Commit 4cdf9988 authored by Shamika Mohanan's avatar Shamika Mohanan

Code to deal with loading intronic regions. Error message added to convey that...

Code to deal with loading intronic regions. Error message added to convey that a larger set of clones should be loaded.
parent c08c7331
......@@ -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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