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1 package Bio::Roary::AccessoryBinaryFasta;
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2
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3 # ABSTRACT: Output a FASTA file which represents the binary presence and absence of genes in the accessory genome
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4
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5 =head1 SYNOPSIS
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6
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7 Output a FASTA file which represents the binary presence and absence of genes in the accessory genome
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8 use Bio::Roary::AccessoryBinaryFasta;
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9 my $obj = Bio::Roary::AccessoryBinaryFasta->new(input_files => ['abc','efg'],
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10 groups_to_files => {'group_1' => ['abc'], group_2 => ['abc', 'efg']}
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11 );
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12 $obj->create_accessory_binary_fasta();
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13 =cut
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14
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15 use Moose;
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16 use POSIX;
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17 use Bio::Roary::AnnotateGroups;
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18 use Bio::Roary::AnalyseGroups;
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19 use Bio::Roary::Exceptions;
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20 use Bio::SeqIO;
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21 use File::Basename;
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22
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23 has 'input_files' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
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24 has 'annotate_groups_obj' => ( is => 'ro', isa => 'Bio::Roary::AnnotateGroups', required => 1 );
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25 has 'analyse_groups_obj' => ( is => 'ro', isa => 'Bio::Roary::AnalyseGroups', required => 1 );
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26 has 'output_filename' => ( is => 'ro', isa => 'Str', default => 'accessory_binary_genes.fa' );
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27 has 'lower_bound_percentage' => ( is => 'ro', isa => 'Int', default => 5 );
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28 has 'upper_bound_percentage' => ( is => 'ro', isa => 'Int', default => 5 );
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29 has 'max_accessory_to_include' => ( is => 'ro', isa => 'Int', default => 4000 );
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30 has 'groups_to_files' => ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_build__groups_to_files' );
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31 has '_lower_bound_value' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build__lower_bound_value' );
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32 has '_upper_bound_value' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build__upper_bound_value' );
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33
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34 sub _build__groups_to_files {
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35 my ($self) = @_;
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36 my %groups_to_files;
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37 for my $group ( @{ $self->annotate_groups_obj->_groups } ) {
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38 my $genes = $self->annotate_groups_obj->_groups_to_id_names->{$group};
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39 my %filenames;
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40 for my $gene_name ( @{$genes} ) {
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41 my $filename = $self->analyse_groups_obj->_genes_to_file->{$gene_name};
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42 push( @{ $filenames{$filename} }, $gene_name );
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43 }
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44 $groups_to_files{$group} = \%filenames;
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45 }
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46
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47 return \%groups_to_files;
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48 }
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49
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50 sub _build__lower_bound_value {
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51 my ($self) = @_;
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52 my $num_files = @{ $self->input_files };
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53 return ceil( $num_files * ( $self->lower_bound_percentage / 100 ) );
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54 }
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55
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56 sub _build__upper_bound_value {
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57 my ($self) = @_;
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58 my $num_files = @{ $self->input_files };
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59 return $num_files - ceil( $num_files * ( $self->upper_bound_percentage / 100 ) );
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60 }
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61
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62 sub create_accessory_binary_fasta {
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63 my ($self) = @_;
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64 my $out_seq_io = Bio::SeqIO->new( -file => ">" . $self->output_filename, -format => 'Fasta' );
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65
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66 for my $full_filename ( @{ $self->input_files } ) {
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67 my($filename, $dirs, $suffix) = fileparse($full_filename);
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68
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69 my $output_sequence = '';
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70 my $sample_name = $filename;
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71 $sample_name =~ s!\.gff\.proteome\.faa!!;
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72
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73 my $gene_count = 0;
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74 for my $group ( sort keys %{ $self->groups_to_files } ) {
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75 last if($gene_count > $self->max_accessory_to_include);
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76
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77 my @files = keys %{ $self->groups_to_files->{$group} };
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78
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79 next if ( @files <= $self->_lower_bound_value || @files > $self->_upper_bound_value );
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80
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81 my $group_to_file_genes = $self->groups_to_files->{$group}->{$full_filename};
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82 if ( defined($group_to_file_genes) && @{$group_to_file_genes} > 0 ) {
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83 $output_sequence .= 'A';
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84 }
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85 else {
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86 $output_sequence .= 'C';
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87 }
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88 $gene_count++;
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89
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90 }
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91 next if($output_sequence eq '');
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92 $out_seq_io->write_seq( Bio::Seq->new( -display_id => $sample_name, -seq => $output_sequence ) );
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93 }
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94 return 1;
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95 }
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96
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97 no Moose;
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98 __PACKAGE__->meta->make_immutable;
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99
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100 1;
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