Raw content of Bio::EnsEMBL::Analysis::Runnable::Funcgen::Nessie
<![CDATA[# Ensembl module for Bio::EnsEMBL::Analysis::Runnable::Funcgen::Nessie
#
# Copyright (c) 2007 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Analysis::Runnable::Funcgen::Nessie
=head1 SYNOPSIS
my $nessie = Bio::EnsEMBL::Analysis::Runnable::Funcgen::Nessie->new
(
-analysis => $analysis,
-query => 'slice',
-program => 'nessie',
);
$nessie->run;
my @annotated_features = @{$nessie->output};
=head1 DESCRIPTION
Nessie expects to run the program Nessie and predicts features which
can be stored in the predicted_feature table in the eFG database
=head1 AUTHOR
This module was created by Stefan Graf. It is part of the
Ensembl project: /
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::Analysis::Runnable::Funcgen::Nessie;
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 stack_trace_dump);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Analysis::Runnable::Funcgen);
=head2 run_analysis
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::Nessie
Arg [2] : string, program name
Usage :
Description :
Returns :
Exceptions :
=cut
sub run_analysis {
print "Analysis::Runnable::Funcgen::Nessie::run_analysis\n";
my ($self, $program) = @_;
if(!$program){
$program = $self->program;
}
throw($program." is not executable Nessie::run_analysis ")
unless($program && -x $program);
(my $outfile = $self->infile()) =~ s/\.dat$/.out/;
my @fields = (0..2,4);
$self->output_fields(\@fields);
(my $resultsfile = $self->infile()) =~ s/\.dat$/_peaks.out/;
my $replicates = scalar(keys %{$self->result_features});
if ($replicates == 1) { $replicates=2 }
my ($nessie_parameters, $peak_parameters) = split('; ', $self->options);
print Dumper ($nessie_parameters, $peak_parameters);
my $command = $self->program.' --data="'.$self->infile().'" '.
'--replicates='.$replicates.$nessie_parameters.' > '.$outfile;
warn("Running analysis " . $command . "\n");
eval { system($command) };
throw("FAILED to run $command: ", $@) if ($@);
my $parser = 'oligo_peaks.pl --sang --autonorm '. $peak_parameters .
' -l '.$outfile.' '.$self->infile.' > '.$resultsfile;
warn("Running parser " . $parser . "\n");
eval { system($parser) };
throw("FAILED to run $parser: ", $@) if ($@);
throw("No peak resultfile.") if (! -e $resultsfile);
$self->resultsfile($resultsfile);
}
=head2 write_infile
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::Nessie
Arg [2] : filename
Description :
Returntype :
Exceptions :
Example :
=cut
sub write_infile {
print "Analysis::Runnable::Funcgen::Nessie::write_infile\n";
my ($self, $filename) = @_;
warn("workdir : ".$self->workdir);
if (! $filename) {
$filename = $self->infile();
}
warn("filename: ".$filename);
foreach my $rset_name (sort keys %{$self->result_features})
{
#print Dumper $self->query->[0]->name, $rset_name, $filename;
#print $self->result_features->{$rset_name}, "\n";
my $datafile = $self->workdir.'/cache/'.$self->query->[0]->name.'.'.$rset_name.'.dat';
warn("datafile: ".$datafile);
unless ( -e $datafile ) {
open(F, ">".$datafile)
or throw("Can't open file $datafile.");
#foreach (keys %{$self->result_features}) {
# next unless ($datafile =~ m/$_/);
foreach my $ft (@{$self->result_features->{$rset_name}}) {
#print join("\t", @$ft), "\n";
print F join("\t", @$ft), "\n";
}
# last;
#}
close F;
}
$self->datafiles($datafile);
}
#print Dumper $self->datafiles;
$self->write_filelist();
map {$self->files_to_delete($_)} @{$self->datafiles};
return $filename;
}
=head2 datafiles
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::Nessie
Arg [2] : filename (string)
Description : will hold/add a list of filename
Returntype : listref of filenames
Exceptions : none
Example :
=cut
sub datafiles{
my ($self, $filename) = @_;
if(! $self->{'datafiles'}){
$self->{'datafiles'} = [];
}
if($filename){
push @{$self->{'datafiles'}}, $filename;
}
return \@{$self->{'datafiles'}};
}
=head2 write_filelist
Arg [1] : Bio::EnsEMBL::Analysis::Runnable::Nessie
Description : writes the nessie specific wrapper file containing a
list of replicate data file names
Returntype : none
Exceptions :
Example :
=cut
sub write_filelist {
my ($self) = shift;
throw("No infile found") if (! $self->infile());
open(F, ">".$self->infile())
or throw("Can't open file ".$self->infile);
foreach my $f (@{$self->datafiles}) {
print F $f, "\n";
}
# nessie hack: if there is only one replicate data set we duplicate this one ...
if (scalar(@{$self->datafiles}) == 1) {
warn("Duplicating input data file.");
print F ${$self->datafiles}[0], "\n";
}
close F;
}
1;
]]>