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lib/Bio/MLST/Spreadsheet/Row.pm  view on Meta::CPAN

package Bio::MLST::Spreadsheet::Row;
# ABSTRACT: Create a row representation of the ST results for a single fasta file.
$Bio::MLST::Spreadsheet::Row::VERSION = '2.1.1706216';

use Data::Dumper;
use Text::CSV;

use Bio::MLST::FilterAlleles qw(only_keep_alleles);

use Moose;

has 'sequence_type_obj'  => ( is => 'ro', isa => 'Bio::MLST::SequenceType',     required => 1 ); 
has 'compare_alleles'    => ( is => 'ro', isa => 'Bio::MLST::CompareAlleles',   required => 1 ); 
has 'show_contamination_instead_of_alt_matches' => ( is => 'ro', isa => 'Bool',   default => 1 ); 
                        
has 'allele_numbers_row' => ( is => 'ro', isa => 'ArrayRef', lazy => 1, builder => '_build_allele_numbers_row'); 
has 'genomic_row'        => ( is => 'ro', isa => 'ArrayRef', lazy => 1, builder => '_build_genomic_row'); 
has 'header_row'         => ( is => 'ro', isa => 'ArrayRef', lazy => 1, builder => '_build_header_row'); 
has '_common_cells'      => ( is => 'ro', isa => 'ArrayRef', lazy => 1, builder => '_build__common_cells'); 
has '_allele_order'      => ( is => 'ro', isa => 'ArrayRef', lazy => 1, builder => '_build__allele_order'); 

sub _build__common_cells
{
  my($self) = @_;
  
  #cause the variable to be built.
  $self->sequence_type_obj->sequence_type;
  my $new_st_cell = '';
  if($self->compare_alleles->new_st )
  {
     $new_st_cell = "Unknown";
  }
  elsif($self->sequence_type_obj->nearest_sequence_type)
  {
     $new_st_cell = "Novel ST";
  }

  my $contamination_cell;
  if($self->show_contamination_instead_of_alt_matches == 1)
  {
    $contamination_cell = ($self->compare_alleles->contamination ? $self->compare_alleles->contamination_alleles : '');
  }
  else
  {
    $contamination_cell = (defined($self->compare_alleles->contamination_sequence_names)) ? join(',',@{$self->compare_alleles->contamination_sequence_names}) : '';
  }
  

  # sequence_type_or_nearest is a Maybe[Int]; if it's undefined csv->print skips it so we need to set it to be an empty string
  my $sequence_type = $self->sequence_type_obj->sequence_type_or_nearest ? $self->sequence_type_obj->sequence_type_or_nearest : '';

  my @common_cells = (
    $self->compare_alleles->sequence_filename_root,
    $sequence_type,
    $new_st_cell,
    $contamination_cell,
  );
  return \@common_cells;
}

sub _build__allele_order {
  my $self = shift;
  my $profile_path = $self->compare_alleles->profiles_filename;
  my $csv = Text::CSV->new({sep_char=>"\t"});

  open( my $profile_fh, '<', $profile_path );

  my @alleles = @{$csv->getline($profile_fh)};
  @alleles = @{only_keep_alleles(\@alleles)};

  my @fixed_alleles;
  foreach my $allele ( @alleles ){
    $allele =~ s/_/-/g;
    $allele =~ s/-$//;
    push( @fixed_alleles, $allele );
  }

  #print "ALLELES FROM PROFILE: ";
  #print Dumper \@fixed_alleles;