Commit 5c6628cc authored by Stephen Keenan's avatar Stephen Keenan
Browse files

making sure this is on the head!

parent 0a6cf7be
#!/usr/local/ensembl/bin/perl
#!/usr/local/bin/perl
# Dump variation information to an XML file for indexing by the EBI's search engine.
#
......@@ -64,21 +64,22 @@ my $dbHash = get_databases();
#warn Dumper $dbcHash;
foreach my $species ( sort keys %$dbHash ) {
my $conf = $dbHash->{$species};
foreach my $index (@indexes) {
# we don't dump compara anymore
next if $index =~/Family/;
my $function = "dump$index";
no strict "refs";
$species =~ s/_/ /g;
if ($index ne 'Family'){
if ($index eq 'Gene'){
&$function( ucfirst($species), $conf );
print $function,"\n";
} elsif ($index eq 'Family' && !$FAMILY_DUMPED) {
&dumpFamily($conf);
} #elsif ($index eq 'Family' && !$FAMILY_DUMPED) {
# &dumpFamily($conf);
}
#}
}
......@@ -152,18 +153,21 @@ sub get_databases {
my @dbnames =
map { $_->[0] } @{ $db->selectall_arrayref("show databases") };
$db->disconnect();
my $latest_release = 0;
my ( $db_species, $db_release, $db_type );
my $compara_hash;
for my $dbname (@dbnames) {
if ( ( $db_species, $db_type, $db_release ) =
$dbname =~ /^([a-z]+_[a-z]+)_([a-z]+)_(\d+)_\w+$/ )
{
next if ( $species ne 'ALL' ) && ( $db_species ne $species );
$latest_release = $db_release if ( $db_release > $latest_release );
$dbHash->{$db_species}->{$db_type}->{$db_release} = $dbname;
......@@ -177,6 +181,8 @@ sub get_databases {
}
map { $dbHash->{$_}->{'compara'} = $compara_hash } keys %$dbHash;
$release = $latest_release if ( $release eq 'LATEST' );
......@@ -662,7 +668,8 @@ sub geneLineXML {
)
);
$cross_references .= qq{</cross_references>};
$cross_references .= qq{
</cross_references>};
my $additional_fields .= qq{
<additional_fields>
......@@ -702,7 +709,8 @@ sub geneLineXML {
)
)
. qq{
</additional_fields>};
</additional_fields>
};
......
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