Raw content of Bio::EnsEMBL::Analysis::Runnable::Funcgen
<![CDATA[# Ensembl module for Bio::EnsEMBL::Analysis::Runnable::Funcgen
#
# Copyright (c) 2007 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Analysis::Runnable::Fungen
=head1 SYNOPSIS
=head1 DESCRIPTION
This module is the base class for Fungen Runnables.
=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;
use strict;
use warnings;
use Data::Dumper;
use Bio::EnsEMBL::Analysis::Runnable;
use Bio::EnsEMBL::Utils::Exception qw( throw warning stack_trace_dump );
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use vars qw( @ISA );
@ISA = qw( Bio::EnsEMBL::Analysis::Runnable );
=head2 new
Arg :
Usage : my $runnable = Bio::EnsEMBL::Analysis::Runnable::Funcgen->new()
Description : Instantiates new Chipotle runnable
Returns : Bio::EnsEMBL::Analysis::Runnable::Funcgen::Nessie object
Exceptions : none
=cut
sub new {
print "Analysis::Runnable::Funcgen::new\n";
my ($class,@args) = @_;
#print Dumper @args;
my $self = $class->SUPER::new(@args);
#warn $self;
my ($result_features, $options, $workdir) = rearrange
(['RESULT_FEATURES', 'OPTIONS', 'WORKDIR'], @args);
$self->result_features($result_features);
$self->workdir($workdir);
$self->checkdir();
warn("workdir ".$self->workdir()." OK!");
#warn('RESULT_FEATURES: '.$self->result_features);
#warn('OPTIONS: '.$self->options);
#warn('OPTIONS: '.$options);
#warn('A_PARAMS: '.$self->analysis->parameters);
return $self;
}
=head2 run
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::Funcgen
Arg [2] : string, directory
Description : Class specific run method. This checks the directory specifed
to run it, write the data to file (tab-delimited), marks the query infile
and results file for deletion, runs the analysis, parses the results and
deletes any files
Returntype : 1
Exceptions : throws if no query sequence is specified
Example :
=cut
sub run {
print "Bio::EnsEMBL::Analysis::Runnable::Funcgen::run\n";
my ($self, $dir) = @_;
#print Dumper $self->options;
#throw("Can't run ".$self." without result features")
# unless($self->result_features);
#print Dumper $self->probe_features;
$self->write_infile();
warn("infile: ".$self->infile);
throw("Input file ".$self->infile." is empty.") if (-z $self->infile);
$self->files_to_delete($self->infile);
$self->run_analysis();
#print "Parsing results ... ";
$self->parse_results();
#print "done!\n";
#$self->delete_files;
return 1;
}
=head2 get_parameters
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::Funcgen
Description : parse analysis parameters
Returntype : hash ref with parameter names as keys
Exceptions : none
Example :
=cut
sub get_parameters {
my ($self) = @_;
my %parameters = ();
throw ("Object needs to be a Bio::EnsEMBL::Analysis::Runnable::Funcgen")
if (! $self->isa("Bio::EnsEMBL::Analysis::Runnable::Funcgen"));
my @parameters = split(/\s+/, $self->analysis->parameters());
map { throw("Parameter $_ has not the correct format.")
if (! m/^(.+)=(.+)/);
$parameters{$1} = $2; } @parameters;
#print Dumper %parameters;
return \%parameters;
}
=head2 infile
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::Funcgen
Arg [2] : filename (string)
Description : will hold a given filename or if one is requested but none
defined it will use the create_filename method to create a filename
Returntype : string, filename
Exceptions : none
Example :
=cut
sub infile{
my ($self, $filename) = @_;
if($filename){
$self->{'infile'} = $filename;
}
if(!$self->{'infile'}){
$self->{'infile'} = $self->create_filename
($self->analysis->module.'/'.$self->analysis->module, 'dat');
(my $dir = $self->{'infile'}) =~ s,/[^/]+$,,;
system("mkdir -p $dir") unless ( -d $dir );
}
return $self->{'infile'};
}
=head2 result_features
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::Funcgen
Arg [2] : arrayref of result features
Description : container for result features
Returntype : arrayref
Exceptions : throws if no probe feature container is defined
Example :
=cut
sub result_features {
my ($self, $features) = @_;
if($features){
$self->{'result_features'} = $features;
}
#throw("No result features available in Runnable.")
# if (!$self->{'result_features'});
return $self->{'result_features'};
}
=head2 output_fields
Arg [1] : Bio::EnsEMBL::Analysis::RunnableDB
Arg [2] : arrayref of output fields
Description : container for outout fields
Returntype : arrayref
Exceptions : throws if no output field container is defined
Example :
=cut
sub output_fields {
my ($self, $array) = @_;
#print Dumper $array;
if($array){
$self->{'outfile_fields'} = $array;
}
throw("No outfile field string set in Runnable.")
if (!$self->{'outfile_fields'});
return $self->{'outfile_fields'};
}
=head2 parse_results
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::Funcgen
Arg [2] : filename (string)
Decription : open and parse resultsfile
Returntype : none
Exceptions : throws
Example :
=cut
sub parse_results{
my ($self, $resultsfile) = @_;
if (! defined $resultsfile) {
$resultsfile = $self->resultsfile;
}
throw ('No resultsfile defined in instance!')
if(! defined $resultsfile);
throw("parse_results: results file ".$resultsfile." does not exist.")
if (! -e $resultsfile);
warn('Resultsfile: '.$resultsfile);
throw("parse_results: can't open file ".$resultsfile.": ". $!)
unless (open(F, $resultsfile));
my @output = ();
while (<F>) {
s/\"//g;
s/^chr//;
next unless (/^[0-9XYM]+\s/);
chomp;
my @ft = split;
push(@output, [ @ft[@{$self->output_fields()}] ]);
}
$self->output(\@output);
#print Dumper $self->output();
throw("parse_results: can't close file ".$resultsfile.".")
unless (close(F));
}
sub query {
my ($self, $query) = @_;
if ( $query ) {
throw("Must pass RunnableDB:Funcgen:query a array ref not a ".
ref($query)) unless (ref($query) eq 'ARRAY');
map {
throw($_->name . " is not a Bio::EnsEMBL::Slice")
unless ($_->isa("Bio::EnsEMBL::Slice"));
} @$query;
$self->{'query'} = $query;
}
return $self->{'query'};
}
1;
]]>