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1 package Bio::Roary::ChunkFastaFile;
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2
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3 # ABSTRACT: Take in a FASTA file and chunk it up into smaller pieces.
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4
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5 =head1 SYNOPSIS
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6
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7 Take in a FASTA file and chunk it up into smaller pieces.
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8 use Bio::Roary::ChunkFastaFile;
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9
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10 my $obj = Bio::Roary::ChunkFastaFile->new(
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11 fasta_file => 'abc.fa',
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12 );
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13 $obj->sequence_file_names;
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14
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15 =cut
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16
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17 use Moose;
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18 use Bio::SeqIO;
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19 use Bio::Roary::Exceptions;
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20 use Cwd;
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21 use File::Temp;
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22
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23 has 'fasta_file' => ( is => 'ro', isa => 'Str', required => 1 );
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24 has 'target_chunk_size' => ( is => 'ro', isa => 'Int', default => 200000 );
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25 has 'sequence_file_names' => ( is => 'ro', isa => 'ArrayRef', lazy => 1, builder => '_build_sequence_file_names' );
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26 has '_working_directory' =>
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27 ( is => 'ro', isa => 'File::Temp::Dir', default => sub { File::Temp->newdir( DIR => getcwd, CLEANUP => 1 ); } );
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28 has '_working_directory_name' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build__working_directory_name' );
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29 has '_input_seqio' => ( is => 'ro', isa => 'Bio::SeqIO', lazy => 1, builder => '_build__input_seqio' );
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30
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31 sub _build__working_directory_name {
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32 my ($self) = @_;
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33 return $self->_working_directory->dirname();
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34 }
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35
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36 sub _build__input_seqio {
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37 my ($self) = @_;
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38 return Bio::SeqIO->new( -file => $self->fasta_file, -format => 'Fasta' );
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39 }
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40
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41 sub _create_next_chunk_file_name {
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42 my ( $self, $chunk_number ) = @_;
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43 return join( '/', ( $self->_working_directory_name, $chunk_number . '.seq' ) );
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44 }
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45
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46 sub _create_next_chunk_seqio {
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47 my ( $self, $chunk_number ) = @_;
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48 return Bio::SeqIO->new( -file => ">".$self->_create_next_chunk_file_name($chunk_number), -format => 'Fasta' );
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49 }
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50
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51 sub _build_sequence_file_names {
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52 my ($self) = @_;
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53 my @sequence_file_names;
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54 my $chunk_number = 0;
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55 my $current_chunk_length = 0;
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56 my $current_chunk_seqio = $self->_create_next_chunk_seqio($chunk_number);
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57 push( @sequence_file_names, $self->_create_next_chunk_file_name($chunk_number) );
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58
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59 while ( my $input_seq = $self->_input_seqio->next_seq() ) {
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60 if ( $current_chunk_length > $self->target_chunk_size ) {
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61
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62 # next chunk
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63 $chunk_number++;
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64 $current_chunk_length = 0;
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65 $current_chunk_seqio = $self->_create_next_chunk_seqio($chunk_number);
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66 push( @sequence_file_names, $self->_create_next_chunk_file_name($chunk_number) );
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67 }
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68 $current_chunk_seqio->write_seq($input_seq);
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69 $current_chunk_length += $input_seq->length();
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70 }
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71 return \@sequence_file_names;
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72 }
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73
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74 no Moose;
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75 __PACKAGE__->meta->make_immutable;
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76
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77 1;
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