Commit a9d4f478 authored by Julio Fernandez Banet's avatar Julio Fernandez Banet
Browse files

Added check for stop codons so transcripts with stops in the translation are ignored

parent c9ee626c
......@@ -73,6 +73,7 @@ SLICE:foreach my $slice(@$slices){
my $genes = $slice->get_all_Genes(undef, undef, 1);
my %canonical;
GENE:foreach my $gene(@$genes){
print "Updating gene: ",$gene->dbID,"\n";
my $transcripts = $gene->get_all_Transcripts;
if(@$transcripts == 1){
$canonical{$gene->dbID} = $transcripts->[0]->dbID;
......@@ -85,7 +86,9 @@ SLICE:foreach my $slice(@$slices){
foreach my $transcript(@$transcripts){
if($transcript->translation && ($gene->biotype ne 'processed_transcript')
&& ($gene->biotype ne 'pseudogene')){
push(@with_translation, $transcript)
unless($transcript->translation->seq =~ /\*/){
push(@with_translation, $transcript);
}
}else{
push(@no_translation, $transcript);
}
......
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