--- /dev/null
+#!/usr/bin/perl
+# geo_downloader downloads expression files from GEO (NCBI)
+# and is released under the terms of the GNU GPL version 3, or any
+# later version, at your option. See the file README and COPYING for
+# more information.
+# Copyright 2013 by Don Armstrong <don@donarmstrong.com>.
+
+
+use warnings;
+use strict;
+
+use Getopt::Long;
+use Pod::Usage;
+
+=head1 NAME
+
+geo_downloader - downloads expression files from GEO (NCBI)
+
+=head1 SYNOPSIS
+
+geo_downloader [options] [GSE...]
+
+ Options:
+ --debug, -d debugging level (Default 0)
+ --help, -h display this help
+ --man, -m display manual
+
+=head1 OPTIONS
+
+=over
+
+=item B<--debug, -d>
+
+Debug verbosity. (Default 0)
+
+=item B<--help, -h>
+
+Display brief usage information.
+
+=item B<--man, -m>
+
+Display this manual.
+
+=back
+
+=head1 EXAMPLES
+
+geo_downloader GSE20400
+
+=cut
+
+
+use vars qw($DEBUG);
+use Net::FTP;
+
+my %options = (debug => 0,
+ help => 0,
+ man => 0,
+ host => 'ftp.ncbi.nlm.nih.gov',
+ );
+
+GetOptions(\%options,
+ 'debug|d+','help|h|?','man|m');
+
+pod2usage() if $options{help};
+pod2usage({verbose=>2}) if $options{man};
+
+$DEBUG = $options{debug};
+
+my @USAGE_ERRORS;
+if (not @ARGV) {
+ push @USAGE_ERRORS,"You must give at least one GEO accession";
+}
+
+if (@ARGV != grep {/^(gpl|gse|gsm|gds)\d+$/i} @ARGV) {
+ push @USAGE_ERRORS,"Invalid GEO accession(s): ".
+ join(',',grep {$_ !~ /^(gpl|gse|gsm)\d+$/} @ARGV);
+}
+
+
+pod2usage(join("\n",@USAGE_ERRORS)) if @USAGE_ERRORS;
+
+my $ftp = Net::FTP->new($options{host},Debug=>$DEBUG,Passive=>1) or
+ die "Unable to create new Net::FTP object";
+print STDERR "Connected\n" if $DEBUG;
+
+$ftp->login('anonymous') or
+ die "Unable to login";
+print STDERR "logged in\n" if $DEBUG;
+
+$ftp->binary();
+print STDERR "binary\n" if $DEBUG;
+
+
+
+for my $geo_acc (@ARGV) {
+ my $geo_directory = geo_directory($geo_acc);
+ $ftp->cwd($geo_directory);
+ print STDERR "changed to $geo_directory\n" if $DEBUG;
+ print STDERR "(really) changed to ".$ftp->pwd()."\n" if $DEBUG;
+ my @files = $ftp->ls();
+ print map {$_."\n"} @files;
+ print STDERR "transferred listing\n" if $DEBUG;
+}
+
+sub geo_directory {
+ my $geo_acc = shift;
+ $geo_acc = uc($geo_acc);
+ my $geo_acc_dir = $geo_acc;
+ $geo_acc_dir =~ s/\d{3}$/nnn/;
+ my $geo_type_dir = undef;
+ if ($geo_acc =~ /^GSE/) {
+ $geo_type_dir = 'series';
+ } elsif ($geo_acc =~ /^GDS/) {
+ $geo_type_dir = 'datasets';
+ } elsif ($geo_acc =~ /^GPL/) {
+ $geo_type_dir = 'platforms';
+ } elsif ($geo_acc =~ /^GSM/) {
+ $geo_type_dir = 'samples';
+ }
+ return "/geo/".$geo_type_dir.'/'.$geo_acc_dir.'/'.$geo_acc;
+}
+
+__END__