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

undef $VERSION;

package Bio::Roary::CommandLine::Roary;
$Bio::Roary::CommandLine::Roary::VERSION = '3.13.0';
# ABSTRACT: Take in FASTA files of proteins and cluster them


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Bio::Roary;
use Bio::Roary::PrepareInputFiles;
use Bio::Roary::QC::Report;
use Bio::Roary::ReformatInputGFFs;
use Bio::Roary::External::CheckTools;
use File::Which;
use File::Path qw(make_path);
use Cwd qw(abs_path getcwd);
use File::Temp;
use File::Basename;
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 'fasta_files' => ( is => 'rw', isa => 'ArrayRef', default => sub { [] } );
has 'output_filename'         => ( is => 'rw', isa => 'Str',  default => 'clustered_proteins' );
has 'output_directory'        => ( is => 'rw', isa => 'Str',  default => '.' );
has '_original_directory'     => ( is => 'rw', isa => 'Str',  default => '.' );
has 'job_runner'              => ( is => 'rw', isa => 'Str',  default => 'Local' );
has 'makeblastdb_exec'        => ( is => 'rw', isa => 'Str',  default => 'makeblastdb' );
has 'blastp_exec'             => ( is => 'rw', isa => 'Str',  default => 'blastp' );
has 'mcxdeblast_exec'         => ( is => 'rw', isa => 'Str',  default => 'mcxdeblast' );
has 'mcl_exec'                => ( is => 'rw', isa => 'Str',  default => 'mcl' );
has 'apply_unknowns_filter'   => ( is => 'rw', isa => 'Bool', default => 1 );
has 'cpus'                    => ( is => 'rw', isa => 'Int',  default => 1 );
has 'output_multifasta_files' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'perc_identity'           => ( is => 'rw', isa => 'Num',  default => 95 );
has 'dont_delete_files'       => ( is => 'rw', isa => 'Bool', default => 0 );
has 'check_dependancies'      => ( is => 'rw', isa => 'Bool', default => 0 );
has 'dont_create_rplots'      => ( is => 'rw', isa => 'Bool', default => 1 );
has 'dont_run_qc'             => ( is => 'rw', isa => 'Bool', default => 0 );
has 'dont_split_groups'       => ( is => 'rw', isa => 'Bool', default => 0 );
has 'verbose_stats'           => ( is => 'rw', isa => 'Bool', default => 0 );
has 'translation_table'       => ( is => 'rw', isa => 'Int',  default => 11 );
has 'mafft'                   => ( is => 'rw', isa => 'Bool', default => 0 );
has 'allow_paralogs'          => ( is => 'rw', isa => 'Bool', default => 0 );
has 'group_limit'             => ( is => 'rw', isa => 'Num',  default => 50000 );
has 'core_definition'         => ( is => 'rw', isa => 'Num',  default => 0.99 );
has 'verbose'                 => ( is => 'rw', isa => 'Bool', default => 0 );
has 'kraken_db' => ( is => 'rw', isa => 'Str',  default => '/lustre/scratch118/infgen/pathogen/pathpipe/kraken/minikraken_20140330/' );
has 'run_qc'    => ( is => 'rw', isa => 'Bool', default => 0 );
has '_working_directory' => ( is => 'rw', isa => 'File::Temp::Dir', lazy => 1, builder => '_build__working_directory' );

has 'inflation_value'             => ( is => 'rw', isa => 'Num',      default  => 1.5 );

sub _build__working_directory
{
	my ($self) = @_;
	return File::Temp->newdir( DIR => getcwd, CLEANUP => 1 );
}

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

    my (
        $fasta_files,           $verbose,           $create_rplots,           $group_limit,   $dont_run_qc,
        $max_threads,           $dont_delete_files, $dont_split_groups,       $perc_identity, $output_filename,
        $job_runner,            $makeblastdb_exec,  $mcxdeblast_exec,         $mcl_exec,      $blastp_exec,
        $apply_unknowns_filter, $cpus,              $output_multifasta_files, $verbose_stats, $translation_table,
        $run_qc,                $core_definition,   $help,                    $kraken_db,     $cmd_version,
        $mafft,                 $output_directory,  $check_dependancies, $inflation_value, $allow_paralogs,
    );

    GetOptionsFromArray(
        $self->args,
        'o|output=s'                => \$output_filename,
        'f|output_directory=s'      => \$output_directory,
        'j|job_runner=s'            => \$job_runner,
        'm|makeblastdb_exec=s'      => \$makeblastdb_exec,
        'b|blastp_exec=s'           => \$blastp_exec,
        'd|mcxdeblast_exec=s'       => \$mcxdeblast_exec,