From 28dea3b5e439ac6faf5073070d9d217b390bbb45 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Mon, 17 Oct 2011 14:15:33 +0000
Subject: [PATCH] remove partupdate mode
---
misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm | 9 ++-------
.../XrefMapper/ornithorhynchus_anatinus.pm | 11 +++--------
.../xref_mapping/XrefMapper/rattus_norvegicus.pm | 13 +++----------
.../XrefMapper/saccharomyces_cerevisiae.pm | 1 -
.../XrefMapper/schizosaccharomyces_pombe.pm | 1 -
.../XrefMapper/tetraodon_nigroviridis.pm | 5 +----
.../xref_mapping/XrefMapper/xenopus_tropicalis.pm | 10 ++--------
7 files changed, 11 insertions(+), 39 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm b/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm
index 3e051655b5..24a424fb16 100644
--- a/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm
@@ -92,11 +92,8 @@ sub transcript_display_xref_sources {
my %ignore;
- if(!$fullmode){
- $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
- }
- else{
- $ignore{"EntrezGene"} =(<<'IEG');
+
+ $ignore{"EntrezGene"} =(<<'IEG');
SELECT DISTINCT ox.object_xref_id
FROM object_xref ox, dependent_xref dx,
xref xmas, xref xdep,
@@ -118,8 +115,6 @@ SELECT object_xref_id
AND priority_description = 'protein_evidence_gt_3'
BIGN
- }
-
return [\@list,\%ignore];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/ornithorhynchus_anatinus.pm b/misc-scripts/xref_mapping/XrefMapper/ornithorhynchus_anatinus.pm
index 3b980282a1..04783b230c 100644
--- a/misc-scripts/xref_mapping/XrefMapper/ornithorhynchus_anatinus.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/ornithorhynchus_anatinus.pm
@@ -29,11 +29,8 @@ sub transcript_display_xref_sources {
EntrezGene);
my %ignore;
- if(!$fullmode){
- $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
- }
- else{
- $ignore{"EntrezGene"} =(<<'IEG');
+
+ $ignore{"EntrezGene"} =(<<'IEG');
SELECT DISTINCT ox.object_xref_id
FROM object_xref ox, dependent_xref dx,
xref xmas, xref xdep,
@@ -48,15 +45,13 @@ SELECT DISTINCT ox.object_xref_id
ox.ox_status = "DUMP_OUT"
IEG
- $ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
+ $ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
SELECT object_xref_id
FROM object_xref JOIN xref USING(xref_id) JOIN source USING(source_id)
WHERE ox_status = 'DUMP_OUT' AND name = 'Uniprot/SPTREMBL'
AND priority_description = 'protein_evidence_gt_3'
BIGN
- }
-
return [\@list,\%ignore];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/rattus_norvegicus.pm b/misc-scripts/xref_mapping/XrefMapper/rattus_norvegicus.pm
index b87e2a68bb..9d90638046 100644
--- a/misc-scripts/xref_mapping/XrefMapper/rattus_norvegicus.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/rattus_norvegicus.pm
@@ -16,7 +16,6 @@ use vars '@ISA';
sub transcript_display_xref_sources {
my $self = shift;
- my $fullmode = shift;
my @list = qw(RFAM
miRBase
@@ -32,12 +31,8 @@ sub transcript_display_xref_sources {
my %ignore;
-
- if(!$fullmode){
- $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
- }
- else{
- $ignore{"EntrezGene"} =(<<'IEG');
+
+ $ignore{"EntrezGene"} =(<<'IEG');
SELECT DISTINCT ox.object_xref_id
FROM object_xref ox, dependent_xref dx,
xref xmas, xref xdep,
@@ -52,15 +47,13 @@ SELECT DISTINCT ox.object_xref_id
ox.ox_status = "DUMP_OUT"
IEG
- $ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
+ $ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
SELECT object_xref_id
FROM object_xref JOIN xref USING(xref_id) JOIN source USING(source_id)
WHERE ox_status = 'DUMP_OUT' AND name = 'Uniprot/SPTREMBL'
AND priority_description = 'protein_evidence_gt_3'
BIGN
- }
-
return [\@list,\%ignore];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/saccharomyces_cerevisiae.pm b/misc-scripts/xref_mapping/XrefMapper/saccharomyces_cerevisiae.pm
index deb9a063b9..b371716ed8 100644
--- a/misc-scripts/xref_mapping/XrefMapper/saccharomyces_cerevisiae.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/saccharomyces_cerevisiae.pm
@@ -40,7 +40,6 @@ sub build_display_xrefs {
sub transcript_display_xref_sources {
my $self = shift;
- my $fullmode = shift;
my @list = qw(
SGD_GENE
diff --git a/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm b/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm
index 971f14ab46..353ddfffa7 100644
--- a/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm
@@ -39,7 +39,6 @@ sub build_display_xrefs {
sub transcript_display_xref_sources {
my $self = shift;
- my $fullmode = shift;
my @list = qw(
PomBase_GENE
diff --git a/misc-scripts/xref_mapping/XrefMapper/tetraodon_nigroviridis.pm b/misc-scripts/xref_mapping/XrefMapper/tetraodon_nigroviridis.pm
index 7c1284406b..2b79897837 100644
--- a/misc-scripts/xref_mapping/XrefMapper/tetraodon_nigroviridis.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/tetraodon_nigroviridis.pm
@@ -23,17 +23,14 @@ sub transcript_display_xref_sources {
LocusLink);
my %ignore;
-
- if($fullmode){
- $ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
+ $ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
SELECT object_xref_id
FROM object_xref JOIN xref USING(xref_id) JOIN source USING(source_id)
WHERE ox_status = 'DUMP_OUT' AND name = 'Uniprot/SPTREMBL'
AND priority_description = 'protein_evidence_gt_3'
BIGN
- }
return [\@list,\%ignore];
diff --git a/misc-scripts/xref_mapping/XrefMapper/xenopus_tropicalis.pm b/misc-scripts/xref_mapping/XrefMapper/xenopus_tropicalis.pm
index f200fd5507..31f966efbe 100644
--- a/misc-scripts/xref_mapping/XrefMapper/xenopus_tropicalis.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/xenopus_tropicalis.pm
@@ -36,7 +36,6 @@ sub gene_description_sources {
sub transcript_display_xref_sources {
my $self = shift;
- my $fullmode = shift;
my @list = qw(Xenopus_Jamboree
MGI
@@ -52,11 +51,7 @@ sub transcript_display_xref_sources {
my %ignore;
- if(!$fullmode){
- $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
- }
- else{
- $ignore{"EntrezGene"} =(<<'IEG');
+ $ignore{"EntrezGene"} =(<<'IEG');
SELECT DISTINCT ox.object_xref_id
FROM object_xref ox, dependent_xref dx,
xref xmas, xref xdep,
@@ -71,14 +66,13 @@ SELECT DISTINCT ox.object_xref_id
ox.ox_status = "DUMP_OUT"
IEG
- $ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
+ $ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
SELECT object_xref_id
FROM object_xref JOIN xref USING(xref_id) JOIN source USING(source_id)
WHERE ox_status = 'DUMP_OUT' AND name = 'Uniprot/SPTREMBL'
AND priority_description = 'protein_evidence_gt_3'
BIGN
- }
return [\@list,\%ignore];
}
--
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