bio-shell 0.0.0

checksums.yaml

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+SHA1:
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+  data.tar.gz: 78252c99bcdf7551b90ff80fd5222fb0c6369ee0
+SHA512:
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data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/pkg/
+/spec/reports/
+/tmp/

data/BSDL

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+Copyright (C) 1993-2013 Yukihiro Matsumoto. All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+1. Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGE.

data/COPYING

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+BioRuby is copyrighted free software by Toshiaki Katayama <k@bioruby.org>.
+You can redistribute it and/or modify it under either the terms of the
+2-clause BSDL (see the file BSDL), or the conditions below:
+
+  1. You may make and give away verbatim copies of the source form of the
+     software without restriction, provided that you duplicate all of the
+     original copyright notices and associated disclaimers.
+
+  2. You may modify your copy of the software in any way, provided that
+     you do at least ONE of the following:
+
+       a) place your modifications in the Public Domain or otherwise
+          make them Freely Available, such as by posting said
+	  modifications to Usenet or an equivalent medium, or by allowing
+	  the author to include your modifications in the software.
+
+       b) use the modified software only within your corporation or
+          organization.
+
+       c) give non-standard binaries non-standard names, with
+          instructions on where to get the original software distribution.
+
+       d) make other distribution arrangements with the author.
+
+  3. You may distribute the software in object code or binary form,
+     provided that you do at least ONE of the following:
+
+       a) distribute the binaries and library files of the software,
+	  together with instructions (in the manual page or equivalent)
+	  on where to get the original distribution.
+
+       b) accompany the distribution with the machine-readable source of
+	  the software.
+
+       c) give non-standard binaries non-standard names, with
+          instructions on where to get the original software distribution.
+
+       d) make other distribution arrangements with the author.
+
+  4. You may modify and include the part of the software into any other
+     software (possibly commercial).  But some files in the distribution
+     are not written by the author, so that they are not under these terms.
+
+     For the list of those files and their copying conditions, see the
+     file LEGAL.
+
+  5. The scripts and library files supplied as input to or produced as 
+     output from the software do not automatically fall under the
+     copyright of the software, but belong to whomever generated them, 
+     and may be sold commercially, and may be aggregated with this
+     software.
+
+  6. THIS SOFTWARE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR
+     IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
+     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+     PURPOSE.

data/COPYING.ja

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+本プログラムはフリーソフトウェアです．2-clause BSDL
+または以下に示す条件で本プログラムを再配布できます
+2-clause BSDLについてはBSDLファイルを参照して下さい．
+
+  1. 複製は制限なく自由です．
+
+  2. 以下の条件のいずれかを満たす時に本プログラムのソースを
+     自由に変更できます．
+
+     (a) ネットニューズにポストしたり，作者に変更を送付する
+         などの方法で，変更を公開する．
+
+     (b) 変更した本プログラムを自分の所属する組織内部だけで
+         使う．
+
+     (c) 変更点を明示したうえ，ソフトウェアの名前を変更する．
+         そのソフトウェアを配布する時には変更前の本プログラ
+         ムも同時に配布する．または変更前の本プログラムのソー
+         スの入手法を明示する．
+
+     (d) その他の変更条件を作者と合意する．
+
+  3. 以下の条件のいずれかを満たす時に本プログラムをコンパイ
+     ルしたオブジェクトコードや実行形式でも配布できます．
+
+     (a) バイナリを受け取った人がソースを入手できるように，
+         ソースの入手法を明示する．
+
+     (b) 機械可読なソースコードを添付する．
+
+     (c) 変更を行ったバイナリは名前を変更したうえ，オリジナ
+         ルのソースコードの入手法を明示する．
+
+     (d) その他の配布条件を作者と合意する．
+
+  4. 他のプログラムへの引用はいかなる目的であれ自由です．た
+     だし，本プログラムに含まれる他の作者によるコードは，そ
+     れぞれの作者の意向による制限が加えられる場合があります．
+
+     それらファイルの一覧とそれぞれの配布条件などに付いては
+     LEGALファイルを参照してください．
+
+  5. 本プログラムへの入力となるスクリプトおよび，本プログラ
+     ムからの出力の権利は本プログラムの作者ではなく，それぞ
+     れの入出力を生成した人に属します．また，本プログラムに
+     組み込まれるための拡張ライブラリについても同様です．
+
+  6. 本プログラムは無保証です．作者は本プログラムをサポート
+     する意志はありますが，プログラム自身のバグあるいは本プ
+     ログラムの実行などから発生するいかなる損害に対しても責
+     任を持ちません．

data/Gemfile

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+source "https://rubygems.org"
+
+git_source(:github) {|repo_name| "https://github.com/#{repo_name}" }
+
+# Specify your gem's dependencies in bio-shell.gemspec
+gemspec

data/LEGAL

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+LEGAL NOTICE INFORMATION
+------------------------
+
+All the files in this distribution are covered under either the Ruby's
+license (see the file COPYING) or public-domain except some files
+mentioned below.
+
+(no files)

data/README.md

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+# BioRuby Shell
+
+[![Build Status](https://secure.travis-ci.org/bioruby/bio-shell.png)](http://travis-ci.org/bioruby/bio-shell)
+
+bio-shell, providing BioRuby Shell, is a command-line interface for
+[BioRuby](http://bioruby.org/), an open source bioinformatics library
+for Ruby.
+
+This code has historically been part of
+[the BioRuby gem](https://github.com/bioruby/bioruby),
+but has been split into its own gem as part of an effort to
+[modularize](http://bioruby.open-bio.org/wiki/Plugins) BioRuby.
+bio-shell and many more plugins are available at
+[biogems.info](http://www.biogems.info/).
+
+
+## Requirements
+
+bio-shell uses the `bio` gem. It will automatically be installed
+during the installation of `bio-shell` in normal cases.
+
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'bio-shell'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install bio-shell
+
+## Usage
+
+See BioRuby documentation at https://github.com/bioruby/documentation
+
+## Development
+
+To install this gem onto your local machine, run `bundle exec rake install`.
+To release a new version, update the version number in `version.rb`,
+and then run `bundle exec rake release`, which will create a git tag
+for the version, push git commits and tags, and push the `.gem` file
+to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at
+https://github.com/bioruby/bio-shell
+
+## Cite
+
+If you use this software, please cite one of
+
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+

data/Rakefile

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+require "bundler/gem_tasks"
+require 'rdoc/task'
+require 'rake/testtask'
+
+task :default => :test
+
+Rake::TestTask.new do |t|
+  t.test_files = FileList["test/unit/**/test_*.rb"]
+end
+
+Rake::RDocTask.new do |r|
+  r.rdoc_dir = "rdoc"
+  r.rdoc_files.include("README.md",
+                       "COPYING", "COPYING.ja", "BSDL", "LEGAL",
+                       "lib/**/*.rb")
+  r.main = "README.md"
+  r.options << '--title' << 'Bio::Shell API documentation'
+  r.options << '--line-numbers'
+end
+

data/bin/bioruby

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+#!/usr/bin/env ruby
+#
+# = BioRuby shell - command line interface for the BioRuby library
+#
+# Copyright::   Copyright (C) 2005, 2006, 2007
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+# $Id:$
+#
+
+gem 'bio-shell'
+gem 'bio', '>=1.5.1'
+
+require 'bio/shell'
+
+# required to run commands (getseq, ls etc.)
+include Bio::Shell
+
+# setup command line options, working directory, and irb configurations
+Bio::Shell::Setup.new
+
+# loading workspace and command history
+Bio::Shell.load_session
+
+# sets default email address for Entrez eUtils.
+Bio::NCBI.default_email ||= 'staff@bioruby.org'
+
+# main loop
+if Bio::Shell.cache[:rails]
+  Bio::Shell.cache[:rails].join
+else
+  Signal.trap("SIGINT") do
+    Bio::Shell.cache[:irb].signal_handle
+  end
+
+  catch(:IRB_EXIT) do
+    Bio::Shell.cache[:irb].eval_input
+  end
+end
+
+# saving workspace, command history and configuration before exit
+Bio::Shell.save_session
+

data/bio-shell.gemspec

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+# coding: utf-8
+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "bio/shell/version"
+
+Gem::Specification.new do |spec|
+  spec.name          = "bio-shell"
+  spec.version       = Bio::Shell::VERSION
+  spec.authors       = ["BioRuby project"]
+  spec.email         = ["staff@bioruby.org"]
+
+  spec.summary       = %q{BioRuby Shell: interactive analysis environment for BioRuby}
+  spec.description   = %q{BioRuby Shell is a command-line based interacitve analysis enviroment for BioRuby open source bioinformatics library.}
+  spec.homepage      = "https://github.com/bioruby/bioruby-shell"
+
+  spec.files         = `git ls-files -z`.split("\x0").reject do |f|
+    f.match(%r{^(test|spec|features)/})
+  end
+  spec.bindir        = "bin"
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_runtime_dependency "bio", ">= 1.5.1"
+
+  spec.add_development_dependency "bundler", "~> 1.15"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rdoc", "~> 5"
+  spec.add_development_dependency "test-unit", "~> 3"
+end

data/lib/bio/shell.rb

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+#
+# = bio/shell.rb - Loading all BioRuby shell features
+#
+# Copyright::   Copyright (C) 2005, 2006
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+# $Id:$
+#
+
+require 'bio'
+require 'yaml'
+require 'open-uri'
+require 'fileutils'
+require 'pp'
+
+module Bio::Shell
+
+  require 'bio/shell/setup'
+  require 'bio/shell/irb'
+  require 'bio/shell/web'
+  require 'bio/shell/script'
+  require 'bio/shell/core'
+  require 'bio/shell/interface'
+  require 'bio/shell/object'
+  require 'bio/shell/demo'
+  require 'bio/shell/plugin/entry'
+  require 'bio/shell/plugin/seq'
+  require 'bio/shell/plugin/midi'
+  require 'bio/shell/plugin/codon'
+  require 'bio/shell/plugin/flatfile'
+  require 'bio/shell/plugin/obda'
+  require 'bio/shell/plugin/das'
+  require 'bio/shell/plugin/emboss'
+  require 'bio/shell/plugin/blast'
+  require 'bio/shell/plugin/psort'
+  require 'bio/shell/plugin/ncbirest'
+  require 'bio/shell/plugin/togows'
+
+  extend Ghost
+
+end
+
+

data/lib/bio/shell/core.rb

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+#
+# = bio/shell/core.rb - internal methods for the BioRuby shell
+#
+# Copyright::   Copyright (C) 2005, 2006
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+#
+
+module Bio::Shell::Core
+
+  SHELLDIR = "shell"
+  DATADIR  = "data"
+  SESSION  = File.join(SHELLDIR, "session")
+  PLUGIN   = File.join(SHELLDIR, "plugin")
+  SCRIPT   = File.join(SHELLDIR, "script.rb")
+  CONFIG   = File.join(SESSION, "config")
+  OBJECT   = File.join(SESSION, "object")
+  HISTORY  = File.join(SESSION, "history")
+  BIOFLAT  = File.join(DATADIR, "bioflat")
+
+  MARSHAL = [ Marshal::MAJOR_VERSION, Marshal::MINOR_VERSION ]
+
+  MESSAGE = "...BioRuby in the shell..."
+
+  ESC_SEQ = {
+    :k => "\e[30m",  :black   => "\e[30m",
+    :r => "\e[31m",  :red     => "\e[31m",  :ruby  => "\e[31m",
+    :g => "\e[32m",  :green   => "\e[32m",
+    :y => "\e[33m",  :yellow  => "\e[33m",
+    :b => "\e[34m",  :blue    => "\e[34m",
+    :m => "\e[35m",  :magenta => "\e[35m",
+    :c => "\e[36m",  :cyan    => "\e[36m",
+    :w => "\e[37m",  :white   => "\e[37m",
+    :n => "\e[00m",  :none    => "\e[00m",  :reset => "\e[00m",
+  }
+
+  def colors
+    ESC_SEQ
+  end
+
+  def shell_dir
+    File.join(@cache[:savedir], SHELLDIR)
+  end
+
+  def data_dir
+    File.join(@cache[:savedir], DATADIR)
+  end
+
+  def session_dir
+    File.join(@cache[:savedir], SESSION)
+  end
+
+  def plugin_dir
+    File.join(@cache[:savedir], PLUGIN)
+  end
+
+  def script_file
+    File.join(@cache[:savedir], SCRIPT)
+  end
+
+  def script_dir
+    File.dirname(script_file)
+  end
+
+  def config_file
+    File.join(@cache[:savedir], CONFIG)
+  end
+
+  def object_file
+    File.join(@cache[:savedir], OBJECT)
+  end
+
+  def history_file
+    File.join(@cache[:savedir], HISTORY)
+  end
+
+  def bioflat_dir
+    File.join(@cache[:savedir], BIOFLAT)
+  end
+
+  def ask_yes_or_no(message)
+    loop do
+      STDERR.print "#{message}"
+      answer = gets
+      if answer.nil?
+        # readline support might be broken
+        return false
+      elsif /^\s*[Nn]/.match(answer)
+        return false
+      elsif /^\s*[Yy]/.match(answer)
+        return true
+      else
+        # loop
+      end
+    end
+  end
+
+end
+
+
+module Bio::Shell::Ghost
+
+  include Bio::Shell::Core
+
+  # A hash to store persistent configurations
+  attr_accessor :config
+
+  # A hash to store temporal (per session) configurations
+  attr_accessor :cache
+
+  ### save/restore the environment
+
+  def configure(savedir)
+    @config = {}
+    @cache  = {
+      :savedir => savedir,
+      :workdir => Dir.pwd,
+    }
+    create_save_dir
+    load_config
+    load_plugin
+  end
+ 
+  def load_session
+    load_object
+    unless @cache[:mode] == :script
+      load_history
+      opening_splash
+      open_history
+    end
+  end
+
+  def save_session
+    unless @cache[:mode] == :script
+      closing_splash
+    end
+    if create_save_dir_ask
+      #save_history	# changed to use our own...
+      close_history
+      save_object
+      save_config
+    end
+    #STDERR.puts "Leaving directory '#{@cache[:workdir]}'"
+  end
+
+  ### directories
+
+  def create_save_dir
+    create_real_dir(session_dir)
+    create_real_dir(plugin_dir)
+    create_real_dir(data_dir)
+  end
+
+  def create_save_dir_ask
+    if File.directory?(session_dir)
+      @cache[:save] = true
+    end
+    unless @cache[:save]
+      if ask_yes_or_no("Save session in '#{@cache[:workdir]}' directory? [y/n] ")
+        create_real_dir(session_dir)
+        create_real_dir(plugin_dir)
+        create_real_dir(data_dir)
+        create_real_dir(bioflat_dir)
+        @cache[:save] = true
+      else
+        @cache[:save] = false
+      end
+    end
+    return @cache[:save]
+  end
+
+  def create_real_dir(dir)
+    unless File.directory?(dir)
+      begin
+        STDERR.print "Creating directory (#{dir}) ... "
+        FileUtils.makedirs(dir)
+        STDERR.puts "done"
+      rescue
+        warn "Error: Failed to create directory (#{dir}) : #{$!}"
+      end
+    end
+  end
+
+  ### bioflat
+
+  def create_flat_dir(dbname)
+    dir = File.join(bioflat_dir, dbname.to_s.strip)
+    unless File.directory?(dir)
+      FileUtils.makedirs(dir)
+    end
+    return dir
+  end
+
+  def find_flat_dir(dbname)
+    dir = File.join(bioflat_dir, dbname.to_s.strip)
+    if File.exist?(dir)
+      return dir
+    else
+      return nil
+    end
+  end
+
+  ### config
+
+  def load_config
+    load_config_file(config_file)
+  end
+
+  def load_config_file(file)
+    if File.exist?(file)
+      STDERR.print "Loading config (#{file}) ... "
+      if hash = YAML.load(File.read(file))
+        @config.update(hash)
+      end
+      STDERR.puts "done"
+    end
+  end
+
+  def save_config
+    save_config_file(config_file)
+  end
+
+  def save_config_file(file)
+    begin
+      STDERR.print "Saving config (#{file}) ... "
+      File.open(file, "w") do |f|
+        f.puts @config.to_yaml
+      end
+      STDERR.puts "done"
+    rescue
+      warn "Error: Failed to save (#{file}) : #{$!}"
+    end
+  end
+
+  def config_show
+    @config.each do |k, v|
+      STDERR.puts "#{k}\t= #{v.inspect}"
+    end
+  end
+
+  def config_echo
+    bind = Bio::Shell.cache[:binding]
+    flag = ! @config[:echo]
+    @config[:echo] = IRB.conf[:ECHO] = flag
+    eval("conf.echo = #{flag}", bind)
+    STDERR.puts "Echo #{flag ? 'on' : 'off'}"
+  end
+
+  def config_color
+    bind = Bio::Shell.cache[:binding]
+    flag = ! @config[:color]
+    @config[:color] = flag
+    if flag
+      IRB.conf[:PROMPT_MODE] = :BIORUBY_COLOR
+      eval("conf.prompt_mode = :BIORUBY_COLOR", bind)
+    else
+      IRB.conf[:PROMPT_MODE] = :BIORUBY
+      eval("conf.prompt_mode = :BIORUBY", bind)
+    end
+  end
+
+  def config_pager(cmd = nil)
+    @config[:pager] = cmd
+  end
+
+  def config_splash
+    flag = ! @config[:splash]
+    @config[:splash] = flag
+    STDERR.puts "Splash #{flag ? 'on' : 'off'}"
+    opening_splash
+  end
+
+  def config_message(str = nil)
+    str ||= MESSAGE
+    @config[:message] = str
+    opening_splash
+  end
+
+  ### plugin
+
+  def load_plugin
+    load_plugin_dir(plugin_dir)
+  end
+
+  def load_plugin_dir(dir)
+    if File.directory?(dir)
+      Dir.glob("#{dir}/*.rb").sort.each do |file|
+        STDERR.print "Loading plugin (#{file}) ... "
+        load file
+        STDERR.puts "done"
+      end
+    end
+  end
+
+  ### object
+
+  def check_marshal
+    if @config[:marshal] and @config[:marshal] != MARSHAL
+      raise "Marshal version mismatch"
+    end
+  end
+
+  def load_object
+    begin
+      check_marshal
+      load_object_file(object_file)
+    rescue
+      warn "Error: Load aborted : #{$!}"
+    end
+  end
+
+  def load_object_file(file)
+    if File.exist?(file)
+      STDERR.print "Loading object (#{file}) ... "
+      begin
+        bind = Bio::Shell.cache[:binding]
+        hash = Marshal.load(File.read(file))
+        hash.each do |k, v|
+          begin
+            Thread.current[:restore_value] = v
+            eval("#{k} = Thread.current[:restore_value]", bind)
+          rescue
+            STDERR.puts "Warning: object '#{k}' couldn't be loaded : #{$!}"
+          end
+        end
+      rescue
+        warn "Error: Failed to load (#{file}) : #{$!}"
+      end
+      STDERR.puts "done"
+    end
+  end
+
+  def save_object
+    save_object_file(object_file)
+  end
+
+  def save_object_file(file)
+    begin
+      STDERR.print "Saving object (#{file}) ... "
+      File.rename(file, "#{file}.old") if File.exist?(file)
+      File.open(file, "w") do |f|
+        bind = Bio::Shell.cache[:binding]
+        list = eval("local_variables", bind)
+        list.collect! { |x| x.to_s }
+        list -= ["_"]
+        hash = {}
+        list.each do |elem|
+          value = eval(elem, bind)
+          if value
+            begin
+              Marshal.dump(value)
+              hash[elem] = value
+            rescue
+              # value could not be dumped.
+            end
+          end
+        end
+        Marshal.dump(hash, f)
+        @config[:marshal] = MARSHAL
+      end
+      STDERR.puts "done"
+    rescue
+      File.rename("#{file}.old", file) if File.exist?("#{file}.old")
+      warn "Error: Failed to save (#{file}) : #{$!}"
+    end
+  end
+
+  ### history
+
+  def open_history
+    @cache[:histfile] = File.open(history_file, "a")
+    @cache[:histfile].sync = true
+  end
+
+  def store_history(line)
+    Bio::Shell.cache[:histfile].puts "# #{Time.now}"
+    Bio::Shell.cache[:histfile].puts line
+  end
+
+  def close_history
+    if @cache[:histfile]
+      STDERR.print "Saving history (#{history_file}) ... "
+      @cache[:histfile].close
+      STDERR.puts "done"
+    end
+  end
+
+  def load_history
+    if @cache[:readline]
+      load_history_file(history_file)
+    end
+  end
+
+  def load_history_file(file)
+    if File.exist?(file)
+      STDERR.print "Loading history (#{file}) ... "
+      File.open(file).each do |line|
+        unless line[/^# /]
+          Readline::HISTORY.push line.chomp
+        end
+      end
+      STDERR.puts "done"
+    end
+  end
+  
+  # not used (use open_history/close_history instead)
+  def save_history
+    if @cache[:readline]
+      save_history_file(history_file)
+    end
+  end
+
+  def save_history_file(file)
+    begin
+      STDERR.print "Saving history (#{file}) ... "
+      File.open(file, "w") do |f|
+        f.puts Readline::HISTORY.to_a
+      end
+      STDERR.puts "done"
+    rescue
+      warn "Error: Failed to save (#{file}) : #{$!}"
+    end
+  end
+
+  ### script
+
+  def script(mode = nil)
+    case mode
+    when :begin, "begin", :start, "start"
+      @cache[:script] = true
+      script_begin
+    when :end, "end", :stop, "stop"
+      @cache[:script] = false
+      script_end
+      save_script
+    else
+      if @cache[:script]
+        @cache[:script] = false
+        script_end
+        save_script
+      else
+        @cache[:script] = true
+        script_begin
+      end
+    end
+  end
+
+  def script_begin
+    STDERR.puts "-- 8< -- 8< -- 8< --  Script  -- 8< -- 8< -- 8< --"
+    @script_begin = Readline::HISTORY.size
+  end
+
+  def script_end
+    STDERR.puts "-- >8 -- >8 -- >8 --  Script  -- >8 -- >8 -- >8 --"
+    @script_end = Readline::HISTORY.size - 2
+  end
+
+  def save_script
+    if @script_begin and @script_end and @script_begin <= @script_end
+      if File.exist?(script_file)
+        message = "Overwrite script file (#{script_file})? [y/n] "
+      else
+        message = "Save script file (#{script_file})? [y/n] "
+      end
+      if ask_yes_or_no(message)
+        save_script_file(script_file)
+      else
+        STDERR.puts " ... save aborted."
+      end
+    elsif @script_begin and @script_end and @script_begin - @script_end == 1
+      STDERR.puts " ... script aborted."
+    else
+      STDERR.puts "Error: Script range #{@script_begin}..#{@script_end} is invalid"
+    end
+  end
+
+  def save_script_file(file)
+    begin
+      STDERR.print "Saving script (#{file}) ... "
+      File.open(file, "w") do |f|
+        f.puts "#!/usr/bin/env bioruby"
+        f.puts
+        f.puts Readline::HISTORY.to_a[@script_begin..@script_end]
+        f.puts
+      end
+      STDERR.puts "done"
+    rescue
+      @script_begin = nil
+      warn "Error: Failed to save (#{file}) : #{$!}"
+    end
+  end
+
+  ### splash
+
+  def splash_message
+    @config[:message] ||= MESSAGE
+    @config[:message].to_s.split(//).join(" ")
+  end
+
+  def splash_message_color
+    str = splash_message
+    ruby = colors[:ruby]
+    none = colors[:none]
+    return str.sub(/R u b y/) { "#{ruby}R u b y#{none}" }
+  end
+
+  def splash_message_action(message = nil)
+    s = message || splash_message
+    l = s.length
+    x = " "
+    0.step(l,2) do |i|
+      l1 = l-i;  l2 = l1/2;  l4 = l2/2
+      STDERR.print "#{s[0,i]}#{x*l1}#{s[i,1]}\r"
+      sleep(0.001)
+      STDERR.print "#{s[0,i]}#{x*l2}#{s[i,1]}#{x*(l1-l2)}\r"
+      sleep(0.002)
+      STDERR.print "#{s[0,i]}#{x*l4}#{s[i,1]}#{x*(l2-l4)}\r"
+      sleep(0.004)
+      STDERR.print "#{s[0,i+1]}#{x*l4}\r"
+      sleep(0.008)
+    end
+  end
+
+  def splash_message_action_color(message = nil)
+    s = message || splash_message
+    l = s.length
+    c = colors
+    x = " "
+    0.step(l,2) do |i|
+      l1 = l-i;  l2 = l1/2;  l4 = l2/2
+      STDERR.print "#{c[:n]}#{s[0,i]}#{x*l1}#{c[:y]}#{s[i,1]}\r"
+      sleep(0.001)
+      STDERR.print "#{c[:n]}#{s[0,i]}#{x*l2}#{c[:g]}#{s[i,1]}#{x*(l1-l2)}\r"
+      sleep(0.002)
+      STDERR.print "#{c[:n]}#{s[0,i]}#{x*l4}#{c[:r]}#{s[i,1]}#{x*(l2-l4)}\r"
+      sleep(0.004)
+      STDERR.print "#{c[:n]}#{s[0,i+1]}#{x*l4}\r"
+      sleep(0.008)
+    end
+  end
+
+  def opening_splash
+    STDERR.puts
+    if @config[:splash]
+      if @config[:color]
+        splash_message_action_color
+      else
+        splash_message_action
+      end
+    end
+    if @config[:color]
+      STDERR.print splash_message_color
+    else
+      STDERR.print splash_message
+    end
+    STDERR.puts
+    STDERR.puts
+    STDERR.print "  Version : BioRuby #{Bio::BIORUBY_VERSION_ID}"
+    STDERR.print " / Ruby #{RUBY_VERSION}"
+    STDERR.puts
+    STDERR.puts
+  end
+
+  def closing_splash
+    STDERR.puts
+    STDERR.puts
+    if @config[:color]
+      STDERR.print splash_message_color
+    else
+      STDERR.print splash_message
+    end
+    STDERR.puts
+    STDERR.puts
+  end
+
+end
+