bio-shell 0.0.0
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- checksums.yaml +7 -0
- data/.gitignore +8 -0
- data/BSDL +22 -0
- data/COPYING +56 -0
- data/COPYING.ja +51 -0
- data/Gemfile +6 -0
- data/LEGAL +8 -0
- data/README.md +62 -0
- data/Rakefile +20 -0
- data/bin/bioruby +44 -0
- data/bio-shell.gemspec +29 -0
- data/lib/bio/shell.rb +44 -0
- data/lib/bio/shell/core.rb +578 -0
- data/lib/bio/shell/demo.rb +146 -0
- data/lib/bio/shell/interface.rb +217 -0
- data/lib/bio/shell/irb.rb +94 -0
- data/lib/bio/shell/object.rb +71 -0
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +218 -0
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +137 -0
- data/lib/bio/shell/plugin/flatfile.rb +101 -0
- data/lib/bio/shell/plugin/midi.rb +430 -0
- data/lib/bio/shell/plugin/ncbirest.rb +68 -0
- data/lib/bio/shell/plugin/obda.rb +45 -0
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +248 -0
- data/lib/bio/shell/plugin/togows.rb +40 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +11 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +7 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +10 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +108 -0
- data/lib/bio/shell/version.rb +5 -0
- data/lib/bio/shell/web.rb +102 -0
- data/lib/bioruby.rb +34 -0
- metadata +165 -0
checksums.yaml
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SHA1:
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metadata.gz: a00fbd14c9244b1c3bdde2a86815e7c0eae20db8
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data.tar.gz: 78252c99bcdf7551b90ff80fd5222fb0c6369ee0
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SHA512:
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metadata.gz: f9f48890aa062bceeb71948418e32c137f25595e17c21b440335546ff1b1ca2d9f07594ab9b8385952131a80d677522e2fed981716235f0196a4bf5aae1a6cf8
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data.tar.gz: f85f4804b5605247de07c4dcf992fbc0ef040144b3036d2dfbfc8edf0feded9220414c611f2cc572e96a6c500e0e9d606a647f8c69157761f68d060a22e7f3f4
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data/.gitignore
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data/BSDL
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Copyright (C) 1993-2013 Yukihiro Matsumoto. All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions
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are met:
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1. Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
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ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
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OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
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HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
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LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
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OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
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SUCH DAMAGE.
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data/COPYING
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BioRuby is copyrighted free software by Toshiaki Katayama <k@bioruby.org>.
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You can redistribute it and/or modify it under either the terms of the
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2-clause BSDL (see the file BSDL), or the conditions below:
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1. You may make and give away verbatim copies of the source form of the
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software without restriction, provided that you duplicate all of the
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original copyright notices and associated disclaimers.
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2. You may modify your copy of the software in any way, provided that
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you do at least ONE of the following:
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a) place your modifications in the Public Domain or otherwise
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make them Freely Available, such as by posting said
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modifications to Usenet or an equivalent medium, or by allowing
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the author to include your modifications in the software.
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b) use the modified software only within your corporation or
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organization.
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c) give non-standard binaries non-standard names, with
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instructions on where to get the original software distribution.
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d) make other distribution arrangements with the author.
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3. You may distribute the software in object code or binary form,
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provided that you do at least ONE of the following:
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a) distribute the binaries and library files of the software,
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together with instructions (in the manual page or equivalent)
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on where to get the original distribution.
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b) accompany the distribution with the machine-readable source of
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the software.
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c) give non-standard binaries non-standard names, with
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instructions on where to get the original software distribution.
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d) make other distribution arrangements with the author.
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4. You may modify and include the part of the software into any other
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software (possibly commercial). But some files in the distribution
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are not written by the author, so that they are not under these terms.
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For the list of those files and their copying conditions, see the
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file LEGAL.
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5. The scripts and library files supplied as input to or produced as
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output from the software do not automatically fall under the
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copyright of the software, but belong to whomever generated them,
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and may be sold commercially, and may be aggregated with this
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software.
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6. THIS SOFTWARE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR
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IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
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WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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PURPOSE.
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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
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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
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2-clause BSDLについてはBSDLファイルを参照して下さい.
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1. 複製は制限なく自由です.
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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
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自由に変更できます.
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(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
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などの方法で,変更を公開する.
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(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
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使う.
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(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.
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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
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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
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スの入手法を明示する.
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(d) その他の変更条件を作者と合意する.
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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
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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.
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(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,
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ソースの入手法を明示する.
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(b) 機械可読なソースコードを添付する.
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(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
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ルのソースコードの入手法を明示する.
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(d) その他の配布条件を作者と合意する.
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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
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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
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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.
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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
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LEGALファイルを参照してください.
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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
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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
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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
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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.
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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
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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
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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
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任を持ちません.
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data/Gemfile
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data/LEGAL
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data/README.md
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# BioRuby Shell
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[![Build Status](https://secure.travis-ci.org/bioruby/bio-shell.png)](http://travis-ci.org/bioruby/bio-shell)
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bio-shell, providing BioRuby Shell, is a command-line interface for
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[BioRuby](http://bioruby.org/), an open source bioinformatics library
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for Ruby.
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This code has historically been part of
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[the BioRuby gem](https://github.com/bioruby/bioruby),
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but has been split into its own gem as part of an effort to
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[modularize](http://bioruby.open-bio.org/wiki/Plugins) BioRuby.
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bio-shell and many more plugins are available at
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[biogems.info](http://www.biogems.info/).
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## Requirements
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bio-shell uses the `bio` gem. It will automatically be installed
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during the installation of `bio-shell` in normal cases.
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## Installation
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Add this line to your application's Gemfile:
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```ruby
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gem 'bio-shell'
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```
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And then execute:
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$ bundle
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Or install it yourself as:
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$ gem install bio-shell
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## Usage
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See BioRuby documentation at https://github.com/bioruby/documentation
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## Development
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To install this gem onto your local machine, run `bundle exec rake install`.
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To release a new version, update the version number in `version.rb`,
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and then run `bundle exec rake release`, which will create a git tag
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for the version, push git commits and tags, and push the `.gem` file
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to [rubygems.org](https://rubygems.org).
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## Contributing
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Bug reports and pull requests are welcome on GitHub at
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https://github.com/bioruby/bio-shell
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## Cite
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If you use this software, please cite one of
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* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
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* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
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data/Rakefile
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require "bundler/gem_tasks"
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require 'rdoc/task'
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require 'rake/testtask'
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task :default => :test
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Rake::TestTask.new do |t|
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t.test_files = FileList["test/unit/**/test_*.rb"]
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end
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Rake::RDocTask.new do |r|
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r.rdoc_dir = "rdoc"
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r.rdoc_files.include("README.md",
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"COPYING", "COPYING.ja", "BSDL", "LEGAL",
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"lib/**/*.rb")
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r.main = "README.md"
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r.options << '--title' << 'Bio::Shell API documentation'
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r.options << '--line-numbers'
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end
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data/bin/bioruby
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#!/usr/bin/env ruby
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#
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# = BioRuby shell - command line interface for the BioRuby library
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#
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# Copyright:: Copyright (C) 2005, 2006, 2007
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# Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
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# $Id:$
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#
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gem 'bio-shell'
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gem 'bio', '>=1.5.1'
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require 'bio/shell'
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# required to run commands (getseq, ls etc.)
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include Bio::Shell
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# setup command line options, working directory, and irb configurations
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Bio::Shell::Setup.new
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# loading workspace and command history
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Bio::Shell.load_session
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# sets default email address for Entrez eUtils.
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Bio::NCBI.default_email ||= 'staff@bioruby.org'
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# main loop
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if Bio::Shell.cache[:rails]
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Bio::Shell.cache[:rails].join
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else
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Signal.trap("SIGINT") do
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Bio::Shell.cache[:irb].signal_handle
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end
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catch(:IRB_EXIT) do
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Bio::Shell.cache[:irb].eval_input
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end
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end
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# saving workspace, command history and configuration before exit
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Bio::Shell.save_session
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data/bio-shell.gemspec
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# coding: utf-8
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lib = File.expand_path("../lib", __FILE__)
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$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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require "bio/shell/version"
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Gem::Specification.new do |spec|
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spec.name = "bio-shell"
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spec.version = Bio::Shell::VERSION
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spec.authors = ["BioRuby project"]
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spec.email = ["staff@bioruby.org"]
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spec.summary = %q{BioRuby Shell: interactive analysis environment for BioRuby}
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spec.description = %q{BioRuby Shell is a command-line based interacitve analysis enviroment for BioRuby open source bioinformatics library.}
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spec.homepage = "https://github.com/bioruby/bioruby-shell"
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|
+
spec.files = `git ls-files -z`.split("\x0").reject do |f|
|
17
|
+
f.match(%r{^(test|spec|features)/})
|
18
|
+
end
|
19
|
+
spec.bindir = "bin"
|
20
|
+
spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
|
21
|
+
spec.require_paths = ["lib"]
|
22
|
+
|
23
|
+
spec.add_runtime_dependency "bio", ">= 1.5.1"
|
24
|
+
|
25
|
+
spec.add_development_dependency "bundler", "~> 1.15"
|
26
|
+
spec.add_development_dependency "rake", "~> 10.0"
|
27
|
+
spec.add_development_dependency "rdoc", "~> 5"
|
28
|
+
spec.add_development_dependency "test-unit", "~> 3"
|
29
|
+
end
|
data/lib/bio/shell.rb
ADDED
@@ -0,0 +1,44 @@
|
|
1
|
+
#
|
2
|
+
# = bio/shell.rb - Loading all BioRuby shell features
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2005, 2006
|
5
|
+
# Toshiaki Katayama <k@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id:$
|
9
|
+
#
|
10
|
+
|
11
|
+
require 'bio'
|
12
|
+
require 'yaml'
|
13
|
+
require 'open-uri'
|
14
|
+
require 'fileutils'
|
15
|
+
require 'pp'
|
16
|
+
|
17
|
+
module Bio::Shell
|
18
|
+
|
19
|
+
require 'bio/shell/setup'
|
20
|
+
require 'bio/shell/irb'
|
21
|
+
require 'bio/shell/web'
|
22
|
+
require 'bio/shell/script'
|
23
|
+
require 'bio/shell/core'
|
24
|
+
require 'bio/shell/interface'
|
25
|
+
require 'bio/shell/object'
|
26
|
+
require 'bio/shell/demo'
|
27
|
+
require 'bio/shell/plugin/entry'
|
28
|
+
require 'bio/shell/plugin/seq'
|
29
|
+
require 'bio/shell/plugin/midi'
|
30
|
+
require 'bio/shell/plugin/codon'
|
31
|
+
require 'bio/shell/plugin/flatfile'
|
32
|
+
require 'bio/shell/plugin/obda'
|
33
|
+
require 'bio/shell/plugin/das'
|
34
|
+
require 'bio/shell/plugin/emboss'
|
35
|
+
require 'bio/shell/plugin/blast'
|
36
|
+
require 'bio/shell/plugin/psort'
|
37
|
+
require 'bio/shell/plugin/ncbirest'
|
38
|
+
require 'bio/shell/plugin/togows'
|
39
|
+
|
40
|
+
extend Ghost
|
41
|
+
|
42
|
+
end
|
43
|
+
|
44
|
+
|
@@ -0,0 +1,578 @@
|
|
1
|
+
#
|
2
|
+
# = bio/shell/core.rb - internal methods for the BioRuby shell
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2005, 2006
|
5
|
+
# Toshiaki Katayama <k@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
#
|
9
|
+
|
10
|
+
module Bio::Shell::Core
|
11
|
+
|
12
|
+
SHELLDIR = "shell"
|
13
|
+
DATADIR = "data"
|
14
|
+
SESSION = File.join(SHELLDIR, "session")
|
15
|
+
PLUGIN = File.join(SHELLDIR, "plugin")
|
16
|
+
SCRIPT = File.join(SHELLDIR, "script.rb")
|
17
|
+
CONFIG = File.join(SESSION, "config")
|
18
|
+
OBJECT = File.join(SESSION, "object")
|
19
|
+
HISTORY = File.join(SESSION, "history")
|
20
|
+
BIOFLAT = File.join(DATADIR, "bioflat")
|
21
|
+
|
22
|
+
MARSHAL = [ Marshal::MAJOR_VERSION, Marshal::MINOR_VERSION ]
|
23
|
+
|
24
|
+
MESSAGE = "...BioRuby in the shell..."
|
25
|
+
|
26
|
+
ESC_SEQ = {
|
27
|
+
:k => "\e[30m", :black => "\e[30m",
|
28
|
+
:r => "\e[31m", :red => "\e[31m", :ruby => "\e[31m",
|
29
|
+
:g => "\e[32m", :green => "\e[32m",
|
30
|
+
:y => "\e[33m", :yellow => "\e[33m",
|
31
|
+
:b => "\e[34m", :blue => "\e[34m",
|
32
|
+
:m => "\e[35m", :magenta => "\e[35m",
|
33
|
+
:c => "\e[36m", :cyan => "\e[36m",
|
34
|
+
:w => "\e[37m", :white => "\e[37m",
|
35
|
+
:n => "\e[00m", :none => "\e[00m", :reset => "\e[00m",
|
36
|
+
}
|
37
|
+
|
38
|
+
def colors
|
39
|
+
ESC_SEQ
|
40
|
+
end
|
41
|
+
|
42
|
+
def shell_dir
|
43
|
+
File.join(@cache[:savedir], SHELLDIR)
|
44
|
+
end
|
45
|
+
|
46
|
+
def data_dir
|
47
|
+
File.join(@cache[:savedir], DATADIR)
|
48
|
+
end
|
49
|
+
|
50
|
+
def session_dir
|
51
|
+
File.join(@cache[:savedir], SESSION)
|
52
|
+
end
|
53
|
+
|
54
|
+
def plugin_dir
|
55
|
+
File.join(@cache[:savedir], PLUGIN)
|
56
|
+
end
|
57
|
+
|
58
|
+
def script_file
|
59
|
+
File.join(@cache[:savedir], SCRIPT)
|
60
|
+
end
|
61
|
+
|
62
|
+
def script_dir
|
63
|
+
File.dirname(script_file)
|
64
|
+
end
|
65
|
+
|
66
|
+
def config_file
|
67
|
+
File.join(@cache[:savedir], CONFIG)
|
68
|
+
end
|
69
|
+
|
70
|
+
def object_file
|
71
|
+
File.join(@cache[:savedir], OBJECT)
|
72
|
+
end
|
73
|
+
|
74
|
+
def history_file
|
75
|
+
File.join(@cache[:savedir], HISTORY)
|
76
|
+
end
|
77
|
+
|
78
|
+
def bioflat_dir
|
79
|
+
File.join(@cache[:savedir], BIOFLAT)
|
80
|
+
end
|
81
|
+
|
82
|
+
def ask_yes_or_no(message)
|
83
|
+
loop do
|
84
|
+
STDERR.print "#{message}"
|
85
|
+
answer = gets
|
86
|
+
if answer.nil?
|
87
|
+
# readline support might be broken
|
88
|
+
return false
|
89
|
+
elsif /^\s*[Nn]/.match(answer)
|
90
|
+
return false
|
91
|
+
elsif /^\s*[Yy]/.match(answer)
|
92
|
+
return true
|
93
|
+
else
|
94
|
+
# loop
|
95
|
+
end
|
96
|
+
end
|
97
|
+
end
|
98
|
+
|
99
|
+
end
|
100
|
+
|
101
|
+
|
102
|
+
module Bio::Shell::Ghost
|
103
|
+
|
104
|
+
include Bio::Shell::Core
|
105
|
+
|
106
|
+
# A hash to store persistent configurations
|
107
|
+
attr_accessor :config
|
108
|
+
|
109
|
+
# A hash to store temporal (per session) configurations
|
110
|
+
attr_accessor :cache
|
111
|
+
|
112
|
+
### save/restore the environment
|
113
|
+
|
114
|
+
def configure(savedir)
|
115
|
+
@config = {}
|
116
|
+
@cache = {
|
117
|
+
:savedir => savedir,
|
118
|
+
:workdir => Dir.pwd,
|
119
|
+
}
|
120
|
+
create_save_dir
|
121
|
+
load_config
|
122
|
+
load_plugin
|
123
|
+
end
|
124
|
+
|
125
|
+
def load_session
|
126
|
+
load_object
|
127
|
+
unless @cache[:mode] == :script
|
128
|
+
load_history
|
129
|
+
opening_splash
|
130
|
+
open_history
|
131
|
+
end
|
132
|
+
end
|
133
|
+
|
134
|
+
def save_session
|
135
|
+
unless @cache[:mode] == :script
|
136
|
+
closing_splash
|
137
|
+
end
|
138
|
+
if create_save_dir_ask
|
139
|
+
#save_history # changed to use our own...
|
140
|
+
close_history
|
141
|
+
save_object
|
142
|
+
save_config
|
143
|
+
end
|
144
|
+
#STDERR.puts "Leaving directory '#{@cache[:workdir]}'"
|
145
|
+
end
|
146
|
+
|
147
|
+
### directories
|
148
|
+
|
149
|
+
def create_save_dir
|
150
|
+
create_real_dir(session_dir)
|
151
|
+
create_real_dir(plugin_dir)
|
152
|
+
create_real_dir(data_dir)
|
153
|
+
end
|
154
|
+
|
155
|
+
def create_save_dir_ask
|
156
|
+
if File.directory?(session_dir)
|
157
|
+
@cache[:save] = true
|
158
|
+
end
|
159
|
+
unless @cache[:save]
|
160
|
+
if ask_yes_or_no("Save session in '#{@cache[:workdir]}' directory? [y/n] ")
|
161
|
+
create_real_dir(session_dir)
|
162
|
+
create_real_dir(plugin_dir)
|
163
|
+
create_real_dir(data_dir)
|
164
|
+
create_real_dir(bioflat_dir)
|
165
|
+
@cache[:save] = true
|
166
|
+
else
|
167
|
+
@cache[:save] = false
|
168
|
+
end
|
169
|
+
end
|
170
|
+
return @cache[:save]
|
171
|
+
end
|
172
|
+
|
173
|
+
def create_real_dir(dir)
|
174
|
+
unless File.directory?(dir)
|
175
|
+
begin
|
176
|
+
STDERR.print "Creating directory (#{dir}) ... "
|
177
|
+
FileUtils.makedirs(dir)
|
178
|
+
STDERR.puts "done"
|
179
|
+
rescue
|
180
|
+
warn "Error: Failed to create directory (#{dir}) : #{$!}"
|
181
|
+
end
|
182
|
+
end
|
183
|
+
end
|
184
|
+
|
185
|
+
### bioflat
|
186
|
+
|
187
|
+
def create_flat_dir(dbname)
|
188
|
+
dir = File.join(bioflat_dir, dbname.to_s.strip)
|
189
|
+
unless File.directory?(dir)
|
190
|
+
FileUtils.makedirs(dir)
|
191
|
+
end
|
192
|
+
return dir
|
193
|
+
end
|
194
|
+
|
195
|
+
def find_flat_dir(dbname)
|
196
|
+
dir = File.join(bioflat_dir, dbname.to_s.strip)
|
197
|
+
if File.exist?(dir)
|
198
|
+
return dir
|
199
|
+
else
|
200
|
+
return nil
|
201
|
+
end
|
202
|
+
end
|
203
|
+
|
204
|
+
### config
|
205
|
+
|
206
|
+
def load_config
|
207
|
+
load_config_file(config_file)
|
208
|
+
end
|
209
|
+
|
210
|
+
def load_config_file(file)
|
211
|
+
if File.exist?(file)
|
212
|
+
STDERR.print "Loading config (#{file}) ... "
|
213
|
+
if hash = YAML.load(File.read(file))
|
214
|
+
@config.update(hash)
|
215
|
+
end
|
216
|
+
STDERR.puts "done"
|
217
|
+
end
|
218
|
+
end
|
219
|
+
|
220
|
+
def save_config
|
221
|
+
save_config_file(config_file)
|
222
|
+
end
|
223
|
+
|
224
|
+
def save_config_file(file)
|
225
|
+
begin
|
226
|
+
STDERR.print "Saving config (#{file}) ... "
|
227
|
+
File.open(file, "w") do |f|
|
228
|
+
f.puts @config.to_yaml
|
229
|
+
end
|
230
|
+
STDERR.puts "done"
|
231
|
+
rescue
|
232
|
+
warn "Error: Failed to save (#{file}) : #{$!}"
|
233
|
+
end
|
234
|
+
end
|
235
|
+
|
236
|
+
def config_show
|
237
|
+
@config.each do |k, v|
|
238
|
+
STDERR.puts "#{k}\t= #{v.inspect}"
|
239
|
+
end
|
240
|
+
end
|
241
|
+
|
242
|
+
def config_echo
|
243
|
+
bind = Bio::Shell.cache[:binding]
|
244
|
+
flag = ! @config[:echo]
|
245
|
+
@config[:echo] = IRB.conf[:ECHO] = flag
|
246
|
+
eval("conf.echo = #{flag}", bind)
|
247
|
+
STDERR.puts "Echo #{flag ? 'on' : 'off'}"
|
248
|
+
end
|
249
|
+
|
250
|
+
def config_color
|
251
|
+
bind = Bio::Shell.cache[:binding]
|
252
|
+
flag = ! @config[:color]
|
253
|
+
@config[:color] = flag
|
254
|
+
if flag
|
255
|
+
IRB.conf[:PROMPT_MODE] = :BIORUBY_COLOR
|
256
|
+
eval("conf.prompt_mode = :BIORUBY_COLOR", bind)
|
257
|
+
else
|
258
|
+
IRB.conf[:PROMPT_MODE] = :BIORUBY
|
259
|
+
eval("conf.prompt_mode = :BIORUBY", bind)
|
260
|
+
end
|
261
|
+
end
|
262
|
+
|
263
|
+
def config_pager(cmd = nil)
|
264
|
+
@config[:pager] = cmd
|
265
|
+
end
|
266
|
+
|
267
|
+
def config_splash
|
268
|
+
flag = ! @config[:splash]
|
269
|
+
@config[:splash] = flag
|
270
|
+
STDERR.puts "Splash #{flag ? 'on' : 'off'}"
|
271
|
+
opening_splash
|
272
|
+
end
|
273
|
+
|
274
|
+
def config_message(str = nil)
|
275
|
+
str ||= MESSAGE
|
276
|
+
@config[:message] = str
|
277
|
+
opening_splash
|
278
|
+
end
|
279
|
+
|
280
|
+
### plugin
|
281
|
+
|
282
|
+
def load_plugin
|
283
|
+
load_plugin_dir(plugin_dir)
|
284
|
+
end
|
285
|
+
|
286
|
+
def load_plugin_dir(dir)
|
287
|
+
if File.directory?(dir)
|
288
|
+
Dir.glob("#{dir}/*.rb").sort.each do |file|
|
289
|
+
STDERR.print "Loading plugin (#{file}) ... "
|
290
|
+
load file
|
291
|
+
STDERR.puts "done"
|
292
|
+
end
|
293
|
+
end
|
294
|
+
end
|
295
|
+
|
296
|
+
### object
|
297
|
+
|
298
|
+
def check_marshal
|
299
|
+
if @config[:marshal] and @config[:marshal] != MARSHAL
|
300
|
+
raise "Marshal version mismatch"
|
301
|
+
end
|
302
|
+
end
|
303
|
+
|
304
|
+
def load_object
|
305
|
+
begin
|
306
|
+
check_marshal
|
307
|
+
load_object_file(object_file)
|
308
|
+
rescue
|
309
|
+
warn "Error: Load aborted : #{$!}"
|
310
|
+
end
|
311
|
+
end
|
312
|
+
|
313
|
+
def load_object_file(file)
|
314
|
+
if File.exist?(file)
|
315
|
+
STDERR.print "Loading object (#{file}) ... "
|
316
|
+
begin
|
317
|
+
bind = Bio::Shell.cache[:binding]
|
318
|
+
hash = Marshal.load(File.read(file))
|
319
|
+
hash.each do |k, v|
|
320
|
+
begin
|
321
|
+
Thread.current[:restore_value] = v
|
322
|
+
eval("#{k} = Thread.current[:restore_value]", bind)
|
323
|
+
rescue
|
324
|
+
STDERR.puts "Warning: object '#{k}' couldn't be loaded : #{$!}"
|
325
|
+
end
|
326
|
+
end
|
327
|
+
rescue
|
328
|
+
warn "Error: Failed to load (#{file}) : #{$!}"
|
329
|
+
end
|
330
|
+
STDERR.puts "done"
|
331
|
+
end
|
332
|
+
end
|
333
|
+
|
334
|
+
def save_object
|
335
|
+
save_object_file(object_file)
|
336
|
+
end
|
337
|
+
|
338
|
+
def save_object_file(file)
|
339
|
+
begin
|
340
|
+
STDERR.print "Saving object (#{file}) ... "
|
341
|
+
File.rename(file, "#{file}.old") if File.exist?(file)
|
342
|
+
File.open(file, "w") do |f|
|
343
|
+
bind = Bio::Shell.cache[:binding]
|
344
|
+
list = eval("local_variables", bind)
|
345
|
+
list.collect! { |x| x.to_s }
|
346
|
+
list -= ["_"]
|
347
|
+
hash = {}
|
348
|
+
list.each do |elem|
|
349
|
+
value = eval(elem, bind)
|
350
|
+
if value
|
351
|
+
begin
|
352
|
+
Marshal.dump(value)
|
353
|
+
hash[elem] = value
|
354
|
+
rescue
|
355
|
+
# value could not be dumped.
|
356
|
+
end
|
357
|
+
end
|
358
|
+
end
|
359
|
+
Marshal.dump(hash, f)
|
360
|
+
@config[:marshal] = MARSHAL
|
361
|
+
end
|
362
|
+
STDERR.puts "done"
|
363
|
+
rescue
|
364
|
+
File.rename("#{file}.old", file) if File.exist?("#{file}.old")
|
365
|
+
warn "Error: Failed to save (#{file}) : #{$!}"
|
366
|
+
end
|
367
|
+
end
|
368
|
+
|
369
|
+
### history
|
370
|
+
|
371
|
+
def open_history
|
372
|
+
@cache[:histfile] = File.open(history_file, "a")
|
373
|
+
@cache[:histfile].sync = true
|
374
|
+
end
|
375
|
+
|
376
|
+
def store_history(line)
|
377
|
+
Bio::Shell.cache[:histfile].puts "# #{Time.now}"
|
378
|
+
Bio::Shell.cache[:histfile].puts line
|
379
|
+
end
|
380
|
+
|
381
|
+
def close_history
|
382
|
+
if @cache[:histfile]
|
383
|
+
STDERR.print "Saving history (#{history_file}) ... "
|
384
|
+
@cache[:histfile].close
|
385
|
+
STDERR.puts "done"
|
386
|
+
end
|
387
|
+
end
|
388
|
+
|
389
|
+
def load_history
|
390
|
+
if @cache[:readline]
|
391
|
+
load_history_file(history_file)
|
392
|
+
end
|
393
|
+
end
|
394
|
+
|
395
|
+
def load_history_file(file)
|
396
|
+
if File.exist?(file)
|
397
|
+
STDERR.print "Loading history (#{file}) ... "
|
398
|
+
File.open(file).each do |line|
|
399
|
+
unless line[/^# /]
|
400
|
+
Readline::HISTORY.push line.chomp
|
401
|
+
end
|
402
|
+
end
|
403
|
+
STDERR.puts "done"
|
404
|
+
end
|
405
|
+
end
|
406
|
+
|
407
|
+
# not used (use open_history/close_history instead)
|
408
|
+
def save_history
|
409
|
+
if @cache[:readline]
|
410
|
+
save_history_file(history_file)
|
411
|
+
end
|
412
|
+
end
|
413
|
+
|
414
|
+
def save_history_file(file)
|
415
|
+
begin
|
416
|
+
STDERR.print "Saving history (#{file}) ... "
|
417
|
+
File.open(file, "w") do |f|
|
418
|
+
f.puts Readline::HISTORY.to_a
|
419
|
+
end
|
420
|
+
STDERR.puts "done"
|
421
|
+
rescue
|
422
|
+
warn "Error: Failed to save (#{file}) : #{$!}"
|
423
|
+
end
|
424
|
+
end
|
425
|
+
|
426
|
+
### script
|
427
|
+
|
428
|
+
def script(mode = nil)
|
429
|
+
case mode
|
430
|
+
when :begin, "begin", :start, "start"
|
431
|
+
@cache[:script] = true
|
432
|
+
script_begin
|
433
|
+
when :end, "end", :stop, "stop"
|
434
|
+
@cache[:script] = false
|
435
|
+
script_end
|
436
|
+
save_script
|
437
|
+
else
|
438
|
+
if @cache[:script]
|
439
|
+
@cache[:script] = false
|
440
|
+
script_end
|
441
|
+
save_script
|
442
|
+
else
|
443
|
+
@cache[:script] = true
|
444
|
+
script_begin
|
445
|
+
end
|
446
|
+
end
|
447
|
+
end
|
448
|
+
|
449
|
+
def script_begin
|
450
|
+
STDERR.puts "-- 8< -- 8< -- 8< -- Script -- 8< -- 8< -- 8< --"
|
451
|
+
@script_begin = Readline::HISTORY.size
|
452
|
+
end
|
453
|
+
|
454
|
+
def script_end
|
455
|
+
STDERR.puts "-- >8 -- >8 -- >8 -- Script -- >8 -- >8 -- >8 --"
|
456
|
+
@script_end = Readline::HISTORY.size - 2
|
457
|
+
end
|
458
|
+
|
459
|
+
def save_script
|
460
|
+
if @script_begin and @script_end and @script_begin <= @script_end
|
461
|
+
if File.exist?(script_file)
|
462
|
+
message = "Overwrite script file (#{script_file})? [y/n] "
|
463
|
+
else
|
464
|
+
message = "Save script file (#{script_file})? [y/n] "
|
465
|
+
end
|
466
|
+
if ask_yes_or_no(message)
|
467
|
+
save_script_file(script_file)
|
468
|
+
else
|
469
|
+
STDERR.puts " ... save aborted."
|
470
|
+
end
|
471
|
+
elsif @script_begin and @script_end and @script_begin - @script_end == 1
|
472
|
+
STDERR.puts " ... script aborted."
|
473
|
+
else
|
474
|
+
STDERR.puts "Error: Script range #{@script_begin}..#{@script_end} is invalid"
|
475
|
+
end
|
476
|
+
end
|
477
|
+
|
478
|
+
def save_script_file(file)
|
479
|
+
begin
|
480
|
+
STDERR.print "Saving script (#{file}) ... "
|
481
|
+
File.open(file, "w") do |f|
|
482
|
+
f.puts "#!/usr/bin/env bioruby"
|
483
|
+
f.puts
|
484
|
+
f.puts Readline::HISTORY.to_a[@script_begin..@script_end]
|
485
|
+
f.puts
|
486
|
+
end
|
487
|
+
STDERR.puts "done"
|
488
|
+
rescue
|
489
|
+
@script_begin = nil
|
490
|
+
warn "Error: Failed to save (#{file}) : #{$!}"
|
491
|
+
end
|
492
|
+
end
|
493
|
+
|
494
|
+
### splash
|
495
|
+
|
496
|
+
def splash_message
|
497
|
+
@config[:message] ||= MESSAGE
|
498
|
+
@config[:message].to_s.split(//).join(" ")
|
499
|
+
end
|
500
|
+
|
501
|
+
def splash_message_color
|
502
|
+
str = splash_message
|
503
|
+
ruby = colors[:ruby]
|
504
|
+
none = colors[:none]
|
505
|
+
return str.sub(/R u b y/) { "#{ruby}R u b y#{none}" }
|
506
|
+
end
|
507
|
+
|
508
|
+
def splash_message_action(message = nil)
|
509
|
+
s = message || splash_message
|
510
|
+
l = s.length
|
511
|
+
x = " "
|
512
|
+
0.step(l,2) do |i|
|
513
|
+
l1 = l-i; l2 = l1/2; l4 = l2/2
|
514
|
+
STDERR.print "#{s[0,i]}#{x*l1}#{s[i,1]}\r"
|
515
|
+
sleep(0.001)
|
516
|
+
STDERR.print "#{s[0,i]}#{x*l2}#{s[i,1]}#{x*(l1-l2)}\r"
|
517
|
+
sleep(0.002)
|
518
|
+
STDERR.print "#{s[0,i]}#{x*l4}#{s[i,1]}#{x*(l2-l4)}\r"
|
519
|
+
sleep(0.004)
|
520
|
+
STDERR.print "#{s[0,i+1]}#{x*l4}\r"
|
521
|
+
sleep(0.008)
|
522
|
+
end
|
523
|
+
end
|
524
|
+
|
525
|
+
def splash_message_action_color(message = nil)
|
526
|
+
s = message || splash_message
|
527
|
+
l = s.length
|
528
|
+
c = colors
|
529
|
+
x = " "
|
530
|
+
0.step(l,2) do |i|
|
531
|
+
l1 = l-i; l2 = l1/2; l4 = l2/2
|
532
|
+
STDERR.print "#{c[:n]}#{s[0,i]}#{x*l1}#{c[:y]}#{s[i,1]}\r"
|
533
|
+
sleep(0.001)
|
534
|
+
STDERR.print "#{c[:n]}#{s[0,i]}#{x*l2}#{c[:g]}#{s[i,1]}#{x*(l1-l2)}\r"
|
535
|
+
sleep(0.002)
|
536
|
+
STDERR.print "#{c[:n]}#{s[0,i]}#{x*l4}#{c[:r]}#{s[i,1]}#{x*(l2-l4)}\r"
|
537
|
+
sleep(0.004)
|
538
|
+
STDERR.print "#{c[:n]}#{s[0,i+1]}#{x*l4}\r"
|
539
|
+
sleep(0.008)
|
540
|
+
end
|
541
|
+
end
|
542
|
+
|
543
|
+
def opening_splash
|
544
|
+
STDERR.puts
|
545
|
+
if @config[:splash]
|
546
|
+
if @config[:color]
|
547
|
+
splash_message_action_color
|
548
|
+
else
|
549
|
+
splash_message_action
|
550
|
+
end
|
551
|
+
end
|
552
|
+
if @config[:color]
|
553
|
+
STDERR.print splash_message_color
|
554
|
+
else
|
555
|
+
STDERR.print splash_message
|
556
|
+
end
|
557
|
+
STDERR.puts
|
558
|
+
STDERR.puts
|
559
|
+
STDERR.print " Version : BioRuby #{Bio::BIORUBY_VERSION_ID}"
|
560
|
+
STDERR.print " / Ruby #{RUBY_VERSION}"
|
561
|
+
STDERR.puts
|
562
|
+
STDERR.puts
|
563
|
+
end
|
564
|
+
|
565
|
+
def closing_splash
|
566
|
+
STDERR.puts
|
567
|
+
STDERR.puts
|
568
|
+
if @config[:color]
|
569
|
+
STDERR.print splash_message_color
|
570
|
+
else
|
571
|
+
STDERR.print splash_message
|
572
|
+
end
|
573
|
+
STDERR.puts
|
574
|
+
STDERR.puts
|
575
|
+
end
|
576
|
+
|
577
|
+
end
|
578
|
+
|