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view Roary/lib/Bio/Roary/ParseGFFAnnotationRole.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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package Bio::Roary::ParseGFFAnnotationRole; # ABSTRACT: A role for parsing a gff file efficiently =head1 SYNOPSIS with 'Bio::Roary::ParseGFFAnnotationRole'; =cut use Moose::Role; use Bio::Tools::GFF; has 'gff_file' => ( is => 'ro', isa => 'Str', required => 1 ); has '_tags_to_filter' => ( is => 'ro', isa => 'Str', default => 'CDS' ); has '_gff_parser' => ( is => 'ro', isa => 'Bio::Tools::GFF', lazy => 1, builder => '_build__gff_parser' ); has '_awk_filter' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build__awk_filter' ); sub _gff_fh_input_string { my ($self) = @_; return 'sed -n \'/##gff-version 3/,/^>/p\' '.$self->gff_file.'| grep -v \'^>\''." | " . $self->_awk_filter; } sub _build__awk_filter { my ($self) = @_; return 'awk \'BEGIN {FS="\t"};{ if ($3 ~/' . $self->_tags_to_filter . '/) print $9;}\' '; } 1;