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lib/Bio/Roary/CommandLine/AssemblyStatistics.pm  view on Meta::CPAN

undef $VERSION;
package Bio::Roary::CommandLine::AssemblyStatistics;
$Bio::Roary::CommandLine::AssemblyStatistics::VERSION = '3.13.0';
# ABSTRACT: Given a spreadsheet of gene presence and absence calculate some statistics


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Bio::Roary::AssemblyStatistics;
extends 'Bio::Roary::CommandLine::Common';

has 'args'            => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name'     => ( is => 'ro', isa => 'Str',      required => 1 );
has 'help'            => ( is => 'rw', isa => 'Bool',     default  => 0 );
has 'spreadsheet'     => ( is => 'rw', isa => 'Str',      default  => 'gene_presence_absence.csv' );
has 'job_runner'      => ( is => 'rw', isa => 'Str',      default  => 'Local' );
has 'cpus'            => ( is => 'rw', isa => 'Int',      default  => 1 );
has 'output_filename' => ( is => 'rw', isa => 'Str',      default  => 'assembly_statistics.csv' );
has 'version'         => ( is => 'rw', isa => 'Bool',     default  => 0 );
has 'core_definition' => ( is => 'rw', isa => 'Num',      default  => 0.99 );
has 'verbose'         => ( is => 'rw', isa => 'Bool',     default  => 0 );


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

    my (
        $spreadsheet,
		$job_runner,       
		$cpus,
		$output_filename,
		$version,
		$core_definition,
		$verbose,
		$help
    );

    GetOptionsFromArray(
        $self->args,
        'o|output_filename=s'       => \$output_filename,
        'j|job_runner=s'            => \$job_runner,
        'p|processors=i'            => \$cpus,
        'cd|core_definition=f'      => \$core_definition,
        'v|verbose'                 => \$verbose,
		'w|version'                 => \$version,
        'h|help'                    => \$help,
    );

	$self->version($version)                   if ( defined($version) );
    if ( $self->version ) {
        die($self->_version());
    }

    if ( defined($verbose) ) {
        $self->verbose($verbose);
        $self->logger->level(10000);
    }

    $self->help($help) if ( defined($help) );
	( !$self->help ) or die $self->usage_text;
    if(@{$self->args} == 0)
    {
        $self->logger->error("Error: You need to provide a gene_presence_absence.csv spreadsheet");
        die $self->usage_text;
    }
	$self->output_filename($output_filename)   if ( defined($output_filename) );
    $self->job_runner($job_runner)             if ( defined($job_runner) );
    $self->cpus($cpus)                         if ( defined($cpus) );

    if ( $self->cpus > 1 ) {
        $self->job_runner('Parallel');
    }