From 1e5a3806134eedde1d95d90357d3a1fdd8dfca62 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Thu, 6 Oct 2011 13:53:29 +0000
Subject: [PATCH] update ignore hash
---
.../xref_mapping/XrefMapper/drosophila.pm | 17 ++---------------
.../XrefMapper/ixodes_scapularis.pm | 7 -------
.../XrefMapper/neurospora_crassa.pm | 11 -----------
3 files changed, 2 insertions(+), 33 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/drosophila.pm b/misc-scripts/xref_mapping/XrefMapper/drosophila.pm
index a667360c30..acbb0e1773 100644
--- a/misc-scripts/xref_mapping/XrefMapper/drosophila.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/drosophila.pm
@@ -61,27 +61,14 @@ sub gene_display_xref_sources {
my $self = shift;
my $fullmode = shift;
- my @list = qw(
- FlyBaseName_gene
+ my @list = qw(FlyBaseName_gene
FlyBaseCGID_gene
- flybase_gene_id
- );
+ flybase_gene_id);
my %ignore;
print "Get FlyBase Gene display_xrefs_sources with fullmode=$fullmode\n" if ($self->verbose);
- # Both methods
-
- if(!$fullmode){
- $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
- }
- else{
- $ignore{"EntrezGene"} = 'select ox.object_xref_id from object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2 where ox.object_xref_id = dx.object_xref_id and dx.dependent_xref_id = x1.xref_id and x1.source_id = s1.source_id and s1.name = "EntrezGene" and x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id and (s2.name like "Refseq_dna_predicted" or s2.name like "RefSeq_peptide_predicted") and ox.ox_status = "DUMP_OUT"';
-
- }
-
-
return [\@list,\%ignore];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm b/misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm
index 1a8fe16d39..c6d95e0a3b 100644
--- a/misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm
@@ -27,13 +27,6 @@ sub transcript_display_xref_sources {
);
my %ignore;
- if(!$fullmode){
- $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
- }
- else{
- $ignore{"EntrezGene"} = 'select ox.object_xref_id from object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2 where ox.object_xref_id = dx.object_xref_id and dx.dependent_xref_id = x1.xref_id and x1.source_id = s1.source_id and s1.name = "EntrezGene" and x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id and (s2.name like "Refseq_dna_predicted" or s2.name like "RefSeq_peptide_predicted") and ox.ox_status = "DUMP_OUT"';
-
- }
return [\@list,\%ignore];
diff --git a/misc-scripts/xref_mapping/XrefMapper/neurospora_crassa.pm b/misc-scripts/xref_mapping/XrefMapper/neurospora_crassa.pm
index aaaf470448..f18a93762f 100644
--- a/misc-scripts/xref_mapping/XrefMapper/neurospora_crassa.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/neurospora_crassa.pm
@@ -24,17 +24,6 @@ sub transcript_display_xref_sources {
my %ignore;
-
- # Both methods
-
- if(!$fullmode){
- $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
- }
- else{
- $ignore{"EntrezGene"} = 'select ox.object_xref_id from object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2 where ox.object_xref_id = dx.object_xref_id and dx.dependent_xref_id = x1.xref_id and x1.source_id = s1.source_id and s1.name = "EntrezGene" and x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id and (s2.name like "Refseq_dna_predicted" or s2.name like "RefSeq_peptide_predicted") and ox.ox_status = "DUMP_OUT"';
-
- }
-
return [\@list,\%ignore];
}
--
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