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1 package Bio::Roary::SequenceLengths;
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2
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3 # ABSTRACT: Take in a fasta file and create a hash with the length of each sequence
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4
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5 =head1 SYNOPSIS
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6
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7 Add labels to the groups
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8 use Bio::Roary::SequenceLengths;
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9
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10 my $obj = Bio::Roary::SequenceLengths->new(
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11 fasta_file => 'abc.fa',
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12 );
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13 $obj->sequence_lengths;
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14
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15 =cut
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16
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17 use Moose;
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18 use Bio::SeqIO;
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19 use Bio::Roary::Exceptions;
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20
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21 has 'fasta_file' => ( is => 'ro', isa => 'Str', required => 1 );
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22 has 'sequence_lengths' => ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_build_sequence_lengths' );
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23 has '_input_seqio' => ( is => 'ro', isa => 'Bio::SeqIO', lazy => 1, builder => '_build__input_seqio' );
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24
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25 sub _build__input_seqio {
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26 my ($self) = @_;
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27 return Bio::SeqIO->new( -file => $self->fasta_file, -format => 'Fasta' );
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28 }
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29
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30 sub _build_sequence_lengths {
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31 my ($self) = @_;
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32
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33 my %sequence_lengths;
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34 while ( my $input_seq = $self->_input_seqio->next_seq() ) {
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35 $sequence_lengths{ $input_seq->display_id } = $input_seq->length();
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36 }
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37 return \%sequence_lengths;
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38 }
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39
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40 no Moose;
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41 __PACKAGE__->meta->make_immutable;
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42
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43 1;
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