From 472a146c0f0e1873d2cd10552aa61606c7cd67dd Mon Sep 17 00:00:00 2001
From: Arnaud Kerhornou <arnaud@ebi.ac.uk>
Date: Thu, 16 Aug 2012 12:07:16 +0000
Subject: [PATCH] for method transcript_display_xref_sources, updated the
ignore setup to be consistent with refactoring of DisplayXrefs.pm
---
.../xref_mapping/XrefMapper/eukaryota.pm | 35 +++++++++++++------
1 file changed, 25 insertions(+), 10 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/eukaryota.pm b/misc-scripts/xref_mapping/XrefMapper/eukaryota.pm
index 57f2115fe0..5819eb68f9 100644
--- a/misc-scripts/xref_mapping/XrefMapper/eukaryota.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/eukaryota.pm
@@ -20,7 +20,6 @@ sub set_methods{
sub transcript_display_xref_sources {
my $self = shift;
- my $fullmode = shift;
print STDERR "getting the list of external_dbs for assigning gene names from eukaryota.pm\n";
@@ -46,16 +45,32 @@ sub transcript_display_xref_sources {
my %ignore;
- # Both methods
-
- if(!$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"';
-
- }
+ #don't use EntrezGene labels dependent on predicted RefSeqs
+
+ $ignore{'EntrezGene'} =<<IEG;
+SELECT DISTINCT ox.object_xref_id
+ FROM object_xref ox, dependent_xref dx,
+ xref xmas, xref xdep,
+ source smas, source sdep
+ WHERE ox.xref_id = dx.dependent_xref_id AND
+ dx.dependent_xref_id = xdep.xref_id AND
+ dx.master_xref_id = xmas.xref_id AND
+ xmas.source_id = smas.source_id AND
+ xdep.source_id = sdep.source_id AND
+ smas.name like "Refseq%predicted" AND
+ sdep.name like "EntrezGene" AND
+ ox.ox_status = "DUMP_OUT"
+IEG
+
+ #don't use labels starting with LOC
+
+ $ignore{'LOC_prefix'} =<<LOCP;
+SELECT object_xref_id
+ FROM object_xref JOIN xref USING(xref_id) JOIN source USING(source_id)
+ WHERE ox_status = 'DUMP_OUT' AND label REGEXP '^LOC[[:digit:]]+'
+LOCP
+
return [\@list,\%ignore];
}
--
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