Bio::EnsEMBL::Analysis::Runnable
BaseAbInitio
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Methods description
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::BaseAbInitio
Function : works out which phase to make the exons to get
a complete cds
Returntype: none
Exceptions: throws if it cant find a translation
for a transcript
Example : |
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::BaseAbInitio
Function : use the groups of exons to create prediction transcripts
Returntype: none
Exceptions: none
Example : |
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::BaseAbInitio
Arg [2] : string, group name
Arg [3] : Bio::EnsEMBL::PredictionExon
Function : stores exons in arrayrefs in a hash keyed on group names
Returntype: hashref
Exceptions: throws if passed an exon which isnt a
Bio::EnsEMBL::PredictionExon
Example : |
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::BaseAbInitio
Arg [2] : string, matrix file
Function : container for path to matrix file, when passed a filename it
will use the find_file method to check for its existance
Returntype: string
Exceptions:
Example : |
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::BaseAbInitio
Arg [2] : string, peptide sequence from genscan results
Function : container for the peptides sequences from genscan results
Returntype: arrayref
Exceptions:
Example : |
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::BaseAbInitio
Arg [2] : string, program name
Function : create and open a commandline for one
of the ab initio gene finding programs
Returntype: none
Exceptions: throws if the program in not executable or the system
command fails to execute
Example : |
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::Genscan
Arg [2] : number, start phase,
Arg [3] : arrayref of Bio::EnsEMBL::PredictionExons
Function : starting with the given phase sets of the phase of
each exon on the basis of the end phase of the last. This is done
after ordering them on the basis of there strand
Returntype: arrayref of
Exceptions:
Example : |
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::Genscan
Arg [2] : string, ensembl produced peptides
Arg [3] : string, genscan predicted peptide
Function : makes sure x's and length's of peps are the same
to allow fair comparison
Returntype: string, string
Exceptions:
Example : |
Methods code
sub calculate_phases
{ my ($self) = @_;
my @phases = (0, 1, 2);
my @output;
my $ff = $self->feature_factory;
my $peptides = $self->peptides;
TRANS:foreach my $trans(@{$self->output}){
my @exons = @{$trans->get_all_Exons};
foreach my $phase(@phases){
my @temp_exons = @{$self->set_phases($phase,\@ exons)};
my $new = $ff->create_prediction_transcript(\@temp_exons,
$self->query,
$self->analysis);
my $pep = $new->translate->seq;
my $peptide = $peptides->{$trans->seqname};
my ($ensembl, $genscan) = $self->subsitute_x_codes($pep,
$peptide);
$ensembl =~ s/^x//i;
$ensembl =~ s/x$//i;
$genscan =~ s/^x//i;
$genscan =~ s/x$//i;
if ($ensembl =~ /$genscan/){
push(@output, $new);
next TRANS;
}
}
throw("Failed to find translation for ".$trans." ".$exons[0]->seqname)
}
$self->clean_output;
$self->output(\@output);} | sub create_transcripts
{ my ($self) = @_;
my @transcripts;
my $ff = $self->feature_factory;
my %exon_groups = %{$self->exon_groups};
foreach my $group(keys(%exon_groups)){
my @exons = @{$exon_groups{$group}};
my $transcript = $ff->create_prediction_transcript(\@exons, $self->query,
$self->analysis);
$transcript->seqname($group);
push(@transcripts, $transcript);
}
$self->output(\@transcripts);} | sub exon_groups
{ my ($self, $group, $exon) = @_;
if(!$self->{'exon_groups'}){
$self->{'exon_groups'} = {};
}
if($group && $exon){
if(!$exon->isa('Bio::EnsEMBL::PredictionExon')){
throw("must be passed an exon object ".
"Bio::EnsEMBL::PredictionExon not an $exon ".
"BaseAbInitio:exon_groups");
}
if(!$self->{'exon_groups'}->{$group}){
$self->{'exon_groups'}->{$group} = [];
}
push(@{$self->{'exon_groups'}->{$group}}, $exon);
}
return $self->{'exon_groups'};
}
} | sub matrix
{ my ($self, $matrix) = @_;
if($matrix){
my $file = $self->find_file($matrix);
$self->{'matrix'} = $file;
}
return $self->{'matrix'};} | sub new
{ my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($matrix) = rearrange(['MATRIX'], @args);
$self->matrix($matrix);
return $self;
}
} | sub peptides
{ my ($self, $peptides) = @_;
if($peptides){
$self->{'peptides'} = $peptides;
}
return $self->{'peptides'};} | sub run_analysis
{ my ($self, $program) = @_;
if(!$program){
$program = $self->program;
}
throw($program." is not executable BaseAbInitio::run_analysis ")
unless($program && -x $program);
my $command = $program." ".$self->matrix." ".$self->queryfile." > ".
$self->resultsfile;
print "Running analysis ".$command."\n";
system($command) == 0 or throw("FAILED to run ".$command);} | sub set_phases
{ my ($self, $start_phase, $exons) = @_;
if(@$exons == 0){
throw("Can't set phases if have no exons ".$exons." ".@$exons);
}
if ($exons->[0]->strand == 1) {
@$exons = sort {$a->start <=> $b->start} @$exons;
} else {
@$exons = sort {$b->start <=> $a->start} @$exons;
}
foreach my $e(@$exons){
$e->phase($start_phase);
$start_phase = ($e->phase + $e->length)%3;
}
return $exons;} | sub subsitute_x_codes
{ my ($self, $ensembl_pep, $genscan_pep) = @_;
$genscan_pep =~ s/\*$//;
my $ens_len = length($ensembl_pep);
my $gen_len = length($genscan_pep);
if($ens_len == ($gen_len+1)){
chop($ensembl_pep);
}
if($gen_len == ($ens_len+1)){
chop($genscan_pep);
}
$ens_len = length($ensembl_pep);
$gen_len = length($genscan_pep);
my $x = 0;
while (($x = index($ensembl_pep, 'X', $x)) != -1) {
substr($genscan_pep, $x, 1) = 'X'
if length($genscan_pep) >= length($ensembl_pep);
$x++;
}
$x = 0;
while (($x = index($genscan_pep, 'X', $x)) != -1) {
substr($ensembl_pep, $x, 1) = 'X'
if length($ensembl_pep) >= length($genscan_pep);
$x++;
}
return $ensembl_pep, $genscan_pep;
}
1;} | General documentation
No general documentation available.