From 87ee1a965d0fcd871ca8851931b09d09cadcf9cf Mon Sep 17 00:00:00 2001
From: Arne Stabenau <stabenau@sanger.ac.uk>
Date: Fri, 15 Oct 2004 14:31:02 +0000
Subject: [PATCH] removed probeset column from affy_feature table
---
.../Bio/EnsEMBL/DBSQL/AffyFeatureAdaptor.pm | 13 ++++++-------
modules/t/test_genome.zip | Bin 969526 -> 969512 bytes
2 files changed, 6 insertions(+), 7 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/AffyFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AffyFeatureAdaptor.pm
index f5067d4565..1ca916844d 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AffyFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AffyFeatureAdaptor.pm
@@ -99,8 +99,8 @@ sub store{
my $sth = $self->prepare
("INSERT INTO affy_feature (seq_region_id, seq_region_start, " .
" seq_region_end, seq_region_strand, " .
- " affy_probe_id, analysis_id, mismatches, probeset ) " .
- "VALUES (?,?,?,?,?,?,?,?)" );
+ " affy_probe_id, analysis_id, mismatches ) " .
+ "VALUES (?,?,?,?,?,?,?)" );
my $db = $self->db();
my $analysis_adaptor = $db->get_AnalysisAdaptor();
@@ -132,8 +132,7 @@ sub store{
($af, $seq_region_id) = $self->_pre_store($af);
$sth->execute($seq_region_id, $af->start, $af->end, $af->strand,
- $af->probe->dbID, $af->analysis->dbID, $af->mismatchcount,
- $af->probeset );
+ $af->probe->dbID, $af->analysis->dbID, $af->mismatchcount );
$original->dbID($sth->{'mysql_insertid'});
$original->adaptor($self);
@@ -183,7 +182,7 @@ sub _columns {
my $self = shift;
return qw( af.affy_feature_id af.seq_region_id af.seq_region_start
- af.seq_region_end af.seq_region_strand af.probeset
+ af.seq_region_end af.seq_region_strand
af.mismatches af.affy_probe_id af.analysis_id
aa.name )
@@ -222,11 +221,11 @@ sub _objs_from_sth {
my($affy_feature_id,$seq_region_id, $seq_region_start, $seq_region_end,
- $seq_region_strand, $probeset, $mismatches, $analysis_id,
+ $seq_region_strand, $mismatches, $analysis_id,
$affy_probe_id, $array_name);
$sth->bind_columns(\$affy_feature_id,\$seq_region_id, \$seq_region_start,
- \$seq_region_end, \$seq_region_strand, \$probeset,
+ \$seq_region_end, \$seq_region_strand,
\$mismatches, \$affy_probe_id, \$analysis_id,
\$array_name );
diff --git a/modules/t/test_genome.zip b/modules/t/test_genome.zip
index 79aa4402f60197280e53af2b99c2d43eb59ccdba..45a0b8411f9e1e8c95ffc3f307445b2cd338bd0e 100644
GIT binary patch
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--
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