From d51a835b5377ab7bea31de2df6c7287c36ee5c6d Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Thu, 6 Oct 2011 13:47:58 +0000
Subject: [PATCH] update ignore sql statement for EntrezGene
---
.../xref_mapping/XrefMapper/danio_rerio.pm | 30 ++++++++++++-------
1 file changed, 20 insertions(+), 10 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm b/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm
index 115b242f42..3e051655b5 100644
--- a/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm
@@ -92,16 +92,24 @@ sub transcript_display_xref_sources {
my %ignore;
- $ignore{"EntrezGene"} =(<<AIGN);
-
-SELECT ox.object_xref_id
- FROM object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2
- WHERE ox.object_xref_id = dx.object_xref_id AND dx.dependent_xref_id = x1.xref_id
- AND x1.source_id = s1.source_id and s1.name = 'EntrezGene'
- AND x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id
- AND (s2.name like 'Refseq_dna_predicted' or s2.name like 'RefSeq_peptide_predicted')
- AND ox.ox_status = 'DUMP_OUT'
-AIGN
+ if(!$fullmode){
+ $ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
+ }
+ else{
+ $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
$ignore{"Uniprot/SPTREMBL"} =(<<BIGN);
SELECT object_xref_id
@@ -109,6 +117,8 @@ SELECT object_xref_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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