diff --git a/modules/Bio/EnsEMBL/CircularSlice.pm b/modules/Bio/EnsEMBL/CircularSlice.pm
index df6091da897cdadec8f4a7a94e1490af7e3c5a01..812e86a731202a32634fc9a19c2af1a1aee393a3 100644
--- a/modules/Bio/EnsEMBL/CircularSlice.pm
+++ b/modules/Bio/EnsEMBL/CircularSlice.pm
@@ -798,69 +798,6 @@ sub expand {
} ## end sub expand
-=head2 get_all_Attributes
-
- Arg [1] : optional string $attrib_code
- The code of the attribute type to retrieve values for.
- Example : ($htg_phase) = @{$slice->get_all_Attributes('htg_phase')};
- @slice_attributes = @{$slice->get_all_Attributes()};
- Description: Gets a list of Attributes of this slice''s seq_region.
- Optionally just get Attrubutes for given code.
- Returntype : listref Bio::EnsEMBL::Attribute
- Exceptions : warning if slice does not have attached adaptor
- Caller : general
- Status : Stable
-
-=cut
-
-sub get_all_Attributes {
- my $self = shift;
- my $attrib_code = shift;
-
- my $result;
- my @results;
-
- if ( !$self->adaptor() ) {
- warning('Cannot get attributes without an adaptor.');
- return [];
- }
-
- my $attribute_adaptor = $self->adaptor->db->get_AttributeAdaptor();
-
-## circular BOF
- my ($sl1, $sl2) = $self->_split;
- my $pta_ref = [];
-
- if ( defined $attrib_code ) {
- my @res1 =
- grep { uc( $_->code() ) eq uc($attrib_code) }
- @{ $attribute_adaptor->fetch_all_by_Slice($sl1) };
- my @res2 =
- grep { uc( $_->code() ) eq uc($attrib_code) }
- @{ $attribute_adaptor->fetch_all_by_Slice($sl2) };
- my @res;
- push @res, @res1, @res2;
- $result = \@res;
- } else {
- my @res1 = @{ $attribute_adaptor->fetch_all_by_Slice($sl1) };
- my @res2 = @{ $attribute_adaptor->fetch_all_by_Slice($sl2) };
- my @res;
- push @res, @res1, @res2;
- $result = \@res;
- }
-
-## circular EOF
-
- # if( defined $attrib_code ) {
- # @results = grep { uc($_->code()) eq uc($attrib_code) }
- # @{$attribute_adaptor->fetch_all_by_Slice( $self )};
- # $result = \@results;
- # } else {
- # $result = $attribute_adaptor->fetch_all_by_Slice( $self );
- # }
-
- return $result;
-} ## end sub get_all_Attributes
=head2 get_all_PredictionTranscripts
@@ -1140,174 +1077,6 @@ sub get_all_genotyped_VariationFeatures {
}
-=head2 get_all_Genes
-
- Arg [1] : (optional) string $logic_name
- The name of the analysis used to generate the genes to retrieve
- Arg [2] : (optional) string $dbtype
- The dbtype of genes to obtain. This assumes that the db has
- been added to the DBAdaptor under this name (using the
- DBConnection::add_db_adaptor method).
- Arg [3] : (optional) boolean $load_transcripts
- If set to true, transcripts will be loaded immediately rather
- than being lazy-loaded on request. This will result in a
- significant speed up if the Transcripts and Exons are going to
- be used (but a slow down if they are not).
- Arg [4] : (optional) string $source
- The source of the genes to retrieve.
- Arg [5] : (optional) string $biotype
- The biotype of the genes to retrieve.
- Example : @genes = @{$slice->get_all_Genes};
- Description: Retrieves all genes that overlap this slice.
- Returntype : listref of Bio::EnsEMBL::Genes
- Exceptions : none
- Caller : none
- Status : Stable
-
-=cut
-
-sub get_all_Genes {
- my ( $self, $logic_name, $dbtype, $load_transcripts, $source,
- $biotype )
- = @_;
-
- if ( !$self->adaptor() ) {
- warning('Cannot get Genes without attached adaptor');
- return [];
- }
-
- my $ga;
- if ($dbtype) {
- my $db = $reg->get_db( $self->adaptor()->db(), $dbtype );
- if ( defined($db) ) {
- $ga = $reg->get_adaptor( $db->species(), $db->group(), "Gene" );
- } else {
- $ga = $reg->get_adaptor( $self->adaptor()->db()->species(),
- $dbtype, "Gene" );
- }
- if ( !defined $ga ) {
- warning("$dbtype genes not available");
- return [];
- }
- } else {
- $ga = $self->adaptor->db->get_GeneAdaptor();
- }
-
-## circular BOF
- my ($sl1, $sl2) = $self->_split;
- my ( @arr, @arr1, @arr2 );
- @arr1 = @{
- $ga->fetch_all_by_Slice( $sl1, $logic_name, $load_transcripts,
- $source, $biotype ) };
- @arr2 = @{
- $ga->fetch_all_by_Slice( $sl2, $logic_name, $load_transcripts,
- $source, $biotype ) };
- push @arr, @arr1, @arr2;
- return \@arr;
-
- ## circular EOF
-
-} ## end sub get_all_Genes
-
-
-=head2 get_all_Transcripts
-
- Arg [1] : (optional) boolean $load_exons
- If set to true exons will not be lazy-loaded but will instead
- be loaded right away. This is faster if the exons are
- actually going to be used right away.
- Arg [2] : (optional) string $logic_name
- the logic name of the type of features to obtain
- Arg [3] : (optional) string $db_type
- Example : @transcripts = @{$slice->get_all_Transcripts)_};
- Description: Gets all transcripts which overlap this slice. If you want to
- specify a particular analysis or type, then you are better off
- using get_all_Genes or get_all_Genes_by_type and iterating
- through the transcripts of each gene.
- Returntype : reference to a list of Bio::EnsEMBL::Transcripts
- Exceptions : none
- Caller : general
- Status : Stable
-
-=cut
-
-sub get_all_Transcripts {
- my $self = shift;
- my $load_exons = shift;
- my $logic_name = shift;
- my $dbtype = shift;
- if ( !$self->adaptor() ) {
- warning('Cannot get Transcripts without attached adaptor');
- return [];
- }
-
- my $ta;
- if ($dbtype) {
- my $db = $reg->get_db( $self->adaptor()->db(), $dbtype );
- if ( defined($db) ) {
- $ta =
- $reg->get_adaptor( $db->species(), $db->group(), "Transcript" );
- } else {
- $ta = $reg->get_adaptor( $self->adaptor()->db()->species(),
- $dbtype, "Transcript" );
- }
- if ( !defined $ta ) {
- warning("$dbtype genes not available");
- return [];
- }
- } else {
- $ta = $self->adaptor->db->get_TranscriptAdaptor();
- }
-
-## circular BOF
- my ($sl1, $sl2) = $self->_split;
- my ( @arr, @arr1, @arr2 );
- @arr1 =
- @{ $ta->fetch_all_by_Slice( $sl1, $load_exons, $logic_name ) };
- @arr2 =
- @{ $ta->fetch_all_by_Slice( $sl2, $load_exons, $logic_name ) };
- push @arr, @arr1, @arr2;
- return \@arr;
-## circular EOF
-
-} ## end sub get_all_Transcripts
-
-=head2 get_all_Exons
-
- Arg [1] : none
- Example : @exons = @{$slice->get_all_Exons};
- Description: Gets all exons which overlap this slice. Note that these exons
- will not be associated with any transcripts, so this may not
- be terribly useful.
- Returntype : reference to a list of Bio::EnsEMBL::Exons
- Exceptions : none
- Caller : general
- Status : Stable
-
-=cut
-
-sub get_all_Exons {
- my $self = shift;
-
- if ( !$self->adaptor() ) {
- warning('Cannot get Exons without attached adaptor');
- return [];
- }
-
- ## circular BOF
- my ($sl1, $sl2) = $self->_split;
- my ( @arr, @arr1, @arr2 );
- @arr1 =
- @{ $sl1->adaptor->db->get_ExonAdaptor->fetch_all_by_Slice($sl1) };
- @arr2 =
- @{ $sl2->adaptor->db->get_ExonAdaptor->fetch_all_by_Slice($sl2) };
- push @arr, @arr1, @arr2;
- return \@arr;
- ## circular EOF
-
- #rturn $self->adaptor->db->get_ExonAdaptor->fetch_all_by_Slice($self);
-} ## end sub get_all_Exons
-
=head2 get_all_QtlFeatures
Args : none
diff --git a/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm b/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
index a450ff773b8a2fc7da6e16e37b00723f1b6819bb..0bddbe103f78ba2c51bcc7938b6946ee38f97277 100644
--- a/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
+++ b/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
@@ -68,12 +68,6 @@ sub print_feature {
my @startcs = $self->_make_start_codon_features($transcript);
my @endcs = $self->_make_stop_codon_features($transcript);
my ($hasstart, $hasend) = $self->_check_start_and_stop($transcript);
- #
- # production does not use this option
- #
- # if (!$include_codons) {
- # $hasstart = $hasend = 0;
- # }
# TODO: ask Andy if this is safe
my $dbname = $transcript->adaptor()->dbc()->dbname();
@@ -392,8 +386,7 @@ sub _check_start_and_stop {
return (0,0) unless defined $trans->translation;
- my $tln = $trans->translation;
- my $cds_seq = uc($trans->translateable_seq);
+ my $cds_seq = uc($trans->translateable_seq);
my $startseq = substr($cds_seq, 0, 3);
my $endseq = substr($cds_seq, -3);
@@ -401,7 +394,7 @@ sub _check_start_and_stop {
my $has_start = 1;
my $has_end = 1;
- # reimplemented because verterbrate specific
+ # reimplemented since there are alternatively valid codon tables
$has_start = 0 if ($startseq ne "ATG");
$has_end = 0 if ($endseq ne "TAG" && $endseq ne "TGA" && $endseq ne "TAA");