File Coverage

lib/Bio/Roary/SequenceLengths.pm

Criterion	Covered	Total	%
statement	19	19	100.0
branch			n/a
condition			n/a
subroutine	6	6	100.0
pod			n/a
total	25	25	100.0

package Bio::Roary::SequenceLengths;
$Bio::Roary::SequenceLengths::VERSION = '3.11.0';
# ABSTRACT:  Take in a fasta file and create a hash with the length of each sequence


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;

__END__

=pod

=encoding UTF-8

=head1 NAME

Bio::Roary::SequenceLengths - Take in a fasta file and create a hash with the length of each sequence

=head1 VERSION

version 3.11.0

=head1 SYNOPSIS

Add labels to the groups
   use Bio::Roary::SequenceLengths;

   my $obj = Bio::Roary::SequenceLengths->new(
     fasta_file   => 'abc.fa',
   );
   $obj->sequence_lengths;

=head1 AUTHOR

Andrew J. Page <[e-mail]>

=head1 COPYRIGHT AND LICENSE

This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007

=cut