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

undef $VERSION;
package Bio::Roary::CommandLine::RoaryPostAnalysis;
$Bio::Roary::CommandLine::RoaryPostAnalysis::VERSION = '3.13.0';
# ABSTRACT: Perform the post analysis on the pan genome


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Bio::Roary::PostAnalysis;
use File::Find::Rule;
use Bio::Roary::External::GeneAlignmentFromNucleotides;
use File::Path qw(remove_tree);
use Bio::Roary::External::Fasttree;
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 '_error_message'              => ( is => 'rw', isa => 'Str' );

has 'fasta_files'                 => ( is => 'rw', isa => 'Str',  default  => '_fasta_files' );
has 'input_files'                 => ( is => 'rw', isa => 'Str',  default  => '_gff_files');
has 'output_filename'             => ( is => 'rw', isa => 'Str',  default  => 'clustered_proteins' );
has 'output_pan_geneome_filename' => ( is => 'rw', isa => 'Str',  default  => 'pan_genome.fa' );
has 'output_statistics_filename'  => ( is => 'rw', isa => 'Str',  default  => 'gene_presence_absence.csv' );
has 'output_multifasta_files'     => ( is => 'rw', isa => 'Bool', default  => 0 );
has 'clusters_filename'           => ( is => 'rw', isa => 'Str',  default  => '_clustered.clstr' );
has 'job_runner'                  => ( is => 'rw', isa => 'Str',  default  => 'Local' );
has 'cpus'                        => ( is => 'rw', isa => 'Int',  default => 1 );
has 'dont_delete_files'           => ( is => 'rw', isa => 'Bool', default  => 0 );
has 'dont_create_rplots'          => ( 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 '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 'mafft'                       => ( is => 'rw', isa => 'Bool', default => 0 );
has 'allow_paralogs'              => ( is => 'rw', isa => 'Bool', default => 0 );

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

    my ( 
      $output_filename, $dont_create_rplots, $dont_delete_files, $dont_split_groups, $output_pan_geneome_filename, 
      $job_runner, $output_statistics_filename, $output_multifasta_files, $clusters_filename, $core_definition,
      $fasta_files, $input_files, $verbose_stats, $translation_table, $help, $cpus,$group_limit,$verbose,$mafft, $allow_paralogs
    );


    GetOptionsFromArray(
        $self->args,
        'o|output=s'                => \$output_filename,
        'j|job_runner=s'            => \$job_runner,
        'm|output_multifasta_files' => \$output_multifasta_files,
        'p=s'                       => \$output_pan_geneome_filename,
        's=s'                       => \$output_statistics_filename,
        'c=s'                       => \$clusters_filename,
        'f=s'                       => \$fasta_files,
        'i=s'                       => \$input_files,
        'a|dont_delete_files'       => \$dont_delete_files,
        'b|dont_create_rplots'      => \$dont_create_rplots,
        'd|dont_split_groups'       => \$dont_split_groups,
        'e|verbose_stats'           => \$verbose_stats,
        'z|processors=i'            => \$cpus,
        't|translation_table=i'     => \$translation_table,
        'g|group_limit=i'           => \$group_limit,
        'cd|core_definition=f'      => \$core_definition,
		'v|verbose'                 => \$verbose,
		'n|mafft'                   => \$mafft,
		'q|allow_paralogs'          => \$allow_paralogs,
        'h|help'                    => \$help,
    );
    
    $self->help($help) if(defined($help));
    $self->job_runner($job_runner)                                   if ( defined($job_runner) );