Commit 954a549b authored by Pontus Larsson's avatar Pontus Larsson
Browse files

Fixed consequence typo

parent a2278460
......@@ -197,11 +197,12 @@ if (!defined($file)) {
# Get a TranscriptVariationAdaptor
my $tv_adaptor = $vdb->get_TranscriptVariationAdaptor() or throw("Could not get a TranscriptVariationAdaptor from " . $vdb->dbc->dbname());
my $stop_codons = qq{TGA/TAA/TAG};
my %allele_is_stop;
# For each variation_feature, check that the source, population and minor allele frequencies are 'dbSNP', 'CSHL-HapMap-*' and '>= $FREQUENCY_CUTOFF'
while (my ($transcript_stable_id,$variation_id,$variation_name,$allele_string,$consequence_string,$transcript_variation_id) = $sth->fetchrow_array()) {
my %allele_is_stop;
# Temp fix for getting stable_id from pre-58 variation database
#$stmt = qq{SELECT stable_id FROM transcript_stable_id WHERE transcript_id = $transcript_stable_id LIMIT 1};
#$transcript_stable_id = $cdb->dbc->db_handle->selectall_arrayref($stmt)->[0][0];
......@@ -267,8 +268,8 @@ if (!defined($file)) {
#print $str . "\n";
# Skip this allele if it does not cause the STOP_* event
next if ($n_alleles > 2 && $cons_type =~ m/GAIN/ && !$allele_is_stop{$allele});
next if ($n_alleles > 2 && $cons_type =~ m/LOSS/ && $allele_is_stop{$allele});
next if ($n_alleles > 2 && $cons_type =~ m/GAINED/ && !$allele_is_stop{$allele});
next if ($n_alleles > 2 && $cons_type =~ m/LOST/ && $allele_is_stop{$allele});
push(@null_transcripts,$str);
}
......
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