From 224dd11e9e65fecd0a5f6981d90092eaa354201d Mon Sep 17 00:00:00 2001
From: Derek Wilson <dw8@sanger.ac.uk>
Date: Fri, 4 Jan 2013 15:26:22 +0000
Subject: [PATCH] Added gene_display_xref_sources subroutine.
---
.../xref_mapping/XrefMapper/aedes_aegypti.pm | 37 +++++++-----------
.../XrefMapper/anopheles_gambiae.pm | 17 +-------
.../XrefMapper/culex_quinquefasciatus.pm | 36 ++++++-----------
.../XrefMapper/ixodes_scapularis.pm | 39 ++++++++-----------
4 files changed, 44 insertions(+), 85 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/aedes_aegypti.pm b/misc-scripts/xref_mapping/XrefMapper/aedes_aegypti.pm
index 6a54d7d378..d8b5dc2b3d 100644
--- a/misc-scripts/xref_mapping/XrefMapper/aedes_aegypti.pm
+++ b/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];
diff --git a/misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm b/misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm
index c2a78c3c73..5709b44e3e 100644
--- a/misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm
+++ b/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
diff --git a/misc-scripts/xref_mapping/XrefMapper/culex_quinquefasciatus.pm b/misc-scripts/xref_mapping/XrefMapper/culex_quinquefasciatus.pm
index f96f667ecc..68e3b53549 100644
--- a/misc-scripts/xref_mapping/XrefMapper/culex_quinquefasciatus.pm
+++ b/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];
diff --git a/misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm b/misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm
index b48d640874..f6ca9dd67d 100644
--- a/misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm
+++ b/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;
--
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