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comparison Roary/lib/Bio/Roary/Output/GroupMultifasta.pm @ 0:c47a5f61bc9f draft

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author dereeper
date Fri, 14 May 2021 20:27:06 +0000
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-1:000000000000 0:c47a5f61bc9f
1 package Bio::Roary::Output::GroupMultifasta;
2
3 # ABSTRACT: Take in a group and create a multifasta file
4
5 =head1 SYNOPSIS
6
7 Take in a group and create a multifasta file
8 use Bio::Roary::Output::GroupMultifasta;
9
10 my $obj = Bio::Roary::Output::GroupMultifasta->new(
11 group_name => 'aaa',
12 analyse_groups => $analyse_groups,
13 output_filename_base => 'abc'
14 );
15 $obj->create_file();
16
17 =cut
18
19 use Moose;
20 use Bio::SeqIO;
21 use Bio::Roary::Exceptions;
22 use Bio::Roary::AnalyseGroups;
23
24 has 'group_name' => ( is => 'ro', isa => 'Str', required => 1 );
25 has 'analyse_groups' => ( is => 'ro', isa => 'Bio::Roary::AnalyseGroups', required => 1 );
26 has 'output_filename_base' => ( is => 'ro', isa => 'Str', default => 'output_groups' );
27 has '_genes' => ( is => 'ro', isa => 'ArrayRef', lazy => 1, builder => '_build__genes' );
28 has '_output_seq_io' => ( is => 'ro', lazy => 1, builder => '_build__output_seq_io' );
29
30 sub _build__output_seq_io {
31 my ($self) = @_;
32 my $output_name = $self->output_filename_base . '_' . $self->group_name;
33 $output_name =~ s!\W!_!g;
34 $output_name .= '.fa';
35 return Bio::SeqIO->new( -file => ">" . $output_name, -format => 'Fasta' );
36 }
37
38 sub _build__genes {
39 my ($self) = @_;
40 return $self->analyse_groups->_groups_to_genes->{ $self->group_name };
41 }
42
43 sub _lookup_sequence {
44 my ( $self, $gene, $filename ) = @_;
45 return undef if(! defined($filename));
46 my $fasta_obj = Bio::SeqIO->new( -file => $filename, -format => 'Fasta' );
47 while ( my $seq = $fasta_obj->next_seq() ) {
48 next unless ( $seq->display_id eq $gene );
49 return $seq;
50 }
51 return undef;
52 }
53
54 sub create_file {
55 my ($self) = @_;
56 for my $gene ( @{ $self->_genes } ) {
57 my $seq = $self->_lookup_sequence( $gene, $self->analyse_groups->_genes_to_file->{$gene} );
58 next unless ( defined($seq) );
59 $self->_output_seq_io->write_seq($seq);
60 }
61
62 1;
63 }
64
65 no Moose;
66 __PACKAGE__->meta->make_immutable;
67
68 1;
69