Commit 32e8c5b6 authored by Amonida Zadissa's avatar Amonida Zadissa
Browse files

* 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.
parent faa6a31e
...@@ -65,14 +65,19 @@ $sth->finish; ...@@ -65,14 +65,19 @@ $sth->finish;
$sth = $dba->dbc->prepare("select max(assembly_exception_id) from assembly_exception") $sth = $dba->dbc->prepare("select max(assembly_exception_id) from assembly_exception")
|| die "Could not get max assembly_exception_id"; || 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; my $max_assembly_exception_id;
$sth->bind_columns(\$max_assembly_exception_id) || die "problem binding"; $sth->bind_columns(\$max_assembly_exception_id) || die "problem binding";
$sth->fetch() || die "problem fetching"; $sth->fetch() || die "problem fetching";
$sth->finish; $sth->finish;
print "starting new seq_region at seq_region_id of $max_seq_region_id\n"; 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_seq_region_id++;
$max_assembly_exception_id++; $max_assembly_exception_id++;
...@@ -178,8 +183,8 @@ while (<TYPE>) { ...@@ -178,8 +183,8 @@ while (<TYPE>) {
SCAF: while(<TXT>){ SCAF: while(<TXT>){
if(/^#/){ if(/^#/){
chomp; chomp;
my @arr = split; my @arr = split(/\t/,$_);
my $i = 1;#work around primary and assembly being two words - first three cols never used my $i = 0;
foreach my $name (@arr){ foreach my $name (@arr){
$key_to_index{$name} = $i; $key_to_index{$name} = $i;
$i++; $i++;
...@@ -194,7 +199,8 @@ SCAF: while(<TXT>){ ...@@ -194,7 +199,8 @@ SCAF: while(<TXT>){
} }
} }
else{ else{
my @arr = split; my @arr = split(/\t/,$_);
my $alt_acc = $arr[$key_to_index{'alt_scaf_acc'}]; my $alt_acc = $arr[$key_to_index{'alt_scaf_acc'}];
my $alt_name = $arr[$key_to_index{'alt_scaf_name'}]; my $alt_name = $arr[$key_to_index{'alt_scaf_name'}];
......
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