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package Bio::Tools::PSort::Module::SVMLocApache;
use Bio::Tools::PSort::Constants qw(:all);
use Bio::Tools::PSort::Module::AnalysisI;
use Bio::Tools::PSort::Report::Result;
use LWP;
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 = $class->SUPER::new(@args);
##receive the SVM_MODEL (based on training data) and the Frequent patterns file
my ($url, $module) = $self->_rearrange([qw(URL MODULE)], @args);
$self->{url} = $url ||
$self->throw("URL seems to be blank, where are we pointing?");
$self->{module} = $module ||
$self->throw("Module seems to be blank, what are we fetching?");
$self->{browser} = LWP::UserAgent->new ||
$self->throw("We weren't able to make an LWP Agent, this is bad.");
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 $response = $self->{browser}->post ( $self->{url},
[ 'Module' => $self->{module},
'Seq' => $seq->seq
]
);
$self->throw("Error, wrong content type from SVM Module $self->{module} at $self->{url}, received " . $response->content_type)
unless $response->content_type eq 'text/plain';
# my $loc = $LOCS{'Unknown'};
my $loc = -1;
# Make sure we got a number, if this files $1 will be ''
$response->content =~ /$self->{module}:\s+(\d+)/m;
my $loc = $1;
# Ensure the result is a number and that the previous check did cause it to be ''
$loc = ($loc =~ /\d+/ ? $loc : 10);
# $loc = $1 || 10;
return new Bio::Tools::PSort::Report::Result(-details => [ ],
-score => 0,
-loc => $LOCSR{$loc});
}
1;
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