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Commit 24d38fdb authored by Magali Ruffier's avatar Magali Ruffier
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ENSCORESW-1127: TSL and gencode_basic tags added to gtf dumps as per gencode specifications

parent 8abe38aa
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......@@ -439,12 +439,20 @@ sub _print_attribs {
}
if($transcript && $transcript->isa('Bio::EnsEMBL::Transcript')) {
foreach my $tag (qw/cds_end_NF cds_start_NF mRNA_end_NF mRNA_start_NF/) {
foreach my $tag (qw/cds_end_NF cds_start_NF mRNA_end_NF mRNA_start_NF gencode_basic/) {
my $attributes = $transcript->get_all_Attributes($tag);
if(@{$attributes}) {
print $fh qq{ tag "${tag}";};
my $value = $tag;
$value = "basic" if $tag eq "gencode_basic";
print $fh qq{ tag "${value}";};
}
}
my $attributes = $transcript->get_all_Attributes("TSL");
if (@{$attributes}) {
my $value = $attributes->[0]->value;
$value =~ s/tsl//;
print $fh qq{ transcript_support_level "${value}";};
}
}
return;
......
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