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1 package Bio::Roary::ParseGFFAnnotationRole;
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2
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3 # ABSTRACT: A role for parsing a gff file efficiently
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4
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5 =head1 SYNOPSIS
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6
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7 with 'Bio::Roary::ParseGFFAnnotationRole';
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8
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9 =cut
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10 use Moose::Role;
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11 use Bio::Tools::GFF;
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12
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13 has 'gff_file' => ( is => 'ro', isa => 'Str', required => 1 );
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14
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15 has '_tags_to_filter' => ( is => 'ro', isa => 'Str', default => 'CDS' );
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16 has '_gff_parser' => ( is => 'ro', isa => 'Bio::Tools::GFF', lazy => 1, builder => '_build__gff_parser' );
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17 has '_awk_filter' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build__awk_filter' );
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18
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19 sub _gff_fh_input_string {
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20 my ($self) = @_;
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21 return 'sed -n \'/##gff-version 3/,/^>/p\' '.$self->gff_file.'| grep -v \'^>\''." | " . $self->_awk_filter;
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22 }
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23
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24 sub _build__awk_filter {
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25 my ($self) = @_;
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26 return
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27 'awk \'BEGIN {FS="\t"};{ if ($3 ~/'
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28 . $self->_tags_to_filter
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29 . '/) print $9;}\' ';
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30 }
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31
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32 1;
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