diff --git a/modules/Bio/EnsEMBL/Utils/SeqDumper.pm b/modules/Bio/EnsEMBL/Utils/SeqDumper.pm index 613b0e5b25394863711463dc613f3c45e51795a8..497f42ea408837c02863cbb5500e9d1167e7acc8 100644 --- a/modules/Bio/EnsEMBL/Utils/SeqDumper.pm +++ b/modules/Bio/EnsEMBL/Utils/SeqDumper.pm @@ -829,9 +829,9 @@ sub _dump_feature_table { my $codon_start = $self->transcript_to_codon_start($transcript); $self->write(@ff,'' , qq{/codon_start="${codon_start}"}) if $codon_start > 1; - my $codon_table = $self->_get_codon_table($slice); - if($codon_table > 1){ - $self->write(@ff,'' , '/transl_table='.$codon_table); + my $codon_table_id = $self->_get_codon_table_id($slice); + if($codon_table_id > 1){ + $self->write(@ff,'' , '/transl_table='.$codon_table_id); } $self->write(@ff,'' , '/gene="'.$gene->stable_id_version().'"'); $self->write(@ff,'' , '/protein_id="'.$translation->stable_id_version().'"'); @@ -1009,7 +1009,7 @@ sub transcript_to_codon_start { } -=head2 _get_codon_table +=head2 _get_codon_table_id Arg [1] : Bio::EnsEMBL::Slice slice Example : none @@ -1022,14 +1022,14 @@ sub transcript_to_codon_start { =cut -sub _get_codon_table{ +sub _get_codon_table_id{ my ($self, $slice) = @_; - my $codon_table = 1; + my $codon_table_id = 1; my $codon_table_attributes = $slice->get_all_Attributes("codon_table"); if (@{$codon_table_attributes}) { - $codon_table = $codon_table_attributes->[0]->value; + $codon_table_id = $codon_table_attributes->[0]->value; } - return $codon_table; + return $codon_table_id; } =head2 dump_fasta