From f316cc45db00e4117453ed26e59e89bebe66d8b5 Mon Sep 17 00:00:00 2001
From: Philip Lijnzaad <lijnzaad@sanger.ac.uk>
Date: Wed, 10 Oct 2001 15:30:43 +0000
Subject: [PATCH] GPHit _was_ needed. Also added -N to mysql so we don't get
silly table headers.
---
misc-scripts/utilities/satellite_dbdump_bychr.pl | 16 ++++++++++++++--
1 file changed, 14 insertions(+), 2 deletions(-)
diff --git a/misc-scripts/utilities/satellite_dbdump_bychr.pl b/misc-scripts/utilities/satellite_dbdump_bychr.pl
index 117ab16f6a..917430d60d 100755
--- a/misc-scripts/utilities/satellite_dbdump_bychr.pl
+++ b/misc-scripts/utilities/satellite_dbdump_bychr.pl
@@ -337,9 +337,21 @@ WHERE lg.chr_name = '$chr'
";
dump_data($sql, $satdb, 'Hit');
+# GPHit (i.e., those on the golden path); denormalized table used by contigview
+ $sql="
+SELECT distinct h.*
+FROM $satdb.Hit h,
+ $litedb.gene_snp lgs,
+ $litedb.gene lg
+WHERE lg.chr_name = '$chr'
+ AND lg.gene = lgs.gene
+ AND lgs.refsnpid = h.refsnpid
+"
+ dump_data($sql, $satdb, 'GPHit');
+
+
# ignore these (says Heikki):
# Freq
-# GPHit
# SubPop
} # snp
@@ -584,7 +596,7 @@ sub dump_data {
$sql =~ s/\s+/ /g;
- my $cmd = "echo \"$sql\" | $mysql -q --batch -u $dbuser -p$dbpass $litedb > $destdir/$datfile";
+ my $cmd = "echo \"$sql\" | $mysql -N -q --batch -u $dbuser -p$dbpass $litedb > $destdir/$datfile";
# warn "dumping: $cmd\n"; too verbose
warn "dumping $tablename ...\n";
--
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