bio 1.2.1 → 1.3.0

data/sample/fastagrep.rb

@@ -0,0 +1,72 @@
+#!/usr/bin/env ruby
+#
+# fastagrep: Greps a FASTA file (in fact it can use any flat file input supported
+#            by BIORUBY) and outputs sorted FASTA
+#
+#   Copyright (C) 2008 KATAYAMA Toshiaki <k@bioruby.org> & Pjotr Prins
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  $Id: fastagrep.rb,v 1.1 2008/05/19 12:22:05 pjotr Exp $
+#
+
+require 'bio'
+
+include Bio
+
+usage = <<USAGE
+
+Usage: fastagrep.rb [--skip] [regex] infiles
+
+    -v            Invert the sense of matching, to select non-matching lines.
+
+  Examples:
+
+    Output all sequence descriptors containing 'Arabidopsis' or 'Drosophila'
+    regardless of case
+		
+	    fastagrep.rb "/Arabidopsis|Drosophila/i" *.seq > reduced.fasta
+
+    As the result is a FASTA stream you could pipe it for sorting:
+		
+	    fastagrep.rb "/Arabidopsis|Drosophila/i" *.seq | fastasort.rb
+USAGE
+
+if ARGV.size == 0
+  print usage
+	exit 1
+end
+
+skip = (ARGV[0] == '-v')
+ARGV.shift if skip
+
+# ---- Valid regular expression - if it is not a file
+regex = ARGV[0]
+if regex=~/^\// and !File.exist?(regex)
+  ARGV.shift
+else
+  print usage
+  exit 1
+end
+
+ARGV.each do | fn |
+  Bio::FlatFile.auto(fn).each do | item |
+    if skip
+  		next if eval("item.definition =~ #{regex}")
+    else
+  		next if eval("item.definition !~ #{regex}")
+    end
+    rec = Bio::FastaFormat.new('> '+item.definition.strip+"\n"+item.data)
+    print rec
+  end
+end
+
+

data/sample/fastasort.rb

@@ -0,0 +1,54 @@
+#!/usr/bin/env ruby
+#
+# fastasort: Sorts a FASTA file (in fact it can use any flat file input supported
+#            by BIORUBY) while modifying the definition of each record in the
+#            process so it is suitable for processing with (for example) pal2nal
+#            and PAML.
+#
+#   Copyright (C) 2008 KATAYAMA Toshiaki <k@bioruby.org> & Pjotr Prins
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  $Id: fastasort.rb,v 1.2 2008/05/19 12:22:05 pjotr Exp $
+#
+
+require 'bio'
+
+include Bio
+
+table = Hash.new   # table to sort objects
+ARGV.each do | fn |
+  Bio::FlatFile.auto(fn).each do | item |
+    # Some procession of the definition for external programs (just
+    # an example):
+
+    # strip JALView extension from definition e.g. .../1-212
+    if item.definition =~ /\/\d+-\d+$/
+      item.definition = $`
+    end
+    # substitute slashes:
+    definition = item.definition.gsub(/\//,'-')
+    # substitute quotes and ampersands:
+    definition = item.definition.gsub(/['"&]/,'x')
+    # prefix letters if the first position is a number:
+    definition = 'seq'+definition if definition =~ /^\d/
+
+    # Now add the data to the sort table
+    table[definition] = item.data
+  end
+end
+
+# Output sorted table
+table.sort.each do | definition, data |
+  rec = Bio::FastaFormat.new('> '+definition.strip+"\n"+data)
+  print rec
+end
+

data/sample/gb2fasta.rb

@@ -15,11 +15,10 @@
 #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #  GNU General Public License for more details.
 #
-#  $Id: gb2fasta.rb,v 0.5 2002/07/23 04:51:24 k Exp $
+#  $Id: gb2fasta.rb,v 0.6 2008/02/05 12:11:11 pjotr Exp $
 #
 
-require 'bio/io/flatfile'
-require 'bio/db/genbank'
+require 'bio'
 
 include Bio
 

data/sample/na2aa.rb

@@ -0,0 +1,34 @@
+#!/usr/bin/env ruby
+#
+# translate.rb - translate any NA input into AA FASTA format
+#
+#   Copyright (C) 2008 KATAYAMA Toshiaki <k@bioruby.org> & Pjotr Prins
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  $Id: na2aa.rb,v 1.1 2008/02/06 16:25:53 pjotr Exp $
+#
+
+require 'bio'
+require 'pp'
+
+include Bio
+
+ARGV.each do | fn |
+  Bio::FlatFile.auto(fn).each do | item |
+    seq = Sequence::NA.new(item.data)
+    aa = seq.translate
+    aa.gsub!(/X/,'-')
+    rec = Bio::FastaFormat.new('> '+item.definition+"\n"+aa)
+    print rec
+  end
+end
+

data/setup.rb

@@ -0,0 +1,1596 @@
+#
+# setup.rb
+#
+# Copyright (c) 2000-2006 Minero Aoki
+#
+# This program is free software.
+# You can distribute/modify this program under the terms of
+# the GNU LGPL, Lesser General Public License version 2.1.
+#
+
+unless Enumerable.method_defined?(:map)   # Ruby 1.4.6
+  module Enumerable
+    alias map collect
+  end
+end
+
+unless File.respond_to?(:read)   # Ruby 1.6
+  def File.read(fname)
+    open(fname) {|f|
+      return f.read
+    }
+  end
+end
+
+unless Errno.const_defined?(:ENOTEMPTY)   # Windows?
+  module Errno
+    class ENOTEMPTY
+      # We do not raise this exception, implementation is not needed.
+    end
+  end
+end
+
+def File.binread(fname)
+  open(fname, 'rb') {|f|
+    return f.read
+  }
+end
+
+# for corrupted Windows' stat(2)
+def File.dir?(path)
+  File.directory?((path[-1,1] == '/') ? path : path + '/')
+end
+
+
+class ConfigTable
+
+  include Enumerable
+
+  def initialize(rbconfig)
+    @rbconfig = rbconfig
+    @items = []
+    @table = {}
+    # options
+    @install_prefix = nil
+    @config_opt = nil
+    @verbose = true
+    @no_harm = false
+  end
+
+  attr_accessor :install_prefix
+  attr_accessor :config_opt
+
+  attr_writer :verbose
+
+  def verbose?
+    @verbose
+  end
+
+  attr_writer :no_harm
+
+  def no_harm?
+    @no_harm
+  end
+
+  def [](key)
+    lookup(key).resolve(self)
+  end
+
+  def []=(key, val)
+    lookup(key).set val
+  end
+
+  def names
+    @items.map {|i| i.name }
+  end
+
+  def each(&block)
+    @items.each(&block)
+  end
+
+  def key?(name)
+    @table.key?(name)
+  end
+
+  def lookup(name)
+    @table[name] or setup_rb_error "no such config item: #{name}"
+  end
+
+  def add(item)
+    @items.push item
+    @table[item.name] = item
+  end
+
+  def remove(name)
+    item = lookup(name)
+    @items.delete_if {|i| i.name == name }
+    @table.delete_if {|name, i| i.name == name }
+    item
+  end
+
+  def load_script(path, inst = nil)
+    if File.file?(path)
+      MetaConfigEnvironment.new(self, inst).instance_eval File.read(path), path
+    end
+  end
+
+  def savefile
+    '.config'
+  end
+
+  def load_savefile
+    begin
+      File.foreach(savefile()) do |line|
+        k, v = *line.split(/=/, 2)
+        self[k] = v.strip
+      end
+    rescue Errno::ENOENT
+      setup_rb_error $!.message + "\n#{File.basename($0)} config first"
+    end
+  end
+
+  def save
+    @items.each {|i| i.value }
+    File.open(savefile(), 'w') {|f|
+      @items.each do |i|
+        f.printf "%s=%s\n", i.name, i.value if i.value? and i.value
+      end
+    }
+  end
+
+  def load_standard_entries
+    standard_entries(@rbconfig).each do |ent|
+      add ent
+    end
+  end
+
+  def standard_entries(rbconfig)
+    c = rbconfig
+
+    rubypath = File.join(c['bindir'], c['ruby_install_name'] + c['EXEEXT'])
+
+    major = c['MAJOR'].to_i
+    minor = c['MINOR'].to_i
+    teeny = c['TEENY'].to_i
+    version = "#{major}.#{minor}"
+
+    # ruby ver. >= 1.4.4?
+    newpath_p = ((major >= 2) or
+                 ((major == 1) and
+                  ((minor >= 5) or
+                   ((minor == 4) and (teeny >= 4)))))
+
+    if c['rubylibdir']
+      # V > 1.6.3
+      libruby         = "#{c['prefix']}/lib/ruby"
+      librubyver      = c['rubylibdir']
+      librubyverarch  = c['archdir']
+      siteruby        = c['sitedir']
+      siterubyver     = c['sitelibdir']
+      siterubyverarch = c['sitearchdir']
+    elsif newpath_p
+      # 1.4.4 <= V <= 1.6.3
+      libruby         = "#{c['prefix']}/lib/ruby"
+      librubyver      = "#{c['prefix']}/lib/ruby/#{version}"
+      librubyverarch  = "#{c['prefix']}/lib/ruby/#{version}/#{c['arch']}"
+      siteruby        = c['sitedir']
+      siterubyver     = "$siteruby/#{version}"
+      siterubyverarch = "$siterubyver/#{c['arch']}"
+    else
+      # V < 1.4.4
+      libruby         = "#{c['prefix']}/lib/ruby"
+      librubyver      = "#{c['prefix']}/lib/ruby/#{version}"
+      librubyverarch  = "#{c['prefix']}/lib/ruby/#{version}/#{c['arch']}"
+      siteruby        = "#{c['prefix']}/lib/ruby/#{version}/site_ruby"
+      siterubyver     = siteruby
+      siterubyverarch = "$siterubyver/#{c['arch']}"
+    end
+    parameterize = lambda {|path|
+      path.sub(/\A#{Regexp.quote(c['prefix'])}/, '$prefix')
+    }
+
+    if arg = c['configure_args'].split.detect {|arg| /--with-make-prog=/ =~ arg }
+      makeprog = arg.sub(/'/, '').split(/=/, 2)[1]
+    else
+      makeprog = 'make'
+    end
+
+    [
+      ExecItem.new('installdirs', 'std/site/home',
+                   'std: install under libruby; site: install under site_ruby; home: install under $HOME')\
+          {|val, table|
+            case val
+            when 'std'
+              table['rbdir'] = '$librubyver'
+              table['sodir'] = '$librubyverarch'
+            when 'site'
+              table['rbdir'] = '$siterubyver'
+              table['sodir'] = '$siterubyverarch'
+            when 'home'
+              setup_rb_error '$HOME was not set' unless ENV['HOME']
+              table['prefix'] = ENV['HOME']
+              table['rbdir'] = '$libdir/ruby'
+              table['sodir'] = '$libdir/ruby'
+            end
+          },
+      PathItem.new('prefix', 'path', c['prefix'],
+                   'path prefix of target environment'),
+      PathItem.new('bindir', 'path', parameterize.call(c['bindir']),
+                   'the directory for commands'),
+      PathItem.new('libdir', 'path', parameterize.call(c['libdir']),
+                   'the directory for libraries'),
+      PathItem.new('datadir', 'path', parameterize.call(c['datadir']),
+                   'the directory for shared data'),
+      PathItem.new('mandir', 'path', parameterize.call(c['mandir']),
+                   'the directory for man pages'),
+      PathItem.new('sysconfdir', 'path', parameterize.call(c['sysconfdir']),
+                   'the directory for system configuration files'),
+      PathItem.new('localstatedir', 'path', parameterize.call(c['localstatedir']),
+                   'the directory for local state data'),
+      PathItem.new('libruby', 'path', libruby,
+                   'the directory for ruby libraries'),
+      PathItem.new('librubyver', 'path', librubyver,
+                   'the directory for standard ruby libraries'),
+      PathItem.new('librubyverarch', 'path', librubyverarch,
+                   'the directory for standard ruby extensions'),
+      PathItem.new('siteruby', 'path', siteruby,
+          'the directory for version-independent aux ruby libraries'),
+      PathItem.new('siterubyver', 'path', siterubyver,
+                   'the directory for aux ruby libraries'),
+      PathItem.new('siterubyverarch', 'path', siterubyverarch,
+                   'the directory for aux ruby binaries'),
+      PathItem.new('rbdir', 'path', '$siterubyver',
+                   'the directory for ruby scripts'),
+      PathItem.new('sodir', 'path', '$siterubyverarch',
+                   'the directory for ruby extentions'),
+      PathItem.new('rubypath', 'path', rubypath,
+                   'the path to set to #! line'),
+      ProgramItem.new('rubyprog', 'name', rubypath,
+                      'the ruby program using for installation'),
+      ProgramItem.new('makeprog', 'name', makeprog,
+                      'the make program to compile ruby extentions'),
+      SelectItem.new('shebang', 'all/ruby/never', 'ruby',
+                     'shebang line (#!) editing mode'),
+      BoolItem.new('without-ext', 'yes/no', 'no',
+                   'does not compile/install ruby extentions')
+    ]
+  end
+  private :standard_entries
+
+  def load_multipackage_entries
+    multipackage_entries().each do |ent|
+      add ent
+    end
+  end
+
+  def multipackage_entries
+    [
+      PackageSelectionItem.new('with', 'name,name...', '', 'ALL',
+                               'package names that you want to install'),
+      PackageSelectionItem.new('without', 'name,name...', '', 'NONE',
+                               'package names that you do not want to install')
+    ]
+  end
+  private :multipackage_entries
+
+  ALIASES = {
+    'std-ruby'         => 'librubyver',
+    'stdruby'          => 'librubyver',
+    'rubylibdir'       => 'librubyver',
+    'archdir'          => 'librubyverarch',
+    'site-ruby-common' => 'siteruby',     # For backward compatibility
+    'site-ruby'        => 'siterubyver',  # For backward compatibility
+    'bin-dir'          => 'bindir',
+    'bin-dir'          => 'bindir',
+    'rb-dir'           => 'rbdir',
+    'so-dir'           => 'sodir',
+    'data-dir'         => 'datadir',
+    'ruby-path'        => 'rubypath',
+    'ruby-prog'        => 'rubyprog',
+    'ruby'             => 'rubyprog',
+    'make-prog'        => 'makeprog',
+    'make'             => 'makeprog'
+  }
+
+  def fixup
+    ALIASES.each do |ali, name|
+      @table[ali] = @table[name]
+    end
+  end
+
+  def options_re
+    /\A--(#{@table.keys.join('|')})(?:=(.*))?\z/
+  end
+
+  def parse_opt(opt)
+    m = options_re().match(opt) or setup_rb_error "config: unknown option #{opt}"
+    m.to_a[1,2]
+  end
+
+  def dllext
+    @rbconfig['DLEXT']
+  end
+
+  def value_config?(name)
+    lookup(name).value?
+  end
+
+  class Item
+    def initialize(name, template, default, desc)
+      @name = name.freeze
+      @template = template
+      @value = default
+      @default = default
+      @description = desc
+    end
+
+    attr_reader :name
+    attr_reader :description
+
+    attr_accessor :default
+    alias help_default default
+
+    def help_opt
+      "--#{@name}=#{@template}"
+    end
+
+    def value?
+      true
+    end
+
+    def value
+      @value
+    end
+
+    def resolve(table)
+      @value.gsub(%r<\$([^/]+)>) { table[$1] }
+    end
+
+    def set(val)
+      @value = check(val)
+    end
+
+    private
+
+    def check(val)
+      setup_rb_error "config: --#{name} requires argument" unless val
+      val
+    end
+  end
+
+  class BoolItem < Item
+    def config_type
+      'bool'
+    end
+
+    def help_opt
+      "--#{@name}"
+    end
+
+    private
+
+    def check(val)
+      return 'yes' unless val
+      case val
+      when /\Ay(es)?\z/i, /\At(rue)?\z/i then 'yes'
+      when /\An(o)?\z/i, /\Af(alse)\z/i  then 'no'
+      else
+        setup_rb_error "config: --#{@name} accepts only yes/no for argument"
+      end
+    end
+  end
+
+  class PathItem < Item
+    def config_type
+      'path'
+    end
+
+    private
+
+    def check(path)
+      setup_rb_error "config: --#{@name} requires argument"  unless path
+      path[0,1] == '$' ? path : File.expand_path(path)
+    end
+  end
+
+  class ProgramItem < Item
+    def config_type
+      'program'
+    end
+  end
+
+  class SelectItem < Item
+    def initialize(name, selection, default, desc)
+      super
+      @ok = selection.split('/')
+    end
+
+    def config_type
+      'select'
+    end
+
+    private
+
+    def check(val)
+      unless @ok.include?(val.strip)
+        setup_rb_error "config: use --#{@name}=#{@template} (#{val})"
+      end
+      val.strip
+    end
+  end
+
+  class ExecItem < Item
+    def initialize(name, selection, desc, &block)
+      super name, selection, nil, desc
+      @ok = selection.split('/')
+      @action = block
+    end
+
+    def config_type
+      'exec'
+    end
+
+    def value?
+      false
+    end
+
+    def resolve(table)
+      setup_rb_error "$#{name()} wrongly used as option value"
+    end
+
+    undef set
+
+    def evaluate(val, table)
+      v = val.strip.downcase
+      unless @ok.include?(v)
+        setup_rb_error "invalid option --#{@name}=#{val} (use #{@template})"
+      end
+      @action.call v, table
+    end
+  end
+
+  class PackageSelectionItem < Item
+    def initialize(name, template, default, help_default, desc)
+      super name, template, default, desc
+      @help_default = help_default
+    end
+
+    attr_reader :help_default
+
+    def config_type
+      'package'
+    end
+
+    private
+
+    def check(val)
+      unless File.dir?("packages/#{val}")
+        setup_rb_error "config: no such package: #{val}"
+      end
+      val
+    end
+  end
+
+  class MetaConfigEnvironment
+    def initialize(config, installer)
+      @config = config
+      @installer = installer
+    end
+
+    def config_names
+      @config.names
+    end
+
+    def config?(name)
+      @config.key?(name)
+    end
+
+    def bool_config?(name)
+      @config.lookup(name).config_type == 'bool'
+    end
+
+    def path_config?(name)
+      @config.lookup(name).config_type == 'path'
+    end
+
+    def value_config?(name)
+      @config.lookup(name).config_type != 'exec'
+    end
+
+    def add_config(item)
+      @config.add item
+    end
+
+    def add_bool_config(name, default, desc)
+      @config.add BoolItem.new(name, 'yes/no', default ? 'yes' : 'no', desc)
+    end
+
+    def add_path_config(name, default, desc)
+      @config.add PathItem.new(name, 'path', default, desc)
+    end
+
+    def set_config_default(name, default)
+      @config.lookup(name).default = default
+    end
+
+    def remove_config(name)
+      @config.remove(name)
+    end
+
+    # For only multipackage
+    def packages
+      raise '[setup.rb fatal] multi-package metaconfig API packages() called for single-package; contact application package vendor' unless @installer
+      @installer.packages
+    end
+
+    # For only multipackage
+    def declare_packages(list)
+      raise '[setup.rb fatal] multi-package metaconfig API declare_packages() called for single-package; contact application package vendor' unless @installer
+      @installer.packages = list
+    end
+  end
+
+end   # class ConfigTable
+
+
+# This module requires: #verbose?, #no_harm?
+module FileOperations
+
+  def mkdir_p(dirname, prefix = nil)
+    dirname = prefix + File.expand_path(dirname) if prefix
+    $stderr.puts "mkdir -p #{dirname}" if verbose?
+    return if no_harm?
+
+    # Does not check '/', it's too abnormal.
+    dirs = File.expand_path(dirname).split(%r<(?=/)>)
+    if /\A[a-z]:\z/i =~ dirs[0]
+      disk = dirs.shift
+      dirs[0] = disk + dirs[0]
+    end
+    dirs.each_index do |idx|
+      path = dirs[0..idx].join('')
+      Dir.mkdir path unless File.dir?(path)
+    end
+  end
+
+  def rm_f(path)
+    $stderr.puts "rm -f #{path}" if verbose?
+    return if no_harm?
+    force_remove_file path
+  end
+
+  def rm_rf(path)
+    $stderr.puts "rm -rf #{path}" if verbose?
+    return if no_harm?
+    remove_tree path
+  end
+
+  def remove_tree(path)
+    if File.symlink?(path)
+      remove_file path
+    elsif File.dir?(path)
+      remove_tree0 path
+    else
+      force_remove_file path
+    end
+  end
+
+  def remove_tree0(path)
+    Dir.foreach(path) do |ent|
+      next if ent == '.'
+      next if ent == '..'
+      entpath = "#{path}/#{ent}"
+      if File.symlink?(entpath)
+        remove_file entpath
+      elsif File.dir?(entpath)
+        remove_tree0 entpath
+      else
+        force_remove_file entpath
+      end
+    end
+    begin
+      Dir.rmdir path
+    rescue Errno::ENOTEMPTY
+      # directory may not be empty
+    end
+  end
+
+  def move_file(src, dest)
+    force_remove_file dest
+    begin
+      File.rename src, dest
+    rescue
+      File.open(dest, 'wb') {|f|
+        f.write File.binread(src)
+      }
+      File.chmod File.stat(src).mode, dest
+      File.unlink src
+    end
+  end
+
+  def force_remove_file(path)
+    begin
+      remove_file path
+    rescue
+    end
+  end
+
+  def remove_file(path)
+    File.chmod 0777, path
+    File.unlink path
+  end
+
+  def install(from, dest, mode, prefix = nil)
+    $stderr.puts "install #{from} #{dest}" if verbose?
+    return if no_harm?
+
+    realdest = prefix ? prefix + File.expand_path(dest) : dest
+    realdest = File.join(realdest, File.basename(from)) if File.dir?(realdest)
+    str = File.binread(from)
+    if diff?(str, realdest)
+      verbose_off {
+        rm_f realdest if File.exist?(realdest)
+      }
+      File.open(realdest, 'wb') {|f|
+        f.write str
+      }
+      File.chmod mode, realdest
+
+      File.open("#{objdir_root()}/InstalledFiles", 'a') {|f|
+        if prefix
+          f.puts realdest.sub(prefix, '')
+        else
+          f.puts realdest
+        end
+      }
+    end
+  end
+
+  def diff?(new_content, path)
+    return true unless File.exist?(path)
+    new_content != File.binread(path)
+  end
+
+  def command(*args)
+    $stderr.puts args.join(' ') if verbose?
+    system(*args) or raise RuntimeError,
+        "system(#{args.map{|a| a.inspect }.join(' ')}) failed"
+  end
+
+  def ruby(*args)
+    command config('rubyprog'), *args
+  end
+  
+  def make(task = nil)
+    command(*[config('makeprog'), task].compact)
+  end
+
+  def extdir?(dir)
+    File.exist?("#{dir}/MANIFEST") or File.exist?("#{dir}/extconf.rb")
+  end
+
+  def files_of(dir)
+    Dir.open(dir) {|d|
+      return d.select {|ent| File.file?("#{dir}/#{ent}") }
+    }
+  end
+
+  DIR_REJECT = %w( . .. CVS SCCS RCS CVS.adm .svn )
+
+  def directories_of(dir)
+    Dir.open(dir) {|d|
+      return d.select {|ent| File.dir?("#{dir}/#{ent}") } - DIR_REJECT
+    }
+  end
+
+end
+
+
+# This module requires: #srcdir_root, #objdir_root, #relpath
+module HookScriptAPI
+
+  def get_config(key)
+    @config[key]
+  end
+
+  alias config get_config
+
+  # obsolete: use metaconfig to change configuration
+  def set_config(key, val)
+    @config[key] = val
+  end
+
+  #
+  # srcdir/objdir (works only in the package directory)
+  #
+
+  def curr_srcdir
+    "#{srcdir_root()}/#{relpath()}"
+  end
+
+  def curr_objdir
+    "#{objdir_root()}/#{relpath()}"
+  end
+
+  def srcfile(path)
+    "#{curr_srcdir()}/#{path}"
+  end
+
+  def srcexist?(path)
+    File.exist?(srcfile(path))
+  end
+
+  def srcdirectory?(path)
+    File.dir?(srcfile(path))
+  end
+  
+  def srcfile?(path)
+    File.file?(srcfile(path))
+  end
+
+  def srcentries(path = '.')
+    Dir.open("#{curr_srcdir()}/#{path}") {|d|
+      return d.to_a - %w(. ..)
+    }
+  end
+
+  def srcfiles(path = '.')
+    srcentries(path).select {|fname|
+      File.file?(File.join(curr_srcdir(), path, fname))
+    }
+  end
+
+  def srcdirectories(path = '.')
+    srcentries(path).select {|fname|
+      File.dir?(File.join(curr_srcdir(), path, fname))
+    }
+  end
+
+end
+
+
+class ToplevelInstaller
+
+  Version   = '3.4.1'
+  Copyright = 'Copyright (c) 2000-2006 Minero Aoki'
+
+  TASKS = [
+    [ 'all',      'do config, setup, then install' ],
+    [ 'config',   'saves your configurations' ],
+    [ 'show',     'shows current configuration' ],
+    [ 'setup',    'compiles ruby extentions and others' ],
+    [ 'install',  'installs files' ],
+    [ 'test',     'run all tests in test/' ],
+    [ 'clean',    "does `make clean' for each extention" ],
+    [ 'distclean',"does `make distclean' for each extention" ]
+  ]
+
+  def ToplevelInstaller.invoke
+    config = ConfigTable.new(load_rbconfig())
+    config.load_standard_entries
+    config.load_multipackage_entries if multipackage?
+    config.fixup
+    klass = (multipackage?() ? ToplevelInstallerMulti : ToplevelInstaller)
+    klass.new(File.dirname($0), config).invoke
+  end
+
+  def ToplevelInstaller.multipackage?
+    File.dir?(File.dirname($0) + '/packages')
+  end
+
+  def ToplevelInstaller.load_rbconfig
+    if arg = ARGV.detect {|arg| /\A--rbconfig=/ =~ arg }
+      ARGV.delete(arg)
+      load File.expand_path(arg.split(/=/, 2)[1])
+      $".push 'rbconfig.rb'
+    else
+      require 'rbconfig'
+    end
+    ::Config::CONFIG
+  end
+
+  def initialize(ardir_root, config)
+    @ardir = File.expand_path(ardir_root)
+    @config = config
+    # cache
+    @valid_task_re = nil
+  end
+
+  def config(key)
+    @config[key]
+  end
+
+  def inspect
+    "#<#{self.class} #{__id__()}>"
+  end
+
+  def invoke
+    run_metaconfigs
+    case task = parsearg_global()
+    when nil, 'all'
+      parsearg_config
+      init_installers
+      exec_config
+      exec_setup
+      exec_install
+    else
+      case task
+      when 'config', 'test'
+        ;
+      when 'clean', 'distclean'
+        @config.load_savefile if File.exist?(@config.savefile)
+      else
+        @config.load_savefile
+      end
+      __send__ "parsearg_#{task}"
+      init_installers
+      __send__ "exec_#{task}"
+    end
+  end
+  
+  def run_metaconfigs
+    @config.load_script "#{@ardir}/metaconfig"
+  end
+
+  def init_installers
+    @installer = Installer.new(@config, @ardir, File.expand_path('.'))
+  end
+
+  #
+  # Hook Script API bases
+  #
+
+  def srcdir_root
+    @ardir
+  end
+
+  def objdir_root
+    '.'
+  end
+
+  def relpath
+    '.'
+  end
+
+  #
+  # Option Parsing
+  #
+
+  def parsearg_global
+    while arg = ARGV.shift
+      case arg
+      when /\A\w+\z/
+        setup_rb_error "invalid task: #{arg}" unless valid_task?(arg)
+        return arg
+      when '-q', '--quiet'
+        @config.verbose = false
+      when '--verbose'
+        @config.verbose = true
+      when '--help'
+        print_usage $stdout
+        exit 0
+      when '--version'
+        puts "#{File.basename($0)} version #{Version}"
+        exit 0
+      when '--copyright'
+        puts Copyright
+        exit 0
+      else
+        setup_rb_error "unknown global option '#{arg}'"
+      end
+    end
+    nil
+  end
+
+  def valid_task?(t)
+    valid_task_re() =~ t
+  end
+
+  def valid_task_re
+    @valid_task_re ||= /\A(?:#{TASKS.map {|task,desc| task }.join('|')})\z/
+  end
+
+  def parsearg_no_options
+    unless ARGV.empty?
+      task = caller(0).first.slice(%r<`parsearg_(\w+)'>, 1)
+      setup_rb_error "#{task}: unknown options: #{ARGV.join(' ')}"
+    end
+  end
+
+  alias parsearg_show       parsearg_no_options
+  alias parsearg_setup      parsearg_no_options
+  alias parsearg_test       parsearg_no_options
+  alias parsearg_clean      parsearg_no_options
+  alias parsearg_distclean  parsearg_no_options
+
+  def parsearg_config
+    evalopt = []
+    set = []
+    @config.config_opt = []
+    while i = ARGV.shift
+      if /\A--?\z/ =~ i
+        @config.config_opt = ARGV.dup
+        break
+      end
+      name, value = *@config.parse_opt(i)
+      if @config.value_config?(name)
+        @config[name] = value
+      else
+        evalopt.push [name, value]
+      end
+      set.push name
+    end
+    evalopt.each do |name, value|
+      @config.lookup(name).evaluate value, @config
+    end
+    # Check if configuration is valid
+    set.each do |n|
+      @config[n] if @config.value_config?(n)
+    end
+  end
+
+  def parsearg_install
+    @config.no_harm = false
+    @config.install_prefix = ''
+    while a = ARGV.shift
+      case a
+      when '--no-harm'
+        @config.no_harm = true
+      when /\A--prefix=/
+        path = a.split(/=/, 2)[1]
+        path = File.expand_path(path) unless path[0,1] == '/'
+        @config.install_prefix = path
+      else
+        setup_rb_error "install: unknown option #{a}"
+      end
+    end
+  end
+
+  def print_usage(out)
+    out.puts 'Typical Installation Procedure:'
+    out.puts "  $ ruby #{File.basename $0} config"
+    out.puts "  $ ruby #{File.basename $0} setup"
+    out.puts "  # ruby #{File.basename $0} install (may require root privilege)"
+    out.puts
+    out.puts 'Detailed Usage:'
+    out.puts "  ruby #{File.basename $0} <global option>"
+    out.puts "  ruby #{File.basename $0} [<global options>] <task> [<task options>]"
+
+    fmt = "  %-24s %s\n"
+    out.puts
+    out.puts 'Global options:'
+    out.printf fmt, '-q,--quiet',   'suppress message outputs'
+    out.printf fmt, '   --verbose', 'output messages verbosely'
+    out.printf fmt, '   --help',    'print this message'
+    out.printf fmt, '   --version', 'print version and quit'
+    out.printf fmt, '   --copyright',  'print copyright and quit'
+    out.puts
+    out.puts 'Tasks:'
+    TASKS.each do |name, desc|
+      out.printf fmt, name, desc
+    end
+
+    fmt = "  %-24s %s [%s]\n"
+    out.puts
+    out.puts 'Options for CONFIG or ALL:'
+    @config.each do |item|
+      out.printf fmt, item.help_opt, item.description, item.help_default
+    end
+    out.printf fmt, '--rbconfig=path', 'rbconfig.rb to load',"running ruby's"
+    out.puts
+    out.puts 'Options for INSTALL:'
+    out.printf fmt, '--no-harm', 'only display what to do if given', 'off'
+    out.printf fmt, '--prefix=path',  'install path prefix', ''
+    out.puts
+  end
+
+  #
+  # Task Handlers
+  #
+
+  def exec_config
+    @installer.exec_config
+    @config.save   # must be final
+  end
+
+  def exec_setup
+    @installer.exec_setup
+  end
+
+  def exec_install
+    @installer.exec_install
+  end
+
+  def exec_test
+    @installer.exec_test
+  end
+
+  def exec_show
+    @config.each do |i|
+      printf "%-20s %s\n", i.name, i.value if i.value?
+    end
+  end
+
+  def exec_clean
+    @installer.exec_clean
+  end
+
+  def exec_distclean
+    @installer.exec_distclean
+  end
+
+end   # class ToplevelInstaller
+
+
+class ToplevelInstallerMulti < ToplevelInstaller
+
+  include FileOperations
+
+  def initialize(ardir_root, config)
+    super
+    @packages = directories_of("#{@ardir}/packages")
+    raise 'no package exists' if @packages.empty?
+    @root_installer = Installer.new(@config, @ardir, File.expand_path('.'))
+  end
+
+  def run_metaconfigs
+    @config.load_script "#{@ardir}/metaconfig", self
+    @packages.each do |name|
+      @config.load_script "#{@ardir}/packages/#{name}/metaconfig"
+    end
+  end
+
+  attr_reader :packages
+
+  def packages=(list)
+    raise 'package list is empty' if list.empty?
+    list.each do |name|
+      raise "directory packages/#{name} does not exist"\
+              unless File.dir?("#{@ardir}/packages/#{name}")
+    end
+    @packages = list
+  end
+
+  def init_installers
+    @installers = {}
+    @packages.each do |pack|
+      @installers[pack] = Installer.new(@config,
+                                       "#{@ardir}/packages/#{pack}",
+                                       "packages/#{pack}")
+    end
+    with    = extract_selection(config('with'))
+    without = extract_selection(config('without'))
+    @selected = @installers.keys.select {|name|
+                  (with.empty? or with.include?(name)) \
+                      and not without.include?(name)
+                }
+  end
+
+  def extract_selection(list)
+    a = list.split(/,/)
+    a.each do |name|
+      setup_rb_error "no such package: #{name}"  unless @installers.key?(name)
+    end
+    a
+  end
+
+  def print_usage(f)
+    super
+    f.puts 'Inluded packages:'
+    f.puts '  ' + @packages.sort.join(' ')
+    f.puts
+  end
+
+  #
+  # Task Handlers
+  #
+
+  def exec_config
+    run_hook 'pre-config'
+    each_selected_installers {|inst| inst.exec_config }
+    run_hook 'post-config'
+    @config.save   # must be final
+  end
+
+  def exec_setup
+    run_hook 'pre-setup'
+    each_selected_installers {|inst| inst.exec_setup }
+    run_hook 'post-setup'
+  end
+
+  def exec_install
+    run_hook 'pre-install'
+    each_selected_installers {|inst| inst.exec_install }
+    run_hook 'post-install'
+  end
+
+  def exec_test
+    run_hook 'pre-test'
+    each_selected_installers {|inst| inst.exec_test }
+    run_hook 'post-test'
+  end
+
+  def exec_clean
+    rm_f @config.savefile
+    run_hook 'pre-clean'
+    each_selected_installers {|inst| inst.exec_clean }
+    run_hook 'post-clean'
+  end
+
+  def exec_distclean
+    rm_f @config.savefile
+    run_hook 'pre-distclean'
+    each_selected_installers {|inst| inst.exec_distclean }
+    run_hook 'post-distclean'
+  end
+
+  #
+  # lib
+  #
+
+  def each_selected_installers
+    Dir.mkdir 'packages' unless File.dir?('packages')
+    @selected.each do |pack|
+      $stderr.puts "Processing the package `#{pack}' ..." if verbose?
+      Dir.mkdir "packages/#{pack}" unless File.dir?("packages/#{pack}")
+      Dir.chdir "packages/#{pack}"
+      yield @installers[pack]
+      Dir.chdir '../..'
+    end
+  end
+
+  def run_hook(id)
+    @root_installer.run_hook id
+  end
+
+  # module FileOperations requires this
+  def verbose?
+    @config.verbose?
+  end
+
+  # module FileOperations requires this
+  def no_harm?
+    @config.no_harm?
+  end
+
+end   # class ToplevelInstallerMulti
+
+
+class Installer
+
+  FILETYPES = %w( bin lib ext data conf man )
+
+  include FileOperations
+  include HookScriptAPI
+
+  def initialize(config, srcroot, objroot)
+    @config = config
+    @srcdir = File.expand_path(srcroot)
+    @objdir = File.expand_path(objroot)
+    @currdir = '.'
+  end
+
+  def inspect
+    "#<#{self.class} #{File.basename(@srcdir)}>"
+  end
+
+  def noop(rel)
+  end
+
+  #
+  # Hook Script API base methods
+  #
+
+  def srcdir_root
+    @srcdir
+  end
+
+  def objdir_root
+    @objdir
+  end
+
+  def relpath
+    @currdir
+  end
+
+  #
+  # Config Access
+  #
+
+  # module FileOperations requires this
+  def verbose?
+    @config.verbose?
+  end
+
+  # module FileOperations requires this
+  def no_harm?
+    @config.no_harm?
+  end
+
+  def verbose_off
+    begin
+      save, @config.verbose = @config.verbose?, false
+      yield
+    ensure
+      @config.verbose = save
+    end
+  end
+
+  #
+  # TASK config
+  #
+
+  def exec_config
+    exec_task_traverse 'config'
+  end
+
+  alias config_dir_bin noop
+  alias config_dir_lib noop
+
+  def config_dir_ext(rel)
+    extconf if extdir?(curr_srcdir())
+  end
+
+  alias config_dir_data noop
+  alias config_dir_conf noop
+  alias config_dir_man noop
+
+  def extconf
+    ruby "#{curr_srcdir()}/extconf.rb", *@config.config_opt
+  end
+
+  #
+  # TASK setup
+  #
+
+  def exec_setup
+    exec_task_traverse 'setup'
+  end
+
+  def setup_dir_bin(rel)
+    files_of(curr_srcdir()).each do |fname|
+      update_shebang_line "#{curr_srcdir()}/#{fname}"
+    end
+  end
+
+  alias setup_dir_lib noop
+
+  def setup_dir_ext(rel)
+    make if extdir?(curr_srcdir())
+  end
+
+  alias setup_dir_data noop
+  alias setup_dir_conf noop
+  alias setup_dir_man noop
+
+  def update_shebang_line(path)
+    return if no_harm?
+    return if config('shebang') == 'never'
+    old = Shebang.load(path)
+    if old
+      $stderr.puts "warning: #{path}: Shebang line includes too many args.  It is not portable and your program may not work." if old.args.size > 1
+      new = new_shebang(old)
+      return if new.to_s == old.to_s
+    else
+      return unless config('shebang') == 'all'
+      new = Shebang.new(config('rubypath'))
+    end
+    $stderr.puts "updating shebang: #{File.basename(path)}" if verbose?
+    open_atomic_writer(path) {|output|
+      File.open(path, 'rb') {|f|
+        f.gets if old   # discard
+        output.puts new.to_s
+        output.print f.read
+      }
+    }
+  end
+
+  def new_shebang(old)
+    if /\Aruby/ =~ File.basename(old.cmd)
+      Shebang.new(config('rubypath'), old.args)
+    elsif File.basename(old.cmd) == 'env' and old.args.first == 'ruby'
+      Shebang.new(config('rubypath'), old.args[1..-1])
+    else
+      return old unless config('shebang') == 'all'
+      Shebang.new(config('rubypath'))
+    end
+  end
+
+  def open_atomic_writer(path, &block)
+    tmpfile = File.basename(path) + '.tmp'
+    begin
+      File.open(tmpfile, 'wb', &block)
+      File.rename tmpfile, File.basename(path)
+    ensure
+      File.unlink tmpfile if File.exist?(tmpfile)
+    end
+  end
+
+  class Shebang
+    def Shebang.load(path)
+      line = nil
+      File.open(path) {|f|
+        line = f.gets
+      }
+      return nil unless /\A#!/ =~ line
+      parse(line)
+    end
+
+    def Shebang.parse(line)
+      cmd, *args = *line.strip.sub(/\A\#!/, '').split(' ')
+      new(cmd, args)
+    end
+
+    def initialize(cmd, args = [])
+      @cmd = cmd
+      @args = args
+    end
+
+    attr_reader :cmd
+    attr_reader :args
+
+    def to_s
+      "#! #{@cmd}" + (@args.empty? ? '' : " #{@args.join(' ')}")
+    end
+  end
+
+  #
+  # TASK install
+  #
+
+  def exec_install
+    rm_f 'InstalledFiles'
+    exec_task_traverse 'install'
+  end
+
+  def install_dir_bin(rel)
+    install_files targetfiles(), "#{config('bindir')}/#{rel}", 0755, strip_ext?
+  end
+
+  def strip_ext?
+    /mswin|mingw/ !~ RUBY_PLATFORM
+  end
+
+  def install_dir_lib(rel)
+    install_files libfiles(), "#{config('rbdir')}/#{rel}", 0644
+  end
+
+  def install_dir_ext(rel)
+    return unless extdir?(curr_srcdir())
+    install_files rubyextentions('.'),
+                  "#{config('sodir')}/#{File.dirname(rel)}",
+                  0555
+  end
+
+  def install_dir_data(rel)
+    install_files targetfiles(), "#{config('datadir')}/#{rel}", 0644
+  end
+
+  def install_dir_conf(rel)
+    # FIXME: should not remove current config files
+    # (rename previous file to .old/.org)
+    install_files targetfiles(), "#{config('sysconfdir')}/#{rel}", 0644
+  end
+
+  def install_dir_man(rel)
+    install_files targetfiles(), "#{config('mandir')}/#{rel}", 0644
+  end
+
+  def install_files(list, dest, mode, stripext = false)
+    mkdir_p dest, @config.install_prefix
+    list.each do |fname|
+      if stripext
+        install fname, "#{dest}/#{File.basename(fname, '.*')}",
+                mode, @config.install_prefix
+      else
+        install fname, dest, mode, @config.install_prefix
+      end
+    end
+  end
+
+  def libfiles
+    glob_reject(%w(*.y *.output), targetfiles())
+  end
+
+  def rubyextentions(dir)
+    ents = glob_select("*.#{@config.dllext}", targetfiles())
+    if ents.empty?
+      setup_rb_error "no ruby extention exists: 'ruby #{$0} setup' first"
+    end
+    ents
+  end
+
+  def targetfiles
+    mapdir(existfiles() - hookfiles())
+  end
+
+  def mapdir(ents)
+    ents.map {|ent|
+      if File.exist?(ent)
+      then ent                         # objdir
+      else "#{curr_srcdir()}/#{ent}"   # srcdir
+      end
+    }
+  end
+
+  # picked up many entries from cvs-1.11.1/src/ignore.c
+  JUNK_FILES = %w( 
+    core RCSLOG tags TAGS .make.state
+    .nse_depinfo #* .#* cvslog.* ,* .del-* *.olb
+    *~ *.old *.bak *.BAK *.orig *.rej _$* *$
+
+    *.org *.in .*
+  )
+
+  def existfiles
+    glob_reject(JUNK_FILES, (files_of(curr_srcdir()) | files_of('.')))
+  end
+
+  def hookfiles
+    %w( pre-%s post-%s pre-%s.rb post-%s.rb ).map {|fmt|
+      %w( config setup install clean distclean ).map {|t| sprintf(fmt, t) }
+    }.flatten
+  end
+
+  def glob_select(pat, ents)
+    re = globs2re([pat])
+    ents.select {|ent| re =~ ent }
+  end
+
+  def glob_reject(pats, ents)
+    re = globs2re(pats)
+    ents.reject {|ent| re =~ ent }
+  end
+
+  GLOB2REGEX = {
+    '.' => '\.',
+    '$' => '\$',
+    '#' => '\#',
+    '*' => '.*'
+  }
+
+  def globs2re(pats)
+    /\A(?:#{
+      pats.map {|pat| pat.gsub(/[\.\$\#\*]/) {|ch| GLOB2REGEX[ch] } }.join('|')
+    })\z/
+  end
+
+  #
+  # TASK test
+  #
+
+  TESTDIR = 'test'
+
+  def exec_test
+    unless File.directory?('test')
+      $stderr.puts 'no test in this package' if verbose?
+      return
+    end
+    $stderr.puts 'Running tests...' if verbose?
+    begin
+      require 'test/unit'
+    rescue LoadError
+      setup_rb_error 'test/unit cannot loaded.  You need Ruby 1.8 or later to invoke this task.'
+    end
+    runner = Test::Unit::AutoRunner.new(true)
+    runner.to_run << TESTDIR
+    runner.run
+  end
+
+  #
+  # TASK clean
+  #
+
+  def exec_clean
+    exec_task_traverse 'clean'
+    rm_f @config.savefile
+    rm_f 'InstalledFiles'
+  end
+
+  alias clean_dir_bin noop
+  alias clean_dir_lib noop
+  alias clean_dir_data noop
+  alias clean_dir_conf noop
+  alias clean_dir_man noop
+
+  def clean_dir_ext(rel)
+    return unless extdir?(curr_srcdir())
+    make 'clean' if File.file?('Makefile')
+  end
+
+  #
+  # TASK distclean
+  #
+
+  def exec_distclean
+    exec_task_traverse 'distclean'
+    rm_f @config.savefile
+    rm_f 'InstalledFiles'
+  end
+
+  alias distclean_dir_bin noop
+  alias distclean_dir_lib noop
+
+  def distclean_dir_ext(rel)
+    return unless extdir?(curr_srcdir())
+    make 'distclean' if File.file?('Makefile')
+  end
+
+  alias distclean_dir_data noop
+  alias distclean_dir_conf noop
+  alias distclean_dir_man noop
+
+  #
+  # Traversing
+  #
+
+  def exec_task_traverse(task)
+    run_hook "pre-#{task}"
+    FILETYPES.each do |type|
+      if type == 'ext' and config('without-ext') == 'yes'
+        $stderr.puts 'skipping ext/* by user option' if verbose?
+        next
+      end
+      traverse task, type, "#{task}_dir_#{type}"
+    end
+    run_hook "post-#{task}"
+  end
+
+  def traverse(task, rel, mid)
+    dive_into(rel) {
+      run_hook "pre-#{task}"
+      __send__ mid, rel.sub(%r[\A.*?(?:/|\z)], '')
+      directories_of(curr_srcdir()).each do |d|
+        traverse task, "#{rel}/#{d}", mid
+      end
+      run_hook "post-#{task}"
+    }
+  end
+
+  def dive_into(rel)
+    return unless File.dir?("#{@srcdir}/#{rel}")
+
+    dir = File.basename(rel)
+    Dir.mkdir dir unless File.dir?(dir)
+    prevdir = Dir.pwd
+    Dir.chdir dir
+    $stderr.puts '---> ' + rel if verbose?
+    @currdir = rel
+    yield
+    Dir.chdir prevdir
+    $stderr.puts '<--- ' + rel if verbose?
+    @currdir = File.dirname(rel)
+  end
+
+  def run_hook(id)
+    path = [ "#{curr_srcdir()}/#{id}",
+             "#{curr_srcdir()}/#{id}.rb" ].detect {|cand| File.file?(cand) }
+    return unless path
+    $stderr.puts "invoking hook script #{path}" if verbose?
+    begin
+      instance_eval File.read(path), path, 1
+    rescue
+      raise if $DEBUG
+      setup_rb_error "hook #{path} failed:\n" + $!.message
+    end
+  end
+
+end   # class Installer
+
+
+class SetupError < StandardError; end
+
+def setup_rb_error(msg)
+  raise SetupError, msg
+end
+
+if $0 == __FILE__
+  begin
+    ToplevelInstaller.invoke
+  rescue SetupError
+    raise if $DEBUG
+    $stderr.puts $!.message
+    $stderr.puts "Try 'ruby #{$0} --help' for detailed usage."
+    exit 1
+  end
+end