene);
+                EntrezGene
+                Uniprot_gn);
 
   my %ignore;
 

misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm

@@ -84,17 +84,6 @@ JSQL
 
 }
 
-sub gene_description_sources {
-
-  return ("RFAM",
-	  "miRBase",
-          "ZFIN_ID",
-          "IMGT/GENE_DB",
-	  "Uniprot/SWISSPROT",
-	  "RefSeq_peptide",
-	  "RefSeq_mRNA");
-
-}
 
 
 1;

misc-scripts/xref_mapping/XrefMapper/gallus_gallus.pm

@@ -50,17 +50,5 @@ LOCP
 }
 
 
-sub gene_description_sources {
-
-  return ("miRBase",
-	  "RFAM", 
-	  "CGNC",
-	  "Uniprot/SWISSPROT", 
-	  "Uniprot/Varsplic", 
-	  "RefSeq_peptide", 
-	  "RefSeq_mRNA");
-
-}
-
 
 1;

misc-scripts/xref_mapping/XrefMapper/mus_musculus.pm

@@ -85,21 +85,6 @@ JSQL
 
 }
 
-sub gene_description_sources {
-
-  return ("miRBase",
-	  "RFAM", 
-          "IMGT/GENE_DB",
-	  "MGI_curated_gene",
-	  "MGI_curated_transcript",
-	  "MGI",
-	  "Uniprot/SWISSPROT", 
-	  "Uniprot/Varsplic", 
-	  "RefSeq_peptide", 
-	  "RefSeq_mRNA");
-
-}
-
 sub special_filter {
 
   return ('\(?[0-9A-Z]{10}RIK PROTEIN\)?[ \.]',

misc-scripts/xref_mapping/XrefMapper/xenopus_tropicalis.pm

@@ -34,17 +34,6 @@ sub gene_description_filter_regexps {
 
 }
 
-sub gene_description_sources {
-
-  return ("Xenbase",	  
-	  "RFAM",
-	  "miRBase",
-	  "Uniprot/SWISSPROT",
-	  "RefSeq_peptide",
-	  "RefSeq_mRNA",
-	  "Uniprot/Varsplic");
-}
-
 
 sub gene_display_xref_sources {
   my $self     = shift;