Raw content of Bio::EnsEMBL::Analysis::Runnable::Funcgen::SWEmbl
<![CDATA[# Ensembl module for Bio::EnsEMBL::Analysis::Runnable::Funcgen::SWEmbl
#
# Copyright (c) 2007 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Analysis::Runnable::Funcgen::SWEmbl
=head1 SYNOPSIS
my $runnable = Bio::EnsEMBL::Analysis::Runnable::Funcgen::SWEmbl->new
(
-analysis => $analysis,
-query => 'slice',
-program => 'program.pl',
);
$runnable->run;
my @features = @{$runnable->output};
=head1 DESCRIPTION
SWEmbl expects bed or maq mapview files as input and predicts features which
can be stored in the annotated_feature table in the eFG database
=head1 LICENCE
This code is distributed under an Apache style licence. Please see
/info/about/code_licence.html for details.
=head1 AUTHOR
Stefan Graf, Ensembl Functional Genomics -
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::Analysis::Runnable::Funcgen::SWEmbl;
use strict;
use warnings;
use Data::Dumper;
use Bio::EnsEMBL::Analysis::Runnable;
use Bio::EnsEMBL::Analysis::Runnable::Funcgen;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Analysis::Runnable::Funcgen);
=head2 run
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::SWEmbl
Arg [2] : filename
Description :
Returntype :
Exceptions :
Example :
=cut
sub run {
print "Bio::EnsEMBL::Analysis::Runnable::Funcgen::SWEmbl::run\n";
my ($self, $dir) = @_;
$self->run_analysis;
print "Parsing results ... ";
$self->parse_results();
print "done!\n";
}
=head2 run_analysis
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::SWEmbl
Arg [2] : string, program name
Usage :
Description :
Returns :
Exceptions :
=cut
sub run_analysis {
my ($self, $program) = @_;
if(!$program){
$program = $self->program;
}
throw($program." is not executable SWEmble::run_analysis ")
unless($program && -x $program);
my @fields = (0..2,5);
$self->output_fields(\@fields);
(my $resultsfile = $self->infile());
$self->resultsfile($resultsfile);
warn("RESULTS FILE: ".$resultsfile);
my $command = $self->program . ' -B -z -i ' . $self->query . ' ' .
$self->options . ' -o ' . $resultsfile;
warn("Running analysis " . $command);
eval { system($command) };
throw("FAILED to run $command: ", $@) if ($@);
}
#=head2 infile
#
# Arg [1] : Bio::EnsEMBL::Analysis::Runnable::SWEmble
# Arg [2] : filename (string)
# Description : will hold a given filename or if one is requested but none
# defined it will use the create_filename method to create a filename
# Returntype : string, filename
# Exceptions : none
# Example :
#
#=cut
#
#
#sub infile{
#
# my ($self, $filename) = @_;
#
# if($filename){
# $self->{'infile'} = $filename;
# }
# if(!$self->{'infile'}){
# $self->{'infile'} = $self->create_filename($self->analysis->logic_name, 'dat');
# }
#
# return $self->{'infile'};
#
#}
sub query{
my $self = shift;
$self->{'query'} = shift if(@_);
throw("file ".$self->{'query'}. " doesn't exist") if (! -e $self->{'query'});
return $self->{'query'};
}
sub config_file {
my $self = shift;
$self->{'config_file'} = shift if(@_);
return $self->{'config_file'};
}
1;
]]>