Raw content of InterimExon
<![CDATA[use strict;
use warnings;
package InterimExon;
use Bio::EnsEMBL::Utils::Exception qw(info warning throw);
use StatMsg;
#
# errors which are fatal for exons
#
my @FATAL =
(StatMsg::DELETE | StatMsg::CDS | StatMsg::LONG,
StatMsg::INSERT | StatMsg::CDS | StatMsg::LONG,
StatMsg::DELETE | StatMsg::CDS | StatMsg::MEDIUM | StatMsg::FRAMESHIFT,
StatMsg::INSERT | StatMsg::CDS | StatMsg::MEDIUM | StatMsg::FRAMESHIFT,
StatMsg::STRAND_FLIP,
StatMsg::INVERT,
StatMsg::SCAFFOLD_SPAN,
StatMsg::CONFUSED);
sub new {
my $class = shift;
return bless {'StatMsgs' => [],
'fail' => 0}, $class;
}
#
# returns true if this exon has a 'fatal' error
#
sub is_fatal {
my $self = shift;
foreach my $msg (@{$self->get_all_StatMsgs}) {
foreach my $code (@FATAL) {
if(($msg->code() & $code) == $code) {
#info("Code is Fatal: ". StatMsg::code2str($msg->code()));
return 1;
}
}
#info("Code is NON fatal=". StatMsg::code2str($msg->code()));
}
return 0;
}
sub add_StatMsg {
my $self = shift;
my $statMsg = shift;
push @{$self->{'StatMsgs'}}, $statMsg;
}
sub get_all_StatMsgs {
my $self = shift;
return $self->{'StatMsgs'};
}
sub last_StatMsg {
my $self = shift;
my @msgs = @{$self->{'StatMsgs'}};
return undef if(!@msgs);
return $msgs[$#msgs];
}
sub flush_StatMsgs {
my $self = shift;
$self->{'StatMsgs'} = [];
}
sub stable_id {
my $self = shift;
$self->{'stable_id'} = shift if(@_);
return $self->{'stable_id'};
}
sub start {
my $self = shift;
$self->{'start'} = shift if(@_);
return $self->{'start'};
}
sub end {
my $self = shift;
$self->{'end'} = shift if(@_);
return $self->{'end'};
}
sub length {
my $self = shift;
return $self->end() - $self->start() + 1;
}
sub strand {
my $self = shift;
$self->{'strand'} = shift if(@_);
return $self->{'strand'};
}
sub seq_region {
my $self = shift;
$self->{'seq_region'} = shift if(@_);
return $self->{'seq_region'};
}
sub cdna_start {
my $self = shift;
$self->{'cdna_start'} = shift if(@_);
return $self->{'cdna_start'};
}
sub cdna_end {
my $self = shift;
$self->{'cdna_end'} = shift if(@_);
return $self->{'cdna_end'};
}
sub slice {
my $self = shift;
$self->{'slice'} = shift if(@_);
return $self->{'slice'};
}
sub start_phase {
my $self = shift;
$self->{'start_phase'} = shift if(@_);
return $self->{'start_phase'};
}
sub end_phase {
my $self = shift;
$self->{'end_phase'} = shift if(@_);
return $self->{'end_phase'};
}
sub fail {
my $self = shift;
if(@_) {
my $fail = shift;
#warning("Setting ".$self->stable_id." to failed.\n") if($fail);
$self->{'fail'} = $fail;
}
return $self->{'fail'};
}
#
# This fixes the start and end phases which can get messed up when the
# UTR and CDS move a bit. We maintain correct phase throughout the program
# but there are a couple of problems that may arise:
# * UTR at one end of an exon may be completely deleted so the start/end phase
# needs to change from -1 to 0.
# * CDS may shrink due to a deletion at 5prime or 3prime end of CDS. This
# that exons which had start or end phase to have a start phase of -1 now.
sub fix_phase {
my $exon = shift;
my $transcript = shift;
# do not deal with failed exons, we have no chimp coords for these anyway
# since they were completely lost.
return if($exon->fail());
if(!defined($transcript->cdna_coding_start)) {
throw("cdna coding start not defined!");
}
if(!defined($transcript->cdna_coding_end)) {
throw("cdna coding end not defined.");
}
if(!defined($exon->cdna_end())) {
throw("exons cdna coding end not defined.");
}
if(!defined($exon->cdna_start())) {
throw("exons cdna coding start not defined.");
}
if($exon->start_phase() == -1) {
if($transcript->cdna_coding_start() == $exon->cdna_start()) {
$exon->start_phase(0);
}
} else {
if($transcript->cdna_coding_start() > $exon->cdna_start()) {
$exon->start_phase(-1);
}
}
if($exon->end_phase() == -1) {
if($transcript->cdna_coding_end() == $exon->cdna_end()) {
# no utr left at end of this exon anymore
my $cds_len =
$transcript->cdna_coding_end - $transcript->cdna_coding_start + 1;
$exon->end_phase($cds_len % 3);
}
} else {
if($transcript->cdna_coding_end() < $exon->cdna_end) {
# exon end is now utr
$exon->end_phase(-1);
}
}
}
#
# Fixes exons phases of a newly split exon. The end_phase of the first exon
# and the start_phase of the second exon are set.
#
#
sub set_split_phases {
my $first_exon = shift;
my $second_exon = shift;
my $transcript = shift;
# need to set first exon end phase and second exon start phase
if($first_exon->cdna_end > $transcript->cdna_coding_end()) {
$first_exon->end_phase(-1);
$second_exon->start_phase(-1);
return;
}
if($first_exon->cdna_end() < $transcript->cdna_coding_start()) {
$first_exon->end_phase(-1);
# beginning of CDS could be right at start of second exon
if($second_exon->cdna_start() == $transcript->cdna_coding_start()) {
$second_exon->start_phase(0);
} else {
$second_exon->start_phase(-1);
}
return;
}
my $phase;
if($first_exon->cdna_start() < $transcript->cdna_coding_start()) {
# first exon is partially 5prime UTR
my $coding_len = $first_exon->cdna_end() - $transcript->cdna_coding_start();
$phase = $coding_len % 3;
} else {
# first exon should be all CDS
my $sphase;
# sometimes start phase may be -1 even though this is all CDS.
# this is because we have not fixed the start phase yet and it should
# be 0 due to deletion of the utr
if($first_exon->start_phase() == -1) {
$sphase = 0;
} else {
$sphase = $first_exon->start_phase();
}
$phase = ($first_exon->length() + $sphase) % 3;
}
$first_exon->end_phase($phase);
$second_exon->start_phase($phase);
return;
}
1;
]]>