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lib/Bio/MLST/OutputFasta.pm  view on Meta::CPAN

package Bio::MLST::OutputFasta;
# ABSTRACT: Take in two hashes, both containing sequence names and sequences and output fasta files.
$Bio::MLST::OutputFasta::VERSION = '2.1.1706216';


use Moose;
use File::Basename;
use File::Path qw(make_path);
use Bio::PrimarySeq;
use Bio::SeqIO;
use Bio::MLST::Types;

has 'matching_sequences'      => ( is => 'ro', isa => 'Maybe[HashRef]',      required => 1 ); 
has 'non_matching_sequences'  => ( is => 'ro', isa => 'Maybe[HashRef]',      required => 1 ); 
has 'output_directory'        => ( is => 'ro', isa => 'Str',          required => 1 ); 
has 'input_fasta_file'        => ( is => 'ro', isa => 'Bio::MLST::File',          required => 1 ); 

has '_fasta_filename'         => ( is => 'ro', isa => 'Str',          lazy => 1, builder => '_build__fasta_filename' ); 
has 'concat_sequence'         => ( is => 'rw', isa => 'Maybe[Str]' );


sub _build__fasta_filename
{
  my($self) = @_;
  my $filename  = fileparse($self->input_fasta_file, qr/\.[^.]*$/);
  return $filename;
}

sub _sort_and_join_sequences
{
  my($self, $combined_sequences) = @_;
  my @allele_names = sort keys %{$combined_sequences};
  my @sorted_sequences = map { $combined_sequences->{$_} } @allele_names;
  join("", @sorted_sequences);
}

sub create_files
{
  my($self) = @_;
  make_path($self->output_directory);
  $self->_fasta_filename;
  if((defined($self->matching_sequences) && %{$self->matching_sequences}) ||(defined($self->non_matching_sequences) && %{$self->non_matching_sequences}) )
  {

    my %matching_sequences = %{$self->matching_sequences};
    my %combined_sequences = (%matching_sequences);
    
    if(defined($self->non_matching_sequences) && %{$self->non_matching_sequences})
    {
      my %non_matching_sequences = %{$self->non_matching_sequences};
      %combined_sequences = (%matching_sequences, %non_matching_sequences);
    }
    my $concat_sequence = $self->_sort_and_join_sequences(\%combined_sequences);
    
    $self->concat_sequence($concat_sequence);
  }
  
  if(defined($self->non_matching_sequences) && %{$self->non_matching_sequences})
  {
   # create 1 FASTA file for each unknown allele with a close match to another allele
    for my $sequence_name (keys %{$self->non_matching_sequences})
    {
      next if(length($self->non_matching_sequences->{$sequence_name}) < 2);
      next if($self->_does_sequence_contain_all_unknowns($self->non_matching_sequences->{$sequence_name}));
      my $non_matching_output_filename = join('/',($self->output_directory, $self->_fasta_filename.'.unknown_allele.'.$sequence_name.'.fa'));
      my $out = Bio::SeqIO->new(-file => "+>$non_matching_output_filename" , '-format' => 'Fasta');
      $out->write_seq(Bio::PrimarySeq->new(-seq => $self->non_matching_sequences->{$sequence_name}, -id  => $sequence_name));
    }
  }
  1;
}

sub _does_sequence_contain_all_unknowns
{