AJPAGE / Bio-MLST-Check-2.1.1706216 / bin / download_fasta_database 

            

              
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#!/usr/bin/env perl
package Bio::MLST::Bin::Download;
$Bio::MLST::Bin::Download::VERSION = '2.1.1706216';
# ABSTRACT: Downloads all the MLST databases to disk. It requires access to the Internet.
# PODNAME: download_mlst_databases
BEGIN { unshift( @INC, '../lib' ) }
use lib "/software/pathogen/internal/prod/lib";
use Moose;
use Getopt::Long;
use Bio::MLST::CDC::Convert;
my ($config_file, $base_directory,$url, $species,$gene_name, $help, $version);
GetOptions ('u|url=s'            => \$url,
            'b|base_directory=s' => \$base_directory,
            's|species=s',       => \$species,
            'g|gene_name=s',     => \$gene_name,
            'h|help'             => \$help,
            'v|version'          => \$version,
);
(! $version ) or die "$0 version " . Bio::MLST::Bin::Download->VERSION . "\n";
(! $help)or die <<USAGE;
Usage: $0 [options]
Downloads all the MLST databases to disk
# download everything with defaults
download_mlst_databases
# print version information
download_mlst_databases -v
# XML file containing details of the MLST databases (from pubmlst)
download_mlst_databases -c my_config_file.json
# Pass in a different url to download
download_mlst_databases -u http://example.com/myfasta.fa
# destination base directory defaults to the environment variable \$MLST_DATABASES
download_mlst_databases -b /path/to/destination
USAGE
;
$base_directory ||= $ENV{MLST_DATABASES};
$base_directory ||= '/lustre/scratch108/pathogen/pathpipe/mlst';
$url  ||= 'ftp://ftp.cdc.gov/pub/infectious_diseases/biotech/tsemm/tofasta.tfa';
$species     ||= 'Streptococcus pyogenes emm';
$gene_name   ||= 'emm';
my $convert_fasta = Bio::MLST::CDC::Convert->new(
  species        => $species,
  input_file     => $url,
  gene_name      => $gene_name,
  base_directory => $base_directory
  );
$convert_fasta->create_mlst_files();
__END__
=pod
=encoding UTF-8
=head1 NAME
download_mlst_databases - Downloads all the MLST databases to disk. It requires access to the Internet.
=head1 VERSION
version 2.1.1706216
=head1 SYNOPSIS
Downloads all the MLST databases to disk. It requires access to the Internet.
    # download everything with defaults
    download_mlst_databases
    # print version information
    download_mlst_databases -v
    # XML file containing details of the MLST databases (from pubmlst)
    download_mlst_databases -c my_config_file.json
  
    # Pass in a different url to download
    download_mlst_databases -u http://example.com/myfasta.fa
    # destination base directory defaults to the environment variable \$MLST_DATABASES
    download_mlst_databases -b /path/to/destination
=head1 AUTHOR
Andrew J. Page <ap13@sanger.ac.uk>
=head1 COPYRIGHT AND LICENSE
This software is Copyright (c) 2012 by Wellcome Trust Sanger Institute.
This is free software, licensed under:
  The GNU General Public License, Version 3, June 2007
=cut