From 32e8c5b6e8856d0759337fa6236749d3cb11a5c2 Mon Sep 17 00:00:00 2001
From: Amonida Zadissa <amonida@ebi.ac.uk>
Date: Thu, 27 Sep 2012 14:33:05 +0000
Subject: [PATCH] * Columns are tab-separated, split the rows accordingly and
then there's no need to start the index at '1'. * Don't check the
assembly_exception table if this is the first set of patches to be added.
---
.../assembly_patches/assembly_patch_load.pl | 16 +++++++++++-----
1 file changed, 11 insertions(+), 5 deletions(-)
diff --git a/misc-scripts/assembly_patches/assembly_patch_load.pl b/misc-scripts/assembly_patches/assembly_patch_load.pl
index 7d8c3f0891..9b045c7d02 100644
--- a/misc-scripts/assembly_patches/assembly_patch_load.pl
+++ b/misc-scripts/assembly_patches/assembly_patch_load.pl
@@ -65,14 +65,19 @@ $sth->finish;
$sth = $dba->dbc->prepare("select max(assembly_exception_id) from assembly_exception")
|| die "Could not get max assembly_exception_id";
-$sth->execute || die "problem executing get max sassembly_exception_id";
+$sth->execute || die "problem executing get max assembly_exception_id";
my $max_assembly_exception_id;
$sth->bind_columns(\$max_assembly_exception_id) || die "problem binding";
$sth->fetch() || die "problem fetching";
$sth->finish;
print "starting new seq_region at seq_region_id of $max_seq_region_id\n";
-print "\nTo reset\ndelete from dna where seq_region_id > $max_seq_region_id\ndelete from seq_region where seq_region_id > $max_seq_region_id\ndelete from assembly_exception where assembly_exception_id > $max_assembly_exception_id\n\n";
+
+if (defined( $max_assembly_exception_id ) ) {
+ print "\nTo reset\ndelete from dna where seq_region_id > $max_seq_region_id\ndelete from seq_region where seq_region_id > $max_seq_region_id\ndelete from assembly_exception where assembly_exception_id > $max_assembly_exception_id\n\n";
+} else {
+ print "\nNOTE! assembly_exception table is not populated, probably the first patch release.\n\n";
+}
$max_seq_region_id++;
$max_assembly_exception_id++;
@@ -178,8 +183,8 @@ while (<TYPE>) {
SCAF: while(<TXT>){
if(/^#/){
chomp;
- my @arr = split;
- my $i = 1;#work around primary and assembly being two words - first three cols never used
+ my @arr = split(/\t/,$_);
+ my $i = 0;
foreach my $name (@arr){
$key_to_index{$name} = $i;
$i++;
@@ -194,7 +199,8 @@ SCAF: while(<TXT>){
}
}
else{
- my @arr = split;
+ my @arr = split(/\t/,$_);
+
my $alt_acc = $arr[$key_to_index{'alt_scaf_acc'}];
my $alt_name = $arr[$key_to_index{'alt_scaf_name'}];
--
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