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

sub _build__groups_to_files {
    my ($self) = @_;
    my %groups_to_files;
    for my $group ( @{ $self->annotate_groups_obj->_groups } ) {
        my $genes = $self->annotate_groups_obj->_groups_to_id_names->{$group};
        my %filenames;
        for my $gene_name ( @{$genes} ) {
            my $filename = $self->analyse_groups_obj->_genes_to_file->{$gene_name};
            push( @{ $filenames{$filename} }, $gene_name );
        }
        $groups_to_files{$group} = \%filenames;
    }
    
    return \%groups_to_files;
}

sub _build__files_to_groups
{
  my ($self) = @_;
  my %files_to_groups;
  
  for my $group (keys %{$self->_groups_to_files})
  {
    for my $filename (keys %{$self->_groups_to_files->{$group}})
    {
      push(@{$files_to_groups{$filename}}, $group);
    }
  }
  
  return \%files_to_groups;
}

sub _build__num_files_in_groups
{
	 my ($self) = @_;
 	my %num_files_in_groups;
 	for my $group (@{ $self->annotate_groups_obj->_groups })
 	{
 	  my $num_files = $self->analyse_groups_obj->_count_num_files_in_group( $self->annotate_groups_obj->_groups_to_id_names->{$group});
 	  $num_files_in_groups{$group} = $num_files;
 	}
	return \%num_files_in_groups;
}

sub _row {
    my ( $self, $group ) = @_;
    my $genes = $self->annotate_groups_obj->_groups_to_id_names->{$group};

    my $num_isolates_in_group     = $self->analyse_groups_obj->_count_num_files_in_group($genes);
    my $num_sequences_in_group    = $#{$genes} + 1;
    my $avg_sequences_per_isolate = ceil( ( $num_sequences_in_group / $num_isolates_in_group ) * 100 ) / 100;

    my $annotation           = $self->annotate_groups_obj->consensus_product_for_id_names($genes);
    my $annotated_group_name = $self->annotate_groups_obj->_groups_to_consensus_gene_names->{$group};

    my $duplicate_gene_name = $self->_non_unique_name_for_group($annotated_group_name);
    
    my $genome_number = '';
    my $qc_comment = '';
    my $order_within_fragement = '';
    my $accessory_order_within_fragement = '';
    my $accessory_genome_number = '';
    if(defined($self->groups_to_contigs) && defined($self->groups_to_contigs->{$annotated_group_name}))
    {
      $genome_number = $self->groups_to_contigs->{$annotated_group_name}->{label};
      $qc_comment = $self->groups_to_contigs->{$annotated_group_name}->{comment};
      $order_within_fragement = $self->groups_to_contigs->{$annotated_group_name}->{order};
      
      $accessory_genome_number = $self->groups_to_contigs->{$annotated_group_name}->{accessory_label};
      $accessory_order_within_fragement = $self->groups_to_contigs->{$annotated_group_name}->{accessory_order};
    }
	
	my $group_size = $self->annotate_groups_obj->group_nucleotide_lengths->{$group};
    
    my @row = (
        $annotated_group_name,  $duplicate_gene_name,    $annotation,
        $num_isolates_in_group, $num_sequences_in_group, $avg_sequences_per_isolate,$genome_number,$order_within_fragement,$accessory_genome_number,$accessory_order_within_fragement,$qc_comment,$group_size->{min}, $group_size->{max}, $group_size->{av...
    );
	
	for(my $i =0; $i < @row; $i++)
	{
		if(!defined($row[$i]))
		{
			$row[$i] = '';
		}
	}

    for my $filename ( @{ $self->_sorted_file_names } ) {
        my $group_to_file_genes = $self->_groups_to_files->{$group}->{$filename};

        if ( defined($group_to_file_genes) && @{$group_to_file_genes} > 0 ) {

            push( @row, join( "\t", @{$group_to_file_genes} ) );
            next;
        }
        else {
            push( @row, '' );
        }
    }

    ## ADD INFERENCE AND FULL ANNOTATION IF VERBOSE REQUESTED ##
    if ( $self->_verbose ){
      my ( $full_annotation, $inference );
        $row[2] = $self->annotate_groups_obj->full_annotation($group);
        push( @row, $self->annotate_groups_obj->inference($group) );
    }

    return \@row;
}

sub create_rtab
{
	my ($self) = @_;
    my $presence_absence_matrix_obj = Bio::Roary::PresenceAbsenceMatrix->new(
      output_filename     => $self->output_rtab_filename,
	  annotate_groups_obj => $self->annotate_groups_obj,
      sorted_file_names   => $self->_sorted_file_names,
      groups_to_files     => $self->_groups_to_files,
      num_files_in_groups => $self->_num_files_in_groups,
      sample_headers      => $self->_sample_headers,
    );
    $presence_absence_matrix_obj->create_matrix_file;
	return $self;
}

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

    $self->_text_csv_obj->print( $self->_output_fh, $self->_header );

    for my $group (sort {$self->_num_files_in_groups->{$b}<=>$self->_num_files_in_groups->{$a} || $a cmp $b} keys %{$self->_num_files_in_groups}){
        $self->_text_csv_obj->print( $self->_output_fh, $self->_row($group) );
    }
    close( $self->_output_fh );
}

no Moose;