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package Bio::Tools::PSort::Module::SVMLoc;
use Bio::Tools::PSort::Constants qw(:all);
use Bio::Tools::PSort::Module::AnalysisI;
use Bio::Tools::PSort::Report::Result;
use Bio::Tools::PSort::SVMLoc;
use vars qw(@ISA);
use strict;
@ISA = qw(Bio::Tools::PSort::Module::AnalysisI);
my %LOCMAP = (Cytoplasmic => CYTOPLASM,
CytoplasmicMembrane => CYTOPLASMICMEMBRANE,
Periplasmic => PERIPLASMIC,
OuterMembrane => OUTERMEMBRANE,
Extracellular => EXTRACELLULAR,
Mitochondrial => MITOCHONDRIAL,
Nuclear => NUCLEAR,
Unknown => UNKNOWN,
Membrane => MEMBRANE,
Cellwall => CELLWALL,
Other => OTHER
);
my %LOCS = (Cytoplasmic => 0, CytoplasmicMembrane => 1, Periplasmic => 2,
OuterMembrane => 3, Extracellular => 4, Mitochondrial => 5,
Nuclear => 6, Other => 7,
Membrane => 8, Cellwall => 9, Unknown => 10 );
my %LOCSR = (0 => 'Cytoplasmic', 1 => 'CytoplasmicMembrane', 2 => 'Periplasmic',
3 => 'OuterMembrane', 4 => 'Extracellular', 5 => 'Mitochondrial',
6 => 'Nuclear', 7 => 'Other',
8 => 'Membrane', 9 => 'Cellwall', 10 => 'Unknown');
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
##receive the SVM_MODEL (based on training data) and the Frequent patterns file
my ($model, $patterns) = $self->_rearrange([qw(MODEL PATTERNS)], @args);
$self->{subloc} = new Bio::Tools::PSort::SVMLoc(Model => $model, FreqPatt => $patterns) ||
$self->throw("Couldn't create new Bio::Tools::PSort::SVMLoc object");
return $self;
}
sub run {
my ($self, $seq) = @_;
$self->throw("Not a Bio::Seq object")
if((! ref($seq)) && (! $seq->isa("Bio::Seq")));
$self-throw("No sequence in Bio::Seq object")
unless($seq->seq);
my $loc = $self->{subloc}->classify($seq->seq);
return new Bio::Tools::PSort::Report::Result(-details => [ ],
-score => 0,
-loc => $LOCSR{$loc});
}
1;
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