diff --git a/modules/Bio/EnsEMBL/Utils/SeqDumper.pm b/modules/Bio/EnsEMBL/Utils/SeqDumper.pm index 72ea110dff754b08a39514d6ce55dc96569913f1..348d6c703d45c900ccf808730ce67beb01e6c86f 100644 --- a/modules/Bio/EnsEMBL/Utils/SeqDumper.pm +++ b/modules/Bio/EnsEMBL/Utils/SeqDumper.pm @@ -426,10 +426,10 @@ sub dump_embl { $self->write($FH, $EMBL_HEADER, 'DT', $self->_date_string); $self->print( $FH, "XX\n" ); - my $species = $slice->adaptor->db->get_MetaContainer->get_Species(); - + my $meta_container = $slice->adaptor()->db()->get_MetaContainer(); + #Description - $self->write($FH, $EMBL_HEADER, 'DE', $species->binomial . + $self->write($FH, $EMBL_HEADER, 'DE', $meta_container->get_scientific_name() . " $name_str $start..$end annotated by Ensembl"); $self->print( $FH, "XX\n" ); @@ -438,17 +438,16 @@ sub dump_embl { $self->print( $FH, "XX\n" ); #Species - my $species_name = $species->binomial(); - if(my $cn = $species->common_name()) { + my $species_name = $meta_container->get_scientific_name(); + if(my $cn = $meta_container->get_common_name()) { $species_name .= " ($cn)"; } $self->write($FH, $EMBL_HEADER, 'OS', $species_name); #Classification - my @cls = $species->classification; - shift @cls; #shift off species name - $self->write($FH, $EMBL_HEADER, 'OC', join('; ', reverse(@cls)) . '.'); + my $cls = $meta_container->get_classification(); + $self->write($FH, $EMBL_HEADER, 'OC', join('; ', reverse(@{$cls})) . '.'); $self->print( $FH, "XX\n" ); #References (we are not dumping refereneces) @@ -582,8 +581,7 @@ sub dump_genbank { my $date = $self->_date_string; - my $species = $slice->adaptor->db->get_MetaContainer->get_Species; - + my $meta_container = $slice->adaptor()->db()->get_MetaContainer(); #LOCUS my $tag = 'LOCUS'; @@ -592,7 +590,7 @@ sub dump_genbank { #DEFINITION $tag = "DEFINITION"; - $value = $species->binomial . + $value = $meta_container->get_scientific_name() . " $name_str $start..$end reannotated via EnsEMBL"; $self->write($FH, $GENBANK_HEADER, $tag, $value); @@ -606,12 +604,12 @@ sub dump_genbank { $self->write($FH, $GENBANK_HEADER, 'KEYWORDS', '.'); # SOURCE - $self->write($FH, $GENBANK_HEADER, 'SOURCE', $species->common_name()); + $self->write($FH, $GENBANK_HEADER, 'SOURCE', $meta_container->get_common_name()); #organism - my @cls = $species->classification(); + my @cls = $meta_container->get_classification(); shift @cls; - $self->write($FH, $GENBANK_SUBHEADER, 'ORGANISM', $species->binomial); + $self->write($FH, $GENBANK_SUBHEADER, 'ORGANISM', $meta_container->get_scientific_name()); $self->write($FH, $GENBANK_SUBHEADER, '', join('; ', reverse @cls) . "."); #refereneces @@ -681,16 +679,15 @@ sub _dump_feature_table { my $lite = $slice->adaptor->db->remove_db_adaptor('lite'); my $meta = $slice->adaptor->db->get_MetaContainer; - my $species = $meta->get_Species; #lump file handle and format string together for simpler method calls my @ff = ($FH, $FORMAT); my $value; #source - my $classification = join(', ', $species->classification); + my $classification = join(', ', $meta->get_classification()); $self->write(@ff,'source', "1.." . $slice->length()); - $self->write(@ff,'' , '/organism="'.$species->binomial . '"'); + $self->write(@ff,'' , '/organism="'.$meta->get_scientific_name(). '"'); $self->write(@ff,'' , '/db_xref="taxon:'.$meta->get_taxonomy_id().'"'); #