Mercurial > repos > dereeper > roary_plots
diff Roary/lib/Bio/Roary/SequenceLengths.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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Roary/lib/Bio/Roary/SequenceLengths.pm Fri May 14 20:27:06 2021 +0000 @@ -0,0 +1,43 @@ +package Bio::Roary::SequenceLengths; + +# ABSTRACT: Take in a fasta file and create a hash with the length of each sequence + +=head1 SYNOPSIS + +Add labels to the groups + use Bio::Roary::SequenceLengths; + + my $obj = Bio::Roary::SequenceLengths->new( + fasta_file => 'abc.fa', + ); + $obj->sequence_lengths; + +=cut + +use Moose; +use Bio::SeqIO; +use Bio::Roary::Exceptions; + +has 'fasta_file' => ( is => 'ro', isa => 'Str', required => 1 ); +has 'sequence_lengths' => ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_build_sequence_lengths' ); +has '_input_seqio' => ( is => 'ro', isa => 'Bio::SeqIO', lazy => 1, builder => '_build__input_seqio' ); + +sub _build__input_seqio { + my ($self) = @_; + return Bio::SeqIO->new( -file => $self->fasta_file, -format => 'Fasta' ); +} + +sub _build_sequence_lengths { + my ($self) = @_; + + my %sequence_lengths; + while ( my $input_seq = $self->_input_seqio->next_seq() ) { + $sequence_lengths{ $input_seq->display_id } = $input_seq->length(); + } + return \%sequence_lengths; +} + +no Moose; +__PACKAGE__->meta->make_immutable; + +1;