Bio-Roary

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lib/Bio/Roary/Output/NumberOfGroups.pm  view on Meta::CPAN

$Bio::Roary::Output::NumberOfGroups::VERSION = '3.13.0';
# ABSTRACT: Create raw output files of group counts for turning into plots


use Moose;
use List::Util qw(shuffle);
use Bio::Roary::AnnotateGroups;
use Bio::Roary::GroupStatistics;

has 'group_statistics_obj' => ( is => 'ro', isa => 'Bio::Roary::GroupStatistics', required => 1 );
has 'number_of_iterations' => ( is => 'ro', isa => 'Int', default => 10);
has 'groups_to_contigs'    => ( is => 'ro', isa => 'Maybe[HashRef]' );
has 'annotate_groups_obj'  => ( is => 'ro', isa => 'Bio::Roary::AnnotateGroups', required => 1 );
has 'core_definition'      => ( is => 'ro', isa => 'Num', default  => 1.0 );

has 'output_raw_filename_conserved_genes' => ( is => 'ro', isa => 'Str', default => 'number_of_conserved_genes.Rtab' );
has 'output_raw_filename_unique_genes'    => ( is => 'ro', isa => 'Str', default => 'number_of_unique_genes.Rtab' );
has 'output_raw_filename_total_genes' => ( is => 'ro', isa => 'Str', default => 'number_of_genes_in_pan_genome.Rtab' );
has 'output_raw_filename_new_genes'   => ( is => 'ro', isa => 'Str', default => 'number_of_new_genes.Rtab' );
has '_conserved_genes' => ( is => 'ro', isa => 'ArrayRef', default => sub { [] } );
has '_unique_genes' => ( is => 'ro', isa => 'ArrayRef', default => sub { [] } );
has '_total_genes'  => ( is => 'ro', isa => 'ArrayRef', default => sub { [] } );
has '_new_genes'    => ( is => 'ro', isa => 'ArrayRef', default => sub { [] } );

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

    for ( my $i = 0 ; $i < $self->number_of_iterations ; $i++ ) {
        $self->_single_iteration_gene_expansion;
    }

    $self->_create_raw_output_file( $self->output_raw_filename_conserved_genes, $self->_conserved_genes );
    $self->_create_raw_output_file( $self->output_raw_filename_unique_genes,    $self->_unique_genes );
    $self->_create_raw_output_file( $self->output_raw_filename_total_genes,     $self->_total_genes );
    $self->_create_raw_output_file( $self->output_raw_filename_new_genes,       $self->_new_genes );
    return 1;
}

sub _create_raw_output_file {
    my ( $self, $filename, $output_data ) = @_;
    open( my $fh, '>', $filename );
    for my $iterations ( @{$output_data} ) {
        print {$fh} join( "\t", @{$iterations} );
        print {$fh} "\n";
    }
    close($fh);
}

sub _shuffle_input_files {
    my ($self) = @_;
    my @shuffled_input_files = shuffle( @{ $self->group_statistics_obj->_sorted_file_names } );
    return \@shuffled_input_files;
}

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

use File::Copy qw(move);
use File::Temp;
use File::Basename;
use File::Slurper 'read_lines';
use Cwd;


has 'groupfile'   => ( is => 'ro', isa => 'Str',      required => 1 );
has 'fasta_files' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'outfile'     => ( is => 'ro', isa => 'Str',      required => 1 );
has 'iterations'  => ( is => 'ro', isa => 'Int',      default  => 5 );
has 'dont_delete' => ( is => 'ro', isa => 'Bool',     default  => 0 );

has '_neighbourhood_size' => ( is => 'ro', isa => 'Int', default => 5 );

has '_group_filelist'  => ( is => 'rw', isa => 'ArrayRef', lazy_build => 1 );
has '_tmp_dir_object' => ( is => 'ro', isa => 'File::Temp::Dir', default => sub { File::Temp->newdir( DIR => getcwd, CLEANUP => 1 ); } );
has '_tmp_dir'        => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build__tmp_dir' );

has '_analyse_groups_obj' => ( is => 'ro', lazy_build => 1 );
has '_genes_to_files'     => ( is => 'ro', lazy_build => 1 );

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

sub _build__genes_to_files {
	my ( $self ) = @_;
	return $self->_analyse_groups_obj->_genes_to_file;
}

sub _build__group_filelist {
	my ( $self ) = @_;
	my $tmp = $self->_tmp_dir;

	my @filelist = ( $self->groupfile );
	for my $i ( 1..($self->iterations - 1) ){
		push( @filelist, "$tmp/group_$i" );
	}
	push( @filelist, $self->outfile );

	return \@filelist;
}

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

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

		}
	}
  }
  return \%genes_to_neighbourhood;
}

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

	# iteratively
	for my $x ( 0..($self->iterations - 1) ){
		my ( $in_groups, $out_groups ) = $self->_get_files_for_iteration( $x ); 

		# read in groups, check paralogs and split
		my @newgroups;
		my $any_paralogs = 0;
		$self->_set_genes_to_groups( $in_groups );
		open( my $group_handle, '<', $in_groups );
		while( my $line = <$group_handle> ){
			my @group = split( /\s+/, $line );