Unverified Commit b7cca175 authored by s-mm's avatar s-mm Committed by GitHub

Merge pull request #104 from Ensembl/bugfix/array_error

Bugfix/array error
parents c3d99593 b51fe8e9
......@@ -49,6 +49,7 @@ use Bio::Otter::Lace::ProcessGFF;
use Bio::Otter::Source::Filter;
use Bio::Otter::Utils::Config::Ini qw( config_ini_format );
use XML::Simple;
use Hum::Ace::Assembly;
use Hum::Ace::MethodCollection;
use Hum::ZMapStyleCollection;
......@@ -255,8 +256,27 @@ sub empty_acefile_list {
sub init_AceDatabase {
my ($self) = @_;
my ($locus_key, $transcript_key, $exon_hash);
my $xml_string = $self->Client->get_region_xml($self->slice);
my $xml_data = XMLin($xml_string);
foreach $locus_key(keys %{$xml_data->{sequence_set}->{locus}}) {
if (exists($xml_data->{sequence_set}->{locus}->{$locus_key}->{transcript}->{exon_set})) {
$exon_hash = $xml_data->{sequence_set}->{locus}->{$locus_key}->{transcript}->{exon_set};
if(!%$exon_hash) {
$self->logger->logdie("Cannot load exons for this region. Please reload a larger set of clones. If the issue persists, please report it on JIRA.'")
}
}
else {
foreach $transcript_key(keys %{$xml_data->{sequence_set}->{locus}->{$locus_key}{transcript}}) {
if (exists($xml_data->{sequence_set}->{locus}->{$locus_key}->{transcript}->{$transcript_key}->{exon_set})) {
$exon_hash = $xml_data->{sequence_set}->{locus}->{$locus_key}->{transcript}->{$transcript_key}->{exon_set};
if(!%$exon_hash) {
$self->logger->logdie("Cannot load exons for this region. Please reload a larger set of clones. If the issue persists, please report it on JIRA.'")
}
}
}
}
}
$self->write_file('01_before.xml', $xml_string);
my $parser = Bio::Vega::Transform::XMLToRegion->new;
......
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