Added gene_display_xref_sources subroutine.

misc-scripts/xref_mapping/XrefMapper/aedes_aegypti.pm

@@ -20,33 +20,26 @@ sub set_methods{
 
 
 
-#Reverse order: last one has higher priority!
+#Reverse order: last one has higher priority! <- This comment is wrong (mikkel 12/10/2012)
+# index [0] has higher priority! 
 sub gene_description_sources {
-  return ("VB_External_Description",
-	  "Uniprot/SWISSPROT",
-          "VB_Community_Annotation"
-	  );
+  return qw(
+  	     VB_Community_Annotation
+  	     Uniprot/SWISSPROT
+  	     VB_External_Description
+	     );
 }
-
-sub gene_display_xref_sources {
-  my @list = qw(
-		Uniprot/SWISSPROT
-		VB_Community_Annotation
-                );
-
-  my %ignore;
-
-  return [\@list,\%ignore];
-
-}
-
+#Old order VB_External_Description Uniprot/SWISSPROT VB_Community_Annotation
+# only sources in this list are used when setting  display_xref_id
 sub transcript_display_xref_sources {
   my @list = qw(
-		Uniprot/SWISSPROT
-		VB_Community_Annotation
-                );
-
+  	  	VB_Community_Annotation
+  	  	Uniprot/SWISSPROT
+  	  	VB_External_Description
+		);
+#old VB_External_Description Uniprot/SWISSPROT VB_Community_Annotation
   my %ignore;
+  #$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
 
   return [\@list,\%ignore];
 

misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm

@@ -37,24 +37,9 @@ sub gene_description_sources {
           );
 }
 
-sub gene_display_xref_sources {
-
-  my @list = qw(RFAM
-		miRBase
-		VB_Community_Annotation
-		Uniprot/SWISSPROT
-		VB_RNA_Description
-	       );
-
-  my %ignore;
-  return [\@list,\%ignore];
-
-}
-
 sub transcript_display_xref_sources {
 
-  my @list = qw(RFAM
-		miRBase
+  my @list = qw(
 		VB_Community_Annotation
 		Uniprot/SWISSPROT
 		VB_RNA_Description

misc-scripts/xref_mapping/XrefMapper/culex_quinquefasciatus.pm

@@ -25,34 +25,22 @@ sub set_methods{
 
 sub gene_description_sources {
 
-  return (
-	  "VB_External_Description",
-	  "VB_RNA_Description",
-	  "Uniprot/SWISSPROT",
-	  "VB_Community_Annotation"
-          );
-}
-
-sub gene_display_xref_sources {
-
-  my @list = qw(RFAM
-		miRBase
-		Uniprot/SWISSPROT
-		VB_Community_Annotation
-             );
-
-  my %ignore;
-  return [\@list,\%ignore];
-
+  return qw(
+	    VB_Community_Annotation
+	    Uniprot/SWISSPROT
+	    VB_RNA_Description
+  	    VB_External_Description
+            );
 }
 
 sub transcript_display_xref_sources {
 
-  my @list = qw(RFAM
-		miRBase
-		Uniprot/SWISSPROT
-		VB_Community_Annotation
-             );
+  my @list = qw(	    
+  	  	VB_Community_Annotation
+  	  	Uniprot/SWISSPROT
+  	  	VB_RNA_Description
+  	  	VB_External_Description
+		);
 
   my %ignore;
   return [\@list,\%ignore];

misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm

@@ -9,40 +9,33 @@ use vars '@ISA';
 
 sub set_methods{
  
-  my $default_method = 'ExonerateGappedBest1_55_perc_id';
-  my %override_method_for_source = ( );
+  my $default_method = 'ExonerateGappedBest1';
+  my %override_method_for_source = ( 
+  	  ExonerateGappedBest5 => ['RefSeq_mRNA','RefSeq_mRNA_predicted', 'RefSeq_ncRNA', 'RefSeq_ncRNA_predicted' ],
+  	  );
 
   return $default_method, \%override_method_for_source;
 }
 
-
+#Reverse order: second one has higher priority!
 sub gene_description_sources {
-  return ("Ixodes_ManualAnnotation",
-	  "Uniprot/SWISSPROT",	  
-  ) ;
-}
-
-sub gene_display_xref_sources {
-  my $self     = shift;
-  my $fullmode = shift;
-
-  my @list = qw(Ixodes_ManualAnnotation
-                Uniprot/SWISSPROT		
-                );
-
-  my %ignore;
-
-  return [\@list,\%ignore];
-
+  return qw(
+  	     VB_Community_Annotation
+  	     Uniprot/SWISSPROT
+  	     VB_External_Description
+	     );
 }
 
+#Reverse order: second one has higher priority!
 sub transcript_display_xref_sources {
   my $self     = shift;
   my $fullmode = shift;
 
-  my @list = qw(Ixodes_ManualAnnotation
-                Uniprot/SWISSPROT		
-                );
+  my @list = qw(
+  	  	VB_Community_Annotation
+  	  	Uniprot/SWISSPROT
+  	  	VB_External_Description
+		);
 
   my %ignore;