Skip to content

Commit

Permalink
Added gencode_primary Transcript attribute and removed some tabs/code…
Browse files Browse the repository at this point in the history 
… align issues
  • Loading branch information
@sgiorgetti
sgiorgetti committed Apr 3, 2024
1 parent 7ebe5f6 commit 6731cef
Show file tree
Hide file tree
Showing 2 changed files with 125 additions and 140 deletions.
252 changes: 123 additions & 129 deletions modules/Bio/EnsEMBL/IO/Translator/Feature.pm
View file
Original file line number Diff line number Diff line change
Expand Up @@ -139,13 +139,13 @@ sub end {
# Start and end must be in ascending order for GXF. Circular genomes require the length of
# the circuit to be added on.
if( $object->seq_region_start() > $object->seq_region_end() ) {
if ($object->slice() && $object->slice()->is_circular() ) {
$end = $end + $object->seq_region_length;
}
# non-circular, but end still before start
else {
$end = $object->seq_region_start();
}
if ($object->slice() && $object->slice()->is_circular() ) {
$end = $end + $object->seq_region_length;
}
# non-circular, but end still before start
else {
$end = $object->seq_region_start();
}
}

return $end;
Expand All @@ -162,16 +162,16 @@ sub source {

my $source;
if (ref($object)->isa('Bio::EnsEMBL::Slice') ) {
$source = $object->source || $object->coord_system->version
$source = $object->source || $object->coord_system->version
}
elsif (ref($object)->isa('Bio::EnsEMBL::ExonTranscript') ||
ref($object)->isa('Bio::EnsEMBL::CDS') ||
ref($object)->isa('Bio::EnsEMBL::UTR') ) {
$source = $object->transcript()->source();
ref($object)->isa('Bio::EnsEMBL::CDS') ||
ref($object)->isa('Bio::EnsEMBL::UTR') ) {
$source = $object->transcript()->source();
}
elsif (ref($object)->isa('Bio::EnsEMBL::Feature') &&
defined($object->analysis) && $object->analysis->gff_source() ) {
$source = $object->analysis->gff_source();
defined($object->analysis) && $object->analysis->gff_source() ) {
$source = $object->analysis->gff_source();
}

return $source;
Expand Down Expand Up @@ -226,9 +226,9 @@ sub strand {
my $object = shift;

if( ref($object)->isa('Bio::EnsEMBL::Slice') ) {
return '.';
return '.';
} else {
return ( $self->{_strand_conversion}->{ $object->{strand} } ? $self->{_strand_conversion}->{ $object->strand() } : $object->strand() );
return ( $self->{_strand_conversion}->{ $object->{strand} } ? $self->{_strand_conversion}->{ $object->strand() } : $object->strand() );
}
}

Expand All @@ -250,9 +250,9 @@ sub phase {
my $object = shift;

if (ref($object)->isa('Bio::EnsEMBL::CDS') ) {
return $object->phase();
return $object->phase();
} else {
return '.';
return '.';
}
}

Expand Down Expand Up @@ -281,63 +281,60 @@ sub attributes {
delete $summary{'source'};
delete $summary{'type'};

# my @attrs;
my %attrs;
my @ordered_keys = grep { exists $summary{$_} } qw(id Name Alias Parent Target Gap Derives_from Note Dbxref Ontology_term Is_circular);
my @ordered_values = @summary{@ordered_keys};
while (my $key = shift @ordered_keys) {
my $value = shift @ordered_values;
delete $summary{$key};
if ($value && $value ne '') {
if ($key =~ /id/) {
$key = uc($key);
if ($object->isa('Bio::EnsEMBL::Transcript')) {
$value = 'transcript:' . $value;
} elsif ($object->isa('Bio::EnsEMBL::Gene')) {
$value = 'gene:' . $value;
} elsif ($object->isa('Bio::EnsEMBL::Exon')) {
$key = 'Name';
} elsif ($object->isa('Bio::EnsEMBL::CDS')) {
my $trans_spliced = $object->transcript->get_all_Attributes('trans_spliced');
if (scalar(@$trans_spliced)) {
$value = $self->so_term($object) . ':' . join('_', $value, $object->seq_region_name, $object->seq_region_strand);
} else {
$value = $self->so_term($object) . ':' . $value;
}
} else {
$value = $self->so_term($object) . ':' . $value;
}
}

if ($key eq 'Parent') {
if ($object->isa('Bio::EnsEMBL::Transcript')) {
$value = 'gene:' . $value;
} elsif ($object->isa('Bio::EnsEMBL::Exon') || $object->isa('Bio::EnsEMBL::UTR') || $object->isa('Bio::EnsEMBL::CDS')) {
$value = 'transcript:' . $value;
}
}

if (ref $value eq "ARRAY" && scalar(@{$value}) > 0) {
$attrs{$key} = join (',',map { uri_escape($_,'\t\n\r;=%&,') } grep { defined $_ } @{$value});
} else {
$attrs{$key} = uri_escape($value,'\t\n\r;=%&,');
}
}
my $value = shift @ordered_values;
delete $summary{$key};
if ($value && $value ne '') {
if ($key =~ /id/) {
$key = uc($key);
if ($object->isa('Bio::EnsEMBL::Transcript')) {
$value = 'transcript:' . $value;
} elsif ($object->isa('Bio::EnsEMBL::Gene')) {
$value = 'gene:' . $value;
} elsif ($object->isa('Bio::EnsEMBL::Exon')) {
$key = 'Name';
} elsif ($object->isa('Bio::EnsEMBL::CDS')) {
my $trans_spliced = $object->transcript->get_all_Attributes('trans_spliced');
if (scalar(@$trans_spliced)) {
$value = $self->so_term($object) . ':' . join('_', $value, $object->seq_region_name, $object->seq_region_strand);
} else {
$value = $self->so_term($object) . ':' . $value;
}
} else {
$value = $self->so_term($object) . ':' . $value;
}
}
if ($key eq 'Parent') {
if ($object->isa('Bio::EnsEMBL::Transcript')) {
$value = 'gene:' . $value;
} elsif ($object->isa('Bio::EnsEMBL::Exon') || $object->isa('Bio::EnsEMBL::UTR') || $object->isa('Bio::EnsEMBL::CDS')) {
$value = 'transcript:' . $value;
}
}
if (ref $value eq "ARRAY" && scalar(@{$value}) > 0) {
$attrs{$key} = join (',',map { uri_escape($_,'\t\n\r;=%&,') } grep { defined $_ } @{$value});
} else {
$attrs{$key} = uri_escape($value,'\t\n\r;=%&,');
}
}
}

# Catch the remaining keys, containing whatever else the Feature provided
my @keys = sort keys %summary;
while(my $attribute = shift @keys) {

if (ref $summary{$attribute} eq "ARRAY") {
if (scalar(@{$summary{$attribute}}) > 0) {
$attrs{$attribute} = join (',',map { uri_escape($_,'\t\n\r;=%&,') } grep { defined $_ } @{$summary{$attribute}});
}
} else {
if (defined $summary{$attribute}) {
$attrs{$attribute} = uri_escape($summary{$attribute},'\t\n\r;=%&,');
}
}
if (ref $summary{$attribute} eq "ARRAY") {
if (scalar(@{$summary{$attribute}}) > 0) {
$attrs{$attribute} = join (',',map { uri_escape($_,'\t\n\r;=%&,') } grep { defined $_ } @{$summary{$attribute}});
}
} else {
if (defined $summary{$attribute}) {
$attrs{$attribute} = uri_escape($summary{$attribute},'\t\n\r;=%&,');
}
}
}

return \%attrs;
Expand All @@ -363,53 +360,50 @@ sub gtf_attributes {

my $gene;
if ( $object->isa('Bio::EnsEMBL::Gene') ) {
# For Genes only
$gene = $object;
# For Genes only
$gene = $object;
} else {
# For anything but a Gene
my $transcript;

if ( $object->isa('Bio::EnsEMBL::Transcript') ) {
$transcript = $object;

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}) {
my $value = $tag;
$value = "basic" if $tag eq "gencode_basic";
$self->add_attr($attrs, 'tag', $value);
}
}

} else {
if ( $object->isa('Bio::EnsEMBL::ExonTranscript') ) {

}

$transcript = $object->transcript();
}

# CCDS records
my $ccds_entries = $transcript->get_all_DBEntries('CCDS');
if(@{$ccds_entries}) {
$self->add_attr($attrs, 'tag', 'CCDS');
foreach my $ccds (sort { $a->primary_id() cmp $b->primary_id() } @{$ccds_entries}) {
my $primary_ccds_id = $ccds->primary_id();
$self->add_attr($attrs, 'ccds_id', $primary_ccds_id);
}
}

$attrs->{transcript_id} = $transcript->display_id;
$attrs->{transcript_version} = $transcript->version;
$attrs->{transcript_name} = $transcript->external_name if $transcript->external_name;
$attrs->{transcript_source} = $transcript->source;
$attrs->{transcript_biotype} = $transcript->biotype();
$attrs->{havana_transcript} = $transcript->havana_transcript()->display_id if $transcript->havana_transcript();
$attrs->{havana_version} = $transcript->havana_transcript()->version if $transcript->havana_transcript();
$self->add_attr($attrs, 'tag', 'basic') if $transcript->gencode_basic();
$attrs->{transcript_support_level} = $transcript->tsl() if $transcript->tsl();

$gene = $object->get_Gene();
# For anything but a Gene
my $transcript;

if ( $object->isa('Bio::EnsEMBL::Transcript') ) {
$transcript = $object;

foreach my $tag (qw/cds_end_NF cds_start_NF mRNA_end_NF mRNA_start_NF gencode_basic gencode_primary MANE_Select is_canonical MANE_Plus_Clinical/) {
my $attributes = $transcript->get_all_Attributes($tag);
if(@{$attributes}) {
my $value = $tag;
$value = "basic" if $tag eq "gencode_basic";
$value = "primary" if $tag eq "gencode_primary";
$value = "Ensembl_canonical" if $tag eq "is_canonical";
$self->add_attr($attrs, 'tag', $value);
}
}

} else {
$transcript = $object->transcript();
}

# CCDS records
my $ccds_entries = $transcript->get_all_DBEntries('CCDS');
if(@{$ccds_entries}) {
$self->add_attr($attrs, 'tag', 'CCDS');
foreach my $ccds (sort { $a->primary_id() cmp $b->primary_id() } @{$ccds_entries}) {
my $primary_ccds_id = $ccds->primary_id();
$self->add_attr($attrs, 'ccds_id', $primary_ccds_id);
}
}

$attrs->{transcript_id} = $transcript->display_id;
$attrs->{transcript_version} = $transcript->version;
$attrs->{transcript_name} = $transcript->external_name if $transcript->external_name;
$attrs->{transcript_source} = $transcript->source;
$attrs->{transcript_biotype} = $transcript->biotype();
$attrs->{havana_transcript} = $transcript->havana_transcript()->display_id if $transcript->havana_transcript();
$attrs->{havana_version} = $transcript->havana_transcript()->version if $transcript->havana_transcript();
$attrs->{transcript_support_level} = $transcript->tsl() if $transcript->tsl();

$gene = $object->get_Gene();
}

$attrs->{gene_id} = $gene->display_id;
Expand Down Expand Up @@ -453,14 +447,14 @@ sub add_attr {
my $value = shift;

if (defined($attrs->{$attr})) {
if( ref($attrs->{$attr}) eq 'ARRAY' ) {
my $duplicate = grep {$_ eq $value} @{$attrs->{$attr}};
push @{$attrs->{$attr}}, $value unless $duplicate;
} else {
$attrs->{$attr} = [ $attrs->{$attr}, $value ] unless ($attrs->{$attr} eq $value);
}
if( ref($attrs->{$attr}) eq 'ARRAY' ) {
my $duplicate = grep {$_ eq $value} @{$attrs->{$attr}};
push @{$attrs->{$attr}}, $value unless $duplicate;
} else {
$attrs->{$attr} = [ $attrs->{$attr}, $value ] unless ($attrs->{$attr} eq $value);
}
} else {
$attrs->{$attr} = $value;
$attrs->{$attr} = $value;
}

}
Expand Down Expand Up @@ -502,35 +496,35 @@ sub so_term {

=head2 _default_score
Description: Return the default source type for a feature
Returntype : String
Description: Return the default source type for a feature
Returntype : String
=cut

sub _default_source {
my ($self) = @_;
return $self->{default_source};
my ($self) = @_;
return $self->{default_source};
}


##### SHOULD THIS BE IN THE TRANSLATOR? SURELY IT IS A FORMAT THING?

=head2 strand_conversion
Description: Sets hash giving the strand conversion for this
output type
Args[1] : Reference to hash
Description: Sets hash giving the strand conversion for this
output type
Args[1] : Reference to hash
=cut

sub strand_conversion {
my $self = shift;
my $self = shift;

if( @_ ) {
$self->{_strand_conversion} = shift;
}
if( @_ ) {
$self->{_strand_conversion} = shift;
}

return $self->{_strand_conversion};
return $self->{_strand_conversion};
}

1;
13 changes: 2 additions & 11 deletions modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
View file
Original file line number Diff line number Diff line change
Expand Up @@ -487,25 +487,16 @@ 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 gencode_basic is_canonical gencode_primary/) {
foreach my $tag (qw/cds_end_NF cds_start_NF mRNA_end_NF mRNA_start_NF gencode_basic gencode_primary MANE_Select is_canonical MANE_Plus_Clinical/) {
my $attributes = $transcript->get_all_Attributes($tag);
if(@{$attributes}) {
my $value = $tag;
$value = "basic" if $tag eq "gencode_basic";
$value = "Ensembl_canonical" if $tag eq "is_canonical";
$value = "GENCODE Primary" if $tag eq "gencode_primary";
$value = "Ensembl_canonical" if $tag eq "is_canonical";
print $fh qq{ tag "${value}";};
}
}

# A transcript can have different types of MANE-related attributes (MANE_Select, MANE_Plus_Clinical)
# We depend on the Bio::EnsEMBL::MANE object to get the specific type
my $mane = $transcript->mane_transcript();
if ($mane) {
my $mane_type = $mane->type();
print $fh qq{ tag "${mane_type}";} if ($mane_type);
}

my $attributes = $transcript->get_all_Attributes("TSL");
if (@{$attributes}) {
my $value = $attributes->[0]->value;
Expand Down

0 comments on commit 6731cef

Please sign in to comment.