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

undef $VERSION;
package Bio::Roary::CommandLine::RoaryCoreAlignment;
$Bio::Roary::CommandLine::RoaryCoreAlignment::VERSION = '3.13.0';
# ABSTRACT: Take in the group statistics spreadsheet and the location of the gene multifasta files and create a core alignment.


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Cwd 'abs_path';
use File::Path qw(remove_tree);
use Bio::Roary::ExtractCoreGenesFromSpreadsheet;
use Bio::Roary::LookupGeneFiles;
use Bio::Roary::MergeMultifastaAlignments;
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 'multifasta_base_directory' => ( is => 'rw', isa => 'Str', default => 'pan_genome_sequences' );
has 'spreadsheet_filename'      => ( is => 'rw', isa => 'Str', default => 'gene_presence_absence.csv' );
has 'output_filename'           => ( is => 'rw', isa => 'Str', default => 'core_gene_alignment.aln' );
has 'core_definition'           => ( is => 'rw', isa => 'Num', default => 0.99 );
has 'dont_delete_files'         => ( is => 'rw', isa => 'Bool', default => 0 );
has 'allow_paralogs'            => ( is => 'rw', isa => 'Bool', default => 0 );
has '_error_message'            => ( is => 'rw', isa => 'Str' );
has 'verbose'                   => ( is => 'rw', isa => 'Bool', default => 0 );

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

    my ( $multifasta_base_directory, $spreadsheet_filename, $output_filename, $core_definition,$verbose,  $help, $mafft, $allow_paralogs, $dont_delete_files );

    GetOptionsFromArray(
        $self->args,
        'm|multifasta_base_directory=s' => \$multifasta_base_directory,
        's|spreadsheet_filename=s'      => \$spreadsheet_filename,
        'o|output_filename=s'           => \$output_filename,
        'cd|core_definition=f'          => \$core_definition,
        'z|dont_delete_files'           => \$dont_delete_files,
		'p|allow_paralogs'              => \$allow_paralogs,
		'v|verbose'                     => \$verbose,
        'h|help'                        => \$help,
    );
    
    if ( defined($verbose) ) {
        $self->verbose($verbose);
        $self->logger->level(10000);
    }
    $self->help($help) if(defined($help));
	$self->allow_paralogs($allow_paralogs) if(defined($allow_paralogs));

    if ( defined($multifasta_base_directory) && ( -d $multifasta_base_directory ) ) {
        $self->multifasta_base_directory( abs_path($multifasta_base_directory));
    }
    if(! -d $self->multifasta_base_directory ) 
    {
        $self->_error_message("Error: Cant access the multifasta base directory: ".$self->multifasta_base_directory);
    }
    
    if ( defined($spreadsheet_filename) && ( -e $spreadsheet_filename ) ) {
        $self->spreadsheet_filename( abs_path($spreadsheet_filename));
    }
    if(! -e $self->spreadsheet_filename ) 
    {
        $self->_error_message("Error: Cant access the spreadsheet: ".$self->spreadsheet_filename);
    }
    $self->output_filename( $output_filename ) if ( defined($output_filename) );
    if ( defined($core_definition) ) 
	{
		if($core_definition > 1)
		{
			$self->core_definition( $core_definition/100 );
		}
		else
		{