Mercurial > repos > dereeper > roary_plots
view Roary/lib/Bio/Roary/Output/GroupMultifasta.pm @ 0:c47a5f61bc9f draft
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author | dereeper |
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date | Fri, 14 May 2021 20:27:06 +0000 |
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package Bio::Roary::Output::GroupMultifasta; # ABSTRACT: Take in a group and create a multifasta file =head1 SYNOPSIS Take in a group and create a multifasta file use Bio::Roary::Output::GroupMultifasta; my $obj = Bio::Roary::Output::GroupMultifasta->new( group_name => 'aaa', analyse_groups => $analyse_groups, output_filename_base => 'abc' ); $obj->create_file(); =cut use Moose; use Bio::SeqIO; use Bio::Roary::Exceptions; use Bio::Roary::AnalyseGroups; has 'group_name' => ( is => 'ro', isa => 'Str', required => 1 ); has 'analyse_groups' => ( is => 'ro', isa => 'Bio::Roary::AnalyseGroups', required => 1 ); has 'output_filename_base' => ( is => 'ro', isa => 'Str', default => 'output_groups' ); has '_genes' => ( is => 'ro', isa => 'ArrayRef', lazy => 1, builder => '_build__genes' ); has '_output_seq_io' => ( is => 'ro', lazy => 1, builder => '_build__output_seq_io' ); sub _build__output_seq_io { my ($self) = @_; my $output_name = $self->output_filename_base . '_' . $self->group_name; $output_name =~ s!\W!_!g; $output_name .= '.fa'; return Bio::SeqIO->new( -file => ">" . $output_name, -format => 'Fasta' ); } sub _build__genes { my ($self) = @_; return $self->analyse_groups->_groups_to_genes->{ $self->group_name }; } sub _lookup_sequence { my ( $self, $gene, $filename ) = @_; return undef if(! defined($filename)); my $fasta_obj = Bio::SeqIO->new( -file => $filename, -format => 'Fasta' ); while ( my $seq = $fasta_obj->next_seq() ) { next unless ( $seq->display_id eq $gene ); return $seq; } return undef; } sub create_file { my ($self) = @_; for my $gene ( @{ $self->_genes } ) { my $seq = $self->_lookup_sequence( $gene, $self->analyse_groups->_genes_to_file->{$gene} ); next unless ( defined($seq) ); $self->_output_seq_io->write_seq($seq); } 1; } no Moose; __PACKAGE__->meta->make_immutable; 1;