File Coverage

lib/Bio/Roary/External/Cdhit.pm

Criterion	Covered	Total	%
statement	29	31	93.5
branch	5	6	83.3
condition			n/a
subroutine	6	7	85.7
pod	0	2	0.0
total	40	46	86.9

package Bio::Roary::External::Cdhit;
$Bio::Roary::External::Cdhit::VERSION = '3.11.0';
# ABSTRACT: Wrapper to run cd-hit


use Moose;

with 'Bio::Roary::JobRunner::Role';

has 'input_file'                   => ( is => 'ro', isa => 'Str',  required => 1 );
has 'output_base'                  => ( is => 'ro', isa => 'Str',  default  => 'output' );
has 'exec'                         => ( is => 'ro', isa => 'Str',  default  => 'cd-hit' );
has 'alt_exec'                     => ( is => 'ro', isa => 'Str',  default  => 'cdhit' );
has '_max_available_memory_in_mb'  => ( is => 'ro', isa => 'Int',  lazy => 1, builder => '_build__max_available_memory_in_mb' );
has '_use_most_similar_clustering' => ( is => 'ro', isa => 'Bool', default  => 1 );
has '_length_difference_cutoff'    => ( is => 'ro', isa => 'Num',  default  => 1 );
has '_sequence_identity_threshold' => ( is => 'ro', isa => 'Num',  default  => 1 );
has '_description_length'          => ( is => 'ro', isa => 'Int',  default  => 256 );
has '_logging'                     => ( is => 'ro', isa => 'Str',  default  => '> /dev/null 2>&1' );
has '_max_cpus'                    => ( is => 'ro', isa => 'Int',  default  => 40 );


# Overload Role
has 'memory_in_mb'  => ( is => 'ro', isa => 'Int',  lazy => 1, builder => '_build_memory_in_mb' );

sub _build_memory_in_mb
{
  my ($self) = @_;
  my $filename = $self->input_file;
  my $memory_required = 2000;
  if(-e $filename)
  {
    $memory_required = -s $filename;
    # Convert to mb
    $memory_required = int($memory_required/1000000);
    # Triple memory for worst case senario
    $memory_required *= 5;
    $memory_required = 2000 if($memory_required < 2000);
  }

  return $memory_required;
}

sub _build__max_available_memory_in_mb
{
  my ($self) = @_;
  my $memory_to_cdhit = int($self->memory_in_mb *0.9);
  return $memory_to_cdhit;
}

sub clusters_filename
{
  my ($self) = @_;
  return join('.',($self->output_base,'clstr'));
}

sub _command_to_run {
    my ($self) = @_;

	my $executable = $self->_find_exe([$self->exec, $self->alt_exec]);

	my $cpus = ($self->cpus > $self->_max_cpus) ? $self->_max_cpus :  $self->cpus;
    return join(
        ' ',
        (
            $executable,                        '-i', $self->input_file,                   '-o',
            $self->output_base,                 '-T', $cpus,                               '-M',
            $self->_max_available_memory_in_mb, '-g', $self->_use_most_similar_clustering, '-s',
            $self->_length_difference_cutoff,   '-d', $self->_description_length ,'-c', $self->_sequence_identity_threshold,
            $self->_logging
        )
    );
}

sub run {
    my ($self) = @_;
    my @commands_to_run;

    push(@commands_to_run, $self->_command_to_run() );
    $self->logger->info( "Running command: " . $self->_command_to_run() );
    my $job_runner_obj = $self->_job_runner_class->new( commands_to_run => \@commands_to_run, memory_in_mb => $self->memory_in_mb, queue => $self->_queue, cpus => $self->cpus );
    $job_runner_obj->run();

    1;
}

no Moose;
__PACKAGE__->meta->make_immutable;

1;

__END__

=pod

=encoding UTF-8

=head1 NAME

Bio::Roary::External::Cdhit - Wrapper to run cd-hit

=head1 VERSION

version 3.11.0

=head1 SYNOPSIS

Wrapper to run cd-hit
   use Bio::Roary::External::Cdhit;

   my $obj = Bio::Roary::External::Cdhit->new(
     input_file   => 'abc.fa',
     exec         => 'cd-hit',
     output_base  => 'efg',
   );
  $obj->run;

=head1 AUTHOR

Andrew J. Page <[e-mail]>

=head1 COPYRIGHT AND LICENSE

This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007

=cut