/usr/share/perl5/Bio/Roary/CommandLine/RoaryPostAnalysis.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.
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package Bio::Roary::CommandLine::RoaryPostAnalysis;
$Bio::Roary::CommandLine::RoaryPostAnalysis::VERSION = '3.8.0';
# ABSTRACT: Perform the post analysis on the pan genome
use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Bio::Roary::PostAnalysis;
use File::Find::Rule;
use Bio::Roary::External::GeneAlignmentFromNucleotides;
use File::Path qw(remove_tree);
use Bio::Roary::External::Fasttree;
extends 'Bio::Roary::CommandLine::Common';
has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 );
has 'help' => ( is => 'rw', isa => 'Bool', default => 0 );
has '_error_message' => ( is => 'rw', isa => 'Str' );
has 'fasta_files' => ( is => 'rw', isa => 'Str', default => '_fasta_files' );
has 'input_files' => ( is => 'rw', isa => 'Str', default => '_gff_files');
has 'output_filename' => ( is => 'rw', isa => 'Str', default => 'clustered_proteins' );
has 'output_pan_geneome_filename' => ( is => 'rw', isa => 'Str', default => 'pan_genome.fa' );
has 'output_statistics_filename' => ( is => 'rw', isa => 'Str', default => 'gene_presence_absence.csv' );
has 'output_multifasta_files' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'clusters_filename' => ( is => 'rw', isa => 'Str', default => '_clustered.clstr' );
has 'job_runner' => ( is => 'rw', isa => 'Str', default => 'Local' );
has 'cpus' => ( is => 'rw', isa => 'Int', default => 1 );
has 'dont_delete_files' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'dont_create_rplots' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'dont_split_groups' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'verbose_stats' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'translation_table' => ( is => 'rw', isa => 'Int', default => 11 );
has 'group_limit' => ( is => 'rw', isa => 'Num', default => 50000 );
has 'core_definition' => ( is => 'rw', isa => 'Num', default => 0.99 );
has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'mafft' => ( is => 'rw', isa => 'Bool', default => 0 );
sub BUILD {
my ($self) = @_;
my (
$output_filename, $dont_create_rplots, $dont_delete_files, $dont_split_groups, $output_pan_geneome_filename,
$job_runner, $output_statistics_filename, $output_multifasta_files, $clusters_filename, $core_definition,
$fasta_files, $input_files, $verbose_stats, $translation_table, $help, $cpus,$group_limit,$verbose,$mafft
);
GetOptionsFromArray(
$self->args,
'o|output=s' => \$output_filename,
'j|job_runner=s' => \$job_runner,
'm|output_multifasta_files' => \$output_multifasta_files,
'p=s' => \$output_pan_geneome_filename,
's=s' => \$output_statistics_filename,
'c=s' => \$clusters_filename,
'f=s' => \$fasta_files,
'i=s' => \$input_files,
'a|dont_delete_files' => \$dont_delete_files,
'b|dont_create_rplots' => \$dont_create_rplots,
'd|dont_split_groups' => \$dont_split_groups,
'e|verbose_stats' => \$verbose_stats,
'z|processors=i' => \$cpus,
't|translation_table=i' => \$translation_table,
'g|group_limit=i' => \$group_limit,
'cd|core_definition=f' => \$core_definition,
'v|verbose' => \$verbose,
'n|mafft' => \$mafft,
'h|help' => \$help,
);
$self->help($help) if(defined($help));
$self->job_runner($job_runner) if ( defined($job_runner) );
$self->fasta_files($fasta_files) if ( defined($fasta_files) );
$self->input_files($input_files) if ( defined($input_files) );
$self->output_filename($output_filename) if ( defined($output_filename) );
$self->output_pan_geneome_filename($output_pan_geneome_filename) if ( defined($output_pan_geneome_filename) );
$self->output_statistics_filename($output_statistics_filename) if ( defined($output_statistics_filename) );
$self->output_multifasta_files($output_multifasta_files) if ( defined($output_multifasta_files) );
$self->clusters_filename($clusters_filename) if ( defined($clusters_filename) );
$self->dont_delete_files($dont_delete_files) if ( defined($dont_delete_files) );
$self->dont_create_rplots($dont_create_rplots) if ( defined($dont_create_rplots) );
$self->dont_split_groups($dont_split_groups) if ( defined($dont_split_groups) );
$self->verbose_stats($verbose_stats) if ( defined($verbose_stats));
$self->translation_table($translation_table) if ( defined($translation_table) );
$self->cpus($cpus) if ( defined($cpus) );
$self->group_limit($group_limit) if ( defined($group_limit) );
$self->core_definition( $core_definition/100 ) if ( defined($core_definition) );
$self->mafft($mafft) if ( defined($mafft) );
if ( defined($verbose) ) {
$self->verbose($verbose);
$self->logger->level(10000);
}
}
sub run {
my ($self) = @_;
( !$self->help ) or die $self->usage_text;
if ( defined( $self->_error_message ) ) {
print $self->_error_message . "\n";
die $self->usage_text;
}
my $input_files = $self->_read_file_into_array($self->input_files);
my $obj = Bio::Roary::PostAnalysis->new(
fasta_files => $self->_read_file_into_array($self->fasta_files) ,
input_files => $input_files ,
output_filename => $self->output_filename ,
output_pan_geneome_filename => $self->output_pan_geneome_filename,
output_statistics_filename => $self->output_statistics_filename ,
output_multifasta_files => $self->output_multifasta_files ,
clusters_filename => $self->clusters_filename ,
dont_delete_files => $self->dont_delete_files,
dont_create_rplots => $self->dont_create_rplots,
dont_split_groups => $self->dont_split_groups,
verbose_stats => $self->verbose_stats,
group_limit => $self->group_limit,
verbose => $self->verbose,
cpus => $self->cpus,
logger => $self->logger,
core_definition => $self->core_definition,
);
$obj->run();
if($self->dont_delete_files == 0)
{
unlink('_inflated_unsplit_mcl_groups');
remove_tree('split_groups');
}
if($self->output_multifasta_files == 1)
{
print "Aligning each cluster\n" if($self->verbose);
my $job_runner_to_use = $self->job_runner;
if($self->_is_lsf_job_runner_available && $self->job_runner eq "LSF")
{
$job_runner_to_use = $self->job_runner;
}
else
{
$job_runner_to_use = 'Parallel';
}
my $output_gene_files = $self->_find_input_files;
my $seg = Bio::Roary::External::GeneAlignmentFromNucleotides->new(
fasta_files => $output_gene_files,
job_runner => $job_runner_to_use,
translation_table => $self->translation_table,
core_definition => $self->core_definition,
cpus => $self->cpus,
verbose => $self->verbose,
mafft => $self->mafft,
dont_delete_files => $self->dont_delete_files,
num_input_files => $#{$input_files},
);
$seg->run();
}
}
sub _is_lsf_job_runner_available
{
my ($self) = @_;
my $rc = eval "require Bio::Roary::JobRunner::LSF; 1;";
if(defined($rc) && $rc == 1)
{
return 1;
}
else
{
return 0;
}
}
sub _find_input_files
{
my ($self) = @_;
my @files = File::Find::Rule->file()
->name( '*.fa' )
->in('pan_genome_sequences' );
return \@files;
}
sub _read_file_into_array
{
my ($self, $filename) = @_;
open(my $in_fh, $filename);
my @filenames;
while(<$in_fh>){
chomp;
my $line = $_;
push(@filenames, $line);
}
return \@filenames;
}
sub usage_text {
my ($self) = @_;
return <<USAGE;
Usage: pan_genome_post_analysis [options]
Perform the post analysis on the pan genome. This script is usally only called by another script.
Options: -a dont delete intermediate files
-b dont create R plots
-c STR clusters filename [_clustered.clstr]
-cd FLOAT percentage of isolates a gene must be in to be core [0.99]
-d dont split groups
-e add inference values to gene presence and absence spreadsheet
-f STR file of protein filenames [_fasta_files]
-g INT maximum number of clusters [50000]
-i STR file of GFF filenames [_gff_files]
-m core gene alignement with PRANK
-n fast core gene alignement with MAFFT instead of PRANK
-o STR clusters output filename [clustered_proteins]
-p STR output pan genome filename [pan_genome.fa]
-s STR output gene presence and absence filename [gene_presence_absence.csv]
-t INT translation table [11]
-z INT number of threads [1]
-v verbose output to STDOUT
-h this help message
For further info see: http://sanger-pathogens.github.io/Roary/
USAGE
}
__PACKAGE__->meta->make_immutable;
no Moose;
1;
__END__
=pod
=encoding UTF-8
=head1 NAME
Bio::Roary::CommandLine::RoaryPostAnalysis - Perform the post analysis on the pan genome
=head1 VERSION
version 3.8.0
=head1 SYNOPSIS
Perform the post analysis on the pan genome
=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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