/usr/share/perl5/Bio/Roary/PrepareInputFiles.pm is in roary 3.8.0+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 | package Bio::Roary::PrepareInputFiles;
$Bio::Roary::PrepareInputFiles::VERSION = '3.8.0';
# ABSTRACT: Take in a mixture of FASTA and GFF input files and output FASTA proteomes only
use Moose;
use Bio::Roary::Exceptions;
use Bio::Roary::ExtractProteomeFromGFFs;
use Bio::Roary::FilterUnknownsFromFasta;
use Cwd qw(getcwd);
use File::Temp;
has 'input_files' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'job_runner' => ( is => 'ro', isa => 'Str', default => 'Local' );
has 'cpus' => ( is => 'ro', isa => 'Int', default => 1 );
has '_input_gff_files' => ( is => 'ro', isa => 'Maybe[ArrayRef]', lazy => 1, builder => '_build__input_gff_files' );
has '_input_fasta_files' => ( is => 'ro', isa => 'Maybe[ArrayRef]', lazy => 1, builder => '_build__input_fasta_files' );
has '_input_fasta_files_filtered' =>
( is => 'ro', isa => 'Maybe[ArrayRef]', lazy => 1, builder => '_build__input_fasta_files_filtered' );
has '_input_fasta_files_filtered_obj' =>
( is => 'ro', isa => 'Bio::Roary::FilterUnknownsFromFasta', lazy => 1, builder => '_build__input_fasta_files_filtered_obj' );
has '_derived_fasta_files' =>
( is => 'ro', isa => 'Maybe[ArrayRef]', lazy => 1, builder => '_build__derived_fasta_files' );
has '_extract_proteome_obj' => (
is => 'ro',
isa => 'Bio::Roary::ExtractProteomeFromGFFs',
lazy => 1,
builder => '_build__extract_proteome_obj'
);
has 'apply_unknowns_filter' => ( is => 'rw', isa => 'Bool', default => 1 );
has 'translation_table' => ( is => 'rw', isa => 'Int', default => 11 );
has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 );
has '_fasta_filter_obj' => ( is => 'ro', isa => 'Bio::Roary::FilterUnknowsFromFasta', lazy => 1, builder => '_fasta_filter_obj' );
has 'working_directory' => ( is => 'ro', isa => 'File::Temp::Dir', default => sub { File::Temp->newdir( DIR => getcwd, CLEANUP => 1 ); } );
sub _build__input_gff_files {
my ($self) = @_;
my @gff_files = grep( /\.gff$/, @{ $self->input_files } );
return \@gff_files;
}
sub _build__input_fasta_files {
my ($self) = @_;
my @fasta_files = grep( !/\.gff$/, @{ $self->input_files } );
return \@fasta_files;
}
sub _build__input_fasta_files_filtered_obj {
my ($self) = @_;
return Bio::Roary::FilterUnknownsFromFasta->new( fasta_files => $self->_input_fasta_files );
}
sub _build__input_fasta_files_filtered
{
my ($self) = @_;
return undef if ( !defined( $self->_input_fasta_files ) );
return $self->_input_fasta_files_filtered_obj->filtered_fasta_files();
}
sub _build__extract_proteome_obj {
my ($self) = @_;
return Bio::Roary::ExtractProteomeFromGFFs->new(
gff_files => $self->_input_gff_files,
job_runner => $self->job_runner,
apply_unknowns_filter => $self->apply_unknowns_filter,
translation_table => $self->translation_table,
cpus => $self->cpus,
verbose => $self->verbose,
working_directory => $self->working_directory,
);
}
sub _build__derived_fasta_files {
my ($self) = @_;
return undef if ( !defined( $self->_input_gff_files ) );
return $self->_extract_proteome_obj->fasta_files();
}
sub fasta_files {
my ($self) = @_;
my @output_fasta_files = ( @{ $self->_input_fasta_files_filtered }, @{ $self->_derived_fasta_files } );
return \@output_fasta_files;
}
sub lookup_fasta_files_from_unknown_input_files {
my ( $self, $input_files ) = @_;
$self->fasta_files;
my @output_fasta_files;
for my $input_file ( @{$input_files} ) {
if ( defined( $self->_extract_proteome_obj->fasta_files_to_gff_files->{$input_file} ) ) {
push( @output_fasta_files, $self->_extract_proteome_obj->fasta_files_to_gff_files->{$input_file} );
}
else {
push( @output_fasta_files, $self->_input_fasta_files_filtered_obj->input_fasta_to_output_fasta->{$input_file} );
}
}
return \@output_fasta_files;
}
no Moose;
__PACKAGE__->meta->make_immutable;
1;
__END__
=pod
=encoding UTF-8
=head1 NAME
Bio::Roary::PrepareInputFiles - Take in a mixture of FASTA and GFF input files and output FASTA proteomes only
=head1 VERSION
version 3.8.0
=head1 SYNOPSIS
Take in a mixture of FASTA and GFF input files and output FASTA proteomes only
use Bio::Roary::PrepareInputFiles;
my $obj = Bio::Roary::PrepareInputFiles->new(
input_files => ['abc.gff','ddd.faa'],
);
$obj->fasta_files;
=head1 AUTHOR
Andrew J. Page <ap13@sanger.ac.uk>
=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
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