File Coverage

lib/Bio/MLST/OutputFasta.pm

Criterion	Covered	Total	%
statement	59	59	100.0
branch	11	12	91.6
condition	9	15	60.0
subroutine	11	11	100.0
pod	1	1	100.0
total	91	98	92.8

package Bio::MLST::OutputFasta;
# ABSTRACT: Take in two hashes, both containing sequence names and sequences and output fasta files.
$Bio::MLST::OutputFasta::VERSION = '2.1.1630910';


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
{
  my($self, $sequence) = @_;
  return 1 if($sequence =~ m/^N+$/);
  return 0;
}



no Moose;
__PACKAGE__->meta->make_immutable;
1;

__END__

=pod

=encoding UTF-8

=head1 NAME

Bio::MLST::OutputFasta - Take in two hashes, both containing sequence names and sequences and output fasta files.

=head1 VERSION

version 2.1.1630910

=head1 SYNOPSIS

Take in two hashes, both containing sequence names and sequences and output fasta files.

   use Bio::MLST::OutputFasta;

   my $output_fasta = Bio::MLST::OutputFasta->new(
     matching_sequences     => \%matching_sequences,
     non_matching_sequences => \%non_matching_sequences,
     output_directory => '/path/to/output',
     input_fasta_file => '/path/to/fasta'
   );
   $output_fasta->create_files();

=head1 METHODS

=head2 create_files

Create output fasta files.

=head1 AUTHOR

Andrew J. Page <[e-mail]>

=head1 COPYRIGHT AND LICENSE

This software is Copyright (c) 2012 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007

=cut