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/usr/bin/roary-query_pan_genome is in roary 3.8.0+dfsg-1.

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#!/usr/bin/env perl

package Bio::Roary::Main::QueryRoary;
$Bio::Roary::Main::QueryRoary::VERSION = '3.8.0';
# ABSTRACT: Take in a groups file and the protein fasta files and output selected data
# PODNAME: query_pan_genome


use Cwd qw(abs_path); 
BEGIN { unshift( @INC, abs_path('./lib') ) }
BEGIN { unshift( @INC, abs_path('./t/lib') ) }
use Bio::Roary::CommandLine::QueryRoary;

Bio::Roary::CommandLine::QueryRoary->new(args => \@ARGV, script_name => $0)->run;

__END__

=pod

=encoding UTF-8

=head1 NAME

query_pan_genome - Take in a groups file and the protein fasta files and output selected data

=head1 VERSION

version 3.8.0

=head1 SYNOPSIS

Take in a groups file and the protein fasta files and output selected data

=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