1 # Copyright (C) 2007-2011 Martin A. Hansen.
3 # This program is free software; you can redistribute it and/or
4 # modify it under the terms of the GNU General Public License
5 # as published by the Free Software Foundation; either version 2
6 # of the License, or (at your option) any later version.
8 # This program is distributed in the hope that it will be useful,
9 # but WITHOUT ANY WARRANTY; without even the implied warranty of
10 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
11 # GNU General Public License for more details.
13 # You should have received a copy of the GNU General Public License
14 # along with this program; if not, write to the Free Software
15 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
17 # http://www.gnu.org/copyleft/gpl.html
19 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
21 # This software is part of the Biopieces framework (www.biopieces.org).
23 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
27 # Error class for all exceptions to do with Filesys.
28 class FilesysError < StandardError; end
33 # Class method that returns a path to a unique temporary file.
34 # If no directory is specified reverts to the systems tmp directory.
35 def self.tmpfile(tmp_dir = ENV["TMPDIR"])
39 path = tmp_dir + [user, time + pid, pid].join("_") + ".tmp"
46 options = args.shift || {}
49 case options[:compress]
51 ios, = Open3.pipeline_w("gzip -f", out: file)
53 ios, = Open3.pipeline_w("bzip2 -c", out: file)
55 ios = File.open(file, mode, options)
61 case `file -L #{file}`
63 ios = IO.popen("gzip -cd #{file}")
65 ios = IO.popen("bzcat #{file}")
67 ios = File.open(file, mode, options)
99 # Iterator method for parsing entries.
101 while entry = get_entry do