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comparison Roary/lib/Bio/Roary/ParseGFFAnnotationRole.pm @ 0:c47a5f61bc9f draft

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author dereeper
date Fri, 14 May 2021 20:27:06 +0000
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-1:000000000000 0:c47a5f61bc9f
1 package Bio::Roary::ParseGFFAnnotationRole;
2
3 # ABSTRACT: A role for parsing a gff file efficiently
4
5 =head1 SYNOPSIS
6
7 with 'Bio::Roary::ParseGFFAnnotationRole';
8
9 =cut
10 use Moose::Role;
11 use Bio::Tools::GFF;
12
13 has 'gff_file' => ( is => 'ro', isa => 'Str', required => 1 );
14
15 has '_tags_to_filter' => ( is => 'ro', isa => 'Str', default => 'CDS' );
16 has '_gff_parser' => ( is => 'ro', isa => 'Bio::Tools::GFF', lazy => 1, builder => '_build__gff_parser' );
17 has '_awk_filter' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build__awk_filter' );
18
19 sub _gff_fh_input_string {
20 my ($self) = @_;
21 return 'sed -n \'/##gff-version 3/,/^>/p\' '.$self->gff_file.'| grep -v \'^>\''." | " . $self->_awk_filter;
22 }
23
24 sub _build__awk_filter {
25 my ($self) = @_;
26 return
27 'awk \'BEGIN {FS="\t"};{ if ($3 ~/'
28 . $self->_tags_to_filter
29 . '/) print $9;}\' ';
30 }
31
32 1;