diff --git a/misc-scripts/xref_mapping/XrefMapper/aedes_aegypti.pm b/misc-scripts/xref_mapping/XrefMapper/aedes_aegypti.pm index 86eee2381d0a4e4e717268e793576885461acf25..6a54d7d3785b295d27d758a99e6785f1b7230830 100644 --- a/misc-scripts/xref_mapping/XrefMapper/aedes_aegypti.pm +++ b/misc-scripts/xref_mapping/XrefMapper/aedes_aegypti.pm @@ -28,6 +28,18 @@ sub gene_description_sources { ); } +sub gene_display_xref_sources { + my @list = qw( + Uniprot/SWISSPROT + VB_Community_Annotation + ); + + my %ignore; + + return [\@list,\%ignore]; + +} + sub transcript_display_xref_sources { my @list = qw( Uniprot/SWISSPROT @@ -35,7 +47,6 @@ sub transcript_display_xref_sources { ); my %ignore; - #$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted'; return [\@list,\%ignore]; diff --git a/misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm b/misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm index 8a5157985d7f4a8d5076bc19b987cec1c2d68752..c2a78c3c736a3b9115d9d6b423b6f54beff095b2 100644 --- a/misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm +++ b/misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm @@ -37,6 +37,20 @@ 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 diff --git a/misc-scripts/xref_mapping/XrefMapper/culex_quinquefasciatus.pm b/misc-scripts/xref_mapping/XrefMapper/culex_quinquefasciatus.pm index 9193f32fc67f22bdb7e9a7792a65821f4fe03f91..f96f667ecc1c4f6032f25c9b13036d5141e55a53 100644 --- a/misc-scripts/xref_mapping/XrefMapper/culex_quinquefasciatus.pm +++ b/misc-scripts/xref_mapping/XrefMapper/culex_quinquefasciatus.pm @@ -33,6 +33,19 @@ sub gene_description_sources { ); } +sub gene_display_xref_sources { + + my @list = qw(RFAM + miRBase + Uniprot/SWISSPROT + VB_Community_Annotation + ); + + my %ignore; + return [\@list,\%ignore]; + +} + sub transcript_display_xref_sources { my @list = qw(RFAM diff --git a/misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm b/misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm index 303efe90d59e605b33edb601ef246b048a289aa5..b48d640874a3d4850e1374d2f03f8e444af67f96 100644 --- a/misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm +++ b/misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm @@ -15,20 +15,33 @@ sub set_methods{ return $default_method, \%override_method_for_source; } -#Reverse order: second one has higher priority! + sub gene_description_sources { - return ("Uniprot/SWISSPROT", - "Ixodes_ManualAnnotation", + return ("Ixodes_ManualAnnotation", + "Uniprot/SWISSPROT", ) ; } -#Reverse order: second one has higher priority! +sub gene_display_xref_sources { + my $self = shift; + my $fullmode = shift; + + my @list = qw(Ixodes_ManualAnnotation + Uniprot/SWISSPROT + ); + + my %ignore; + + return [\@list,\%ignore]; + +} + sub transcript_display_xref_sources { my $self = shift; my $fullmode = shift; - my @list = qw(Uniprot/SWISSPROT - Ixodes_ManualAnnotation + my @list = qw(Ixodes_ManualAnnotation + Uniprot/SWISSPROT ); my %ignore; diff --git a/misc-scripts/xref_mapping/XrefMapper/neurospora_crassa.pm b/misc-scripts/xref_mapping/XrefMapper/neurospora_crassa.pm index 7b7ac28ddb89aec248579c9f12d428ba7aa13bf3..1515e2fe852473d1f95c5658e6c54e9024a33288 100644 --- a/misc-scripts/xref_mapping/XrefMapper/neurospora_crassa.pm +++ b/misc-scripts/xref_mapping/XrefMapper/neurospora_crassa.pm @@ -7,9 +7,20 @@ use vars qw(@ISA); @ISA = qw(XrefMapper::BasicMapper); +sub gene_display_xref_sources { + my $self = shift; + + my @list = qw( + Uniprot_genename + ); + + my %ignore; + + return [\@list,\%ignore]; +} + sub transcript_display_xref_sources { my $self = shift; - my $fullmode = shift; my @list = qw( Uniprot_genename diff --git a/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm b/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm index 03307399c0ab3b79412bafd399b00ac1ac6949c1..361ad0eaefbfd03a99df5abf7472df5d6e5751e6 100644 --- a/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm +++ b/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm @@ -41,11 +41,23 @@ sub build_display_xrefs { } -sub transcript_display_xref_sources { +sub gene_display_xref_sources { my $self = shift; my @list = qw( PomBase_GENE + ); + + my %ignore; + + return [\@list,\%ignore]; +} + + +sub transcript_display_xref_sources { + my $self = shift; + + my @list = qw( PomBase_TRANSCRIPT );