/usr/share/perl5/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.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::RoaryReorderSpreadsheet;
$Bio::Roary::CommandLine::RoaryReorderSpreadsheet::VERSION = '3.8.0';
# ABSTRACT: Take in a tree and a spreadsheet and output a reordered spreadsheet
use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Bio::Roary::ReorderSpreadsheet;
extends 'Bio::Roary::CommandLine::Common';
has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 );
has 'help' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'tree_file' => ( is => 'rw', isa => 'Str' );
has 'spreadsheet_filename' => ( is => 'rw', isa => 'Str', default => 'gene_presence_absence.csv' );
has 'output_filename' => ( is => 'rw', isa => 'Str', default => 'reordered_spreadsheet.csv' );
has 'tree_format' => ( is => 'rw', isa => 'Str', default => 'newick' );
has 'search_strategy' => ( is => 'rw', isa => 'Str', default => 'depth' );
has 'sortby' => ( is => 'rw', isa => 'Str', default => 'height');
has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 );
sub BUILD {
my ($self) = @_;
my ( $output_filename, $tree_file,$search_strategy, $sortby, $tree_format, $spreadsheet_filename,$verbose, $help );
GetOptionsFromArray(
$self->args,
'o|output_filename=s' => \$output_filename,
't|tree_file=s' => \$tree_file,
'f|tree_format=s' => \$tree_format,
's|spreadsheet_filename=s' => \$spreadsheet_filename,
'a|search_strategy=s' => \$search_strategy,
'b|sortby=s' => \$sortby,
'v|verbose' => \$verbose,
'h|help' => \$help,
);
if ( defined($verbose) ) {
$self->verbose($verbose);
$self->logger->level(10000);
}
$self->help($help) if(defined($help));
$self->output_filename($output_filename) if ( defined($output_filename) );
$self->tree_file($tree_file) if ( defined($tree_file) );
$self->tree_format($tree_format) if ( defined($tree_format) );
$self->spreadsheet_filename($spreadsheet_filename) if ( defined($spreadsheet_filename) );
$self->sortby($sortby) if ( defined($sortby) );
$self->search_strategy($search_strategy) if ( defined($search_strategy) );
}
sub run {
my ($self) = @_;
( defined($self->spreadsheet_filename) && defined($self->tree_file) && ( -e $self->spreadsheet_filename ) && ( -e $self->tree_file ) && ( !$self->help ) ) or die $self->usage_text;
($self->sortby eq "height" || $self->sortby eq "creation" || $self->sortby eq "alpha" || $self->sortby eq "revalpha") or die $self->usage_text;
($self->search_strategy eq "breadth" || $self->search_strategy eq "depth") or die $self->usage_text;
my $obj = Bio::Roary::ReorderSpreadsheet->new(
tree_file => $self->tree_file,
spreadsheet => $self->spreadsheet_filename,
output_filename => $self->output_filename,
sortby => $self->sortby,
search_strategy => $self->search_strategy
);
$obj->reorder_spreadsheet();
}
sub usage_text {
my ($self) = @_;
return <<USAGE;
Usage: pan_genome_reorder_spreadsheet [options] -t tree.newick
Reorder the columns in the gene presence and absence spreadsheet against a phylogenetic tree.
Options: -t STR tree filename []
-o STR output filename [reordered_spreadsheet.csv]
-f STR tree format (newick/nexus/nhx/svggraph/tabtree/lintree) [newick]
-s STR input gene presence and absence spreadsheet [gene_presence_absence.csv]
-a STR search strategy (depth/breadth) [depth]
-b STR sorting method (height/creation/alpha/revalpha) [height]
-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::RoaryReorderSpreadsheet - Take in a tree and a spreadsheet and output a reordered spreadsheet
=head1 VERSION
version 3.8.0
=head1 SYNOPSIS
Take in a tree and a spreadsheet and output a reordered spreadsheet
=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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