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Commit 9d319d6b authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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More reformatting of my old code.

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modules/Bio/EnsEMBL/Exon.pm
+ 136
− 147
View file @ 9d319d6b
......@@ -376,35 +376,33 @@ sub strand {
=cut
sub cdna_start {
my $self = shift;
my ($transcript) = @_;
if ( !defined $transcript
|| !ref $transcript
|| !$transcript->isa('Bio::EnsEMBL::Transcript') )
{
throw("Argument is not a transcript");
}
my $self = shift;
my ($transcript) = @_;
my $transcript_id = $transcript->dbID();
if ( !defined($transcript)
|| !ref($transcript)
|| !$transcript->isa('Bio::EnsEMBL::Transcript') )
{
throw("Argument is not a transcript");
}
if ( !exists $self->{'cdna_start'}->{$transcript_id} ) {
my @coords =
$transcript->genomic2cdna( $self->start(), $self->end(),
$self->strand() );
my $transcript_id = $transcript->dbID();
if ( @coords && !$coords[0]->isa('Bio::EnsEMBL::Mapper::Gap') )
{
$self->{'cdna_start'}->{$transcript_id} =
$coords[0]->start();
} elsif (@coords) {
throw("First part of exon maps into a gap");
} else {
throw("Can not map exon");
}
if ( !exists( $self->{'cdna_start'}->{$transcript_id} ) ) {
my @coords =
$transcript->genomic2cdna( $self->start(), $self->end(),
$self->strand() );
if ( @coords && !$coords[0]->isa('Bio::EnsEMBL::Mapper::Gap') ) {
$self->{'cdna_start'}->{$transcript_id} = $coords[0]->start();
} elsif (@coords) {
throw("First part of exon maps into a gap");
} else {
throw("Can not map exon");
}
}
return $self->{'cdna_start'}->{$transcript_id};
return $self->{'cdna_start'}->{$transcript_id};
} ## end sub cdna_start
=head2 cdna_end
......@@ -428,34 +426,33 @@ sub cdna_start {
=cut
sub cdna_end {
my $self = shift;
my ($transcript) = @_;
if ( !defined $transcript
|| !ref $transcript
|| !$transcript->isa('Bio::EnsEMBL::Transcript') )
{
throw("Argument is not a transcript");
}
my $self = shift;
my ($transcript) = @_;
if ( !defined($transcript)
|| !ref($transcript)
|| !$transcript->isa('Bio::EnsEMBL::Transcript') )
{
throw("Argument is not a transcript");
}
my $transcript_id = $transcript->dbID();
my $transcript_id = $transcript->dbID();
if ( !exists $self->{'cdna_end'}->{$transcript_id} ) {
my @coords =
$transcript->genomic2cdna( $self->start(), $self->end(),
$self->strand() );
if ( !exists( $self->{'cdna_end'}->{$transcript_id} ) ) {
my @coords =
$transcript->genomic2cdna( $self->start(), $self->end(),
$self->strand() );
if ( @coords && !$coords[-1]->isa('Bio::EnsEMBL::Mapper::Gap') )
{
$self->{'cdna_end'}->{$transcript_id} = $coords[-1]->end();
} elsif (@coords) {
throw("Last part of exon maps into gap");
} else {
throw("Can not map exon");
}
if ( @coords && !$coords[-1]->isa('Bio::EnsEMBL::Mapper::Gap') ) {
$self->{'cdna_end'}->{$transcript_id} = $coords[-1]->end();
} elsif (@coords) {
throw("Last part of exon maps into gap");
} else {
throw("Can not map exon");
}
}
return $self->{'cdna_end'}->{$transcript_id};
return $self->{'cdna_end'}->{$transcript_id};
} ## end sub cdna_end
=head2 cdna_coding_start
......@@ -478,60 +475,56 @@ sub cdna_end {
=cut
sub cdna_coding_start {
my $self = shift;
my ($transcript) = @_;
if ( !defined $transcript
|| !ref $transcript
|| !$transcript->isa('Bio::EnsEMBL::Transcript') )
{
throw("Argument is not a transcript");
}
my $self = shift;
my ($transcript) = @_;
my $transcript_id = $transcript->dbID();
if ( !defined($transcript)
|| !ref($transcript)
|| !$transcript->isa('Bio::EnsEMBL::Transcript') )
{
throw("Argument is not a transcript");
}
my $transcript_id = $transcript->dbID();
if ( !exists( $self->{'cdna_coding_start'}->{$transcript_id} ) ) {
my $transcript_coding_start = $transcript->cdna_coding_start();
if ( !defined($transcript_coding_start) ) {
# This is a non-coding transcript.
$self->{'cdna_coding_start'}->{$transcript_id} = undef;
$self->{'cdna_coding_end'}->{$transcript_id} = undef;
} else {
my $cdna_start = $self->cdna_start($transcript);
if ( $transcript_coding_start < $cdna_start ) {
# Coding region starts upstream of this exon...
if ( !exists $self->{'cdna_coding_start'}->{$transcript_id} ) {
my $transcript_coding_start = $transcript->cdna_coding_start();
if ( $transcript->cdna_coding_end() < $cdna_start ) {
# ... and also ends upstream of this exon.
$self->{'cdna_coding_start'}->{$transcript_id} = undef;
} else {
# ... and does not end upstream of this exon.
$self->{'cdna_coding_start'}->{$transcript_id} = $cdna_start;
}
} else {
# Coding region starts either within or downstream of this
# exon.
if ( !defined $transcript_coding_start ) {
# This is a non-coding transcript.
$self->{'cdna_coding_start'}->{$transcript_id} = undef;
$self->{'cdna_coding_end'}->{$transcript_id} = undef;
if ( $transcript_coding_start <= $self->cdna_end($transcript) )
{
# Coding region starts within this exon.
$self->{'cdna_coding_start'}->{$transcript_id} =
$transcript_coding_start;
} else {
my $cdna_start = $self->cdna_start($transcript);
if ( $transcript_coding_start < $cdna_start ) {
# Coding region starts upstream of this exon...
if ( $transcript->cdna_coding_end() < $cdna_start ) {
# ... and also ends upstream of this exon.
$self->{'cdna_coding_start'}->{$transcript_id} =
undef;
} else {
# ... and does not end upstream of this exon.
$self->{'cdna_coding_start'}->{$transcript_id} =
$cdna_start;
}
} else {
# Coding region starts either within or downstream of this
# exon.
if ( $transcript_coding_start <=
$self->cdna_end($transcript) )
{
# Coding region starts within this exon.
$self->{'cdna_coding_start'}->{$transcript_id} =
$transcript_coding_start;
} else {
# Coding region starts downstream of this exon.
$self->{'cdna_coding_start'}->{$transcript_id} =
undef;
}
}
} ## end else [ if ( !defined $transcript_coding_start)
} ## end if ( !exists $self->{'cdna_coding_start'...
return $self->{'cdna_coding_start'}->{$transcript_id};
# Coding region starts downstream of this exon.
$self->{'cdna_coding_start'}->{$transcript_id} = undef;
}
}
} ## end else [ if ( !defined($transcript_coding_start...
} ## end if ( !exists( $self->{...
return $self->{'cdna_coding_start'}->{$transcript_id};
} ## end sub cdna_coding_start
=head2 cdna_coding_end
......@@ -554,60 +547,56 @@ sub cdna_coding_start {
=cut
sub cdna_coding_end {
my $self = shift;
my ($transcript) = @_;
if ( !defined $transcript
|| !ref $transcript
|| !$transcript->isa('Bio::EnsEMBL::Transcript') )
{
throw("Argument is not a transcript");
}
my $self = shift;
my ($transcript) = @_;
if ( !defined($transcript)
|| !ref($transcript)
|| !$transcript->isa('Bio::EnsEMBL::Transcript') )
{
throw("Argument is not a transcript");
}
my $transcript_id = $transcript->dbID();
my $transcript_id = $transcript->dbID();
if ( !exists $self->{'cdna_coding_end'}->{$transcript_id} ) {
my $transcript_coding_end = $transcript->cdna_coding_end();
if ( !exists( $self->{'cdna_coding_end'}->{$transcript_id} ) ) {
my $transcript_coding_end = $transcript->cdna_coding_end();
if ( !defined $transcript_coding_end ) {
# This is a non-coding transcript.
$self->{'cdna_coding_start'}->{$transcript_id} = undef;
$self->{'cdna_coding_end'}->{$transcript_id} = undef;
if ( !defined($transcript_coding_end) ) {
# This is a non-coding transcript.
$self->{'cdna_coding_start'}->{$transcript_id} = undef;
$self->{'cdna_coding_end'}->{$transcript_id} = undef;
} else {
my $cdna_end = $self->cdna_end($transcript);
if ( $transcript_coding_end > $cdna_end ) {
# Coding region ends downstream of this exon...
if ( $transcript->cdna_coding_start() > $cdna_end ) {
# ... and also starts downstream of this exon.
$self->{'cdna_coding_end'}->{$transcript_id} = undef;
} else {
my $cdna_end = $self->cdna_end($transcript);
if ( $transcript_coding_end > $cdna_end ) {
# Coding region ends downstream of this exon...
if ( $transcript->cdna_coding_start() > $cdna_end ) {
# ... and also starts downstream of this exon.
$self->{'cdna_coding_end'}->{$transcript_id} =
undef;
} else {
# ... and does not start downstream of this exon.
$self->{'cdna_coding_end'}->{$transcript_id} =
$cdna_end;
}
} else {
# Coding region ends either within or upstream of this
# exon.
if ( $transcript_coding_end >=
$self->cdna_start($transcript) )
{
# Coding region ends within this exon.
$self->{'cdna_coding_end'}->{$transcript_id} =
$transcript_coding_end;
} else {
# Coding region ends upstream of this exon.
$self->{'cdna_coding_end'}->{$transcript_id} =
undef;
}
}
} ## end else [ if ( !defined $transcript_coding_end)
} ## end if ( !exists $self->{'cdna_coding_end'...
return $self->{'cdna_coding_end'}->{$transcript_id};
# ... and does not start downstream of this exon.
$self->{'cdna_coding_end'}->{$transcript_id} = $cdna_end;
}
} else {
# Coding region ends either within or upstream of this
# exon.
if ( $transcript_coding_end >= $self->cdna_start($transcript) )
{
# Coding region ends within this exon.
$self->{'cdna_coding_end'}->{$transcript_id} =
$transcript_coding_end;
} else {
# Coding region ends upstream of this exon.
$self->{'cdna_coding_end'}->{$transcript_id} = undef;
}
}
} ## end else [ if ( !defined($transcript_coding_end...
} ## end if ( !exists( $self->{...
return $self->{'cdna_coding_end'}->{$transcript_id};
} ## end sub cdna_coding_end
=head2 coding_region_start
......
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