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1 package Bio::Roary::Output::GroupMultifasta;
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2
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3 # ABSTRACT: Take in a group and create a multifasta file
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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 group and create a multifasta file
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8 use Bio::Roary::Output::GroupMultifasta;
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9
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10 my $obj = Bio::Roary::Output::GroupMultifasta->new(
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11 group_name => 'aaa',
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12 analyse_groups => $analyse_groups,
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13 output_filename_base => 'abc'
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14 );
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15 $obj->create_file();
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16
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17 =cut
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18
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19 use Moose;
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20 use Bio::SeqIO;
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21 use Bio::Roary::Exceptions;
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22 use Bio::Roary::AnalyseGroups;
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23
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24 has 'group_name' => ( is => 'ro', isa => 'Str', required => 1 );
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25 has 'analyse_groups' => ( is => 'ro', isa => 'Bio::Roary::AnalyseGroups', required => 1 );
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26 has 'output_filename_base' => ( is => 'ro', isa => 'Str', default => 'output_groups' );
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27 has '_genes' => ( is => 'ro', isa => 'ArrayRef', lazy => 1, builder => '_build__genes' );
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28 has '_output_seq_io' => ( is => 'ro', lazy => 1, builder => '_build__output_seq_io' );
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29
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30 sub _build__output_seq_io {
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31 my ($self) = @_;
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32 my $output_name = $self->output_filename_base . '_' . $self->group_name;
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33 $output_name =~ s!\W!_!g;
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34 $output_name .= '.fa';
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35 return Bio::SeqIO->new( -file => ">" . $output_name, -format => 'Fasta' );
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36 }
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37
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38 sub _build__genes {
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39 my ($self) = @_;
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40 return $self->analyse_groups->_groups_to_genes->{ $self->group_name };
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41 }
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42
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43 sub _lookup_sequence {
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44 my ( $self, $gene, $filename ) = @_;
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45 return undef if(! defined($filename));
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46 my $fasta_obj = Bio::SeqIO->new( -file => $filename, -format => 'Fasta' );
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47 while ( my $seq = $fasta_obj->next_seq() ) {
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48 next unless ( $seq->display_id eq $gene );
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49 return $seq;
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50 }
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51 return undef;
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52 }
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53
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54 sub create_file {
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55 my ($self) = @_;
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56 for my $gene ( @{ $self->_genes } ) {
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57 my $seq = $self->_lookup_sequence( $gene, $self->analyse_groups->_genes_to_file->{$gene} );
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58 next unless ( defined($seq) );
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59 $self->_output_seq_io->write_seq($seq);
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60 }
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61
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62 1;
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63 }
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64
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65 no Moose;
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66 __PACKAGE__->meta->make_immutable;
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67
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68 1;
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69
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