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package Bio::Tools::PSort::Module::Profile;
use Bio::Tools::PSort::Module::AnalysisI;
use Bio::Tools::PSort::Report::Result;
use Bio::Tools::PSort::Profile;
use vars qw(@ISA);
@ISA = qw(Bio::Tools::PSort::Module::AnalysisI);
use strict;
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
#profile module must receive: 1 the path to the prosite profiles 2. the path to pfscan, 3. the path to the file containing the SCL's for each of the profile_ids
my ($profiledb, $pfscan, $profileids) = $self->_rearrange([qw(DATABASE PROGRAM PROFILEIDS)], @args);
#pass up the paths to Bio::Tools::Profile.
$self->{profile} = new Bio::Tools::PSort::Profile(-database => $profiledb,
-program => $pfscan,
-profileids => $profileids) ||
$self->throw("Couldn't create new Bio::Tools::PSort::Profile object");
return $self;
}
sub run {
my ($self, $seq) = @_;
my @res = map {
my $detail = "matched " . $_->profile_id . ": " . $_->comment;
new Bio::Tools::PSort::Report::Result(-details => [ $detail ],
-score => 0,
-loc => $_->localization);
} $self->{profile}->match($seq);
@res ? @res : new Bio::Tools::PSort::Report::Result(-loc => 'Unknown',
-details => ['No matches to profiles found']);
}
1;
=head1 NAME
=head1 SYNOPSIS
=head1 DESCRIPTION
=head1 CONSTRUCTOR
=head1 METHODS
=head1 SEE ALSO
=head1 AUTHOR
Fiona Brinkman, Chris Walsh, Matthew Laird <psort-mail@sfu.ca>
Brinkman Lab, Simon Fraser University, Canada
=cut
__END__
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