bio-executables 0.0.0
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- checksums.yaml +7 -0
- data/.gitignore +9 -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 +63 -0
- data/Rakefile +20 -0
- data/bin/br_biofetch.rb +71 -0
- data/bin/br_bioflat.rb +293 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +422 -0
- data/bio-executables.gemspec +30 -0
- data/lib/bio-executables/version.rb +5 -0
- metadata +147 -0
checksums.yaml
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SHA1:
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SHA512:
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data.tar.gz: a01c3a332a2ee4a7d50234300a46307a740afe8bfd20b8ca19ed771e7f53fec323c15ac6ad091cf59a269500fc889aceca6a2479442e7a2adab82c142897a0db
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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
ADDED
data/LEGAL
ADDED
data/README.md
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# BioRuby Executables
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[![Build Status](https://secure.travis-ci.org/bioruby/bio-executables.png)](http://travis-ci.org/bioruby/bio-executables)
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bio-executables is a collection of miscellaneous utilities for bioinformatics
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that were formerly part of the [BioRuby](http://bioruby.org/) core ("bio" gem).
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Because of reducing complexity, they were moved to this gem.
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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-executables 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-executables uses `bio` and `bio-old-biofetch-emulator` gems.
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They will automatically be installed during the installation of
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`bio-executables` 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-executables'
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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-executables
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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/bioruby-executables
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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/**/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' << 'BioRuby Executables API documentation'
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r.options << '--line-numbers'
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end
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data/bin/br_biofetch.rb
ADDED
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#!/usr/bin/env ruby
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#
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# = biofetch - BioFetch client
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#
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# Copyright:: Copyright (C) 2002
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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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#
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begin
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require 'rubygems'
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rescue LoadError
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end
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require 'bio/io/fetch'
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def require_bio_old_biofetch_emulator(mandatory = true)
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begin
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require 'bio-old-biofetch-emulator'
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rescue LoadError
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if mandatory then
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$stderr.puts "Error: please install bio-old-biofetch-emulator gem."
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exit 1
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end
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end
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end
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def default_url
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'http://bioruby.org/cgi-bin/biofetch.rb'
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end
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def another_url
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'http://www.ebi.ac.uk/cgi-bin/dbfetch'
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end
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def usage
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puts "#{$0} [-s[erver] #{another_url}] db id [style] [format]"
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puts " server : URL of the BioFetch CGI (default is #{default_url})"
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puts " db : database name (embl, genbank, etc.)"
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puts " id : entry id"
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puts " style : 'raw' or 'html' (default is 'raw')"
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puts " format : change the output format ('default', 'fasta', etc.)"
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end
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if ARGV.empty? or ARGV[0] =~ /^--?h/
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usage
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exit 1
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end
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case ARGV[0]
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when /^--?s/ # User specified server
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require_bio_old_biofetch_emulator(false)
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ARGV.shift
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serv = Bio::Fetch.new(ARGV.shift)
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puts serv.fetch(*ARGV)
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when /^--?e/ # EBI server
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ARGV.shift
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serv = Bio::Fetch.new(another_url)
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puts serv.fetch(*ARGV)
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when /^--?r/ # BioRuby server
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require_bio_old_biofetch_emulator
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ARGV.shift
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serv = Bio::Fetch.new(default_url)
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puts serv.fetch(*ARGV)
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else # Default server
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require_bio_old_biofetch_emulator
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puts Bio::Fetch.query(*ARGV)
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end
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data/bin/br_bioflat.rb
ADDED
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#!/usr/bin/env ruby
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#
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# = bioflat - OBDA flat file indexer (executable)
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#
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# Copyright:: Copyright (C) 2002
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# Naohisa Goto <ng@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: br_bioflat.rb,v 1.17 2007/04/05 23:35:39 trevor Exp $
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#
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require 'bio'
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def usage
|
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print <<EOM
|
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Search:
|
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#{$0} [--search] [options...] [DIR/]DBNAME KEYWORDS
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or
|
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#{$0} [--search] --location DIR --dbname DBNAME [options...] KEYWORDS
|
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+
|
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Search options:
|
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--namespace NAME set serch namespace to NAME
|
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(or --name NAME) You can set this option many times to specify
|
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more than one namespace.
|
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+
|
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Create index:
|
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#{$0} --create --location DIR --dbname DBNAME [--format <genbank|embl|fasta>] [options...] [--files] FILES
|
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Update index:
|
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#{$0} --update --location DIR --dbname DBNAME [options...] [--files] FILES
|
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+
|
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Create index options:
|
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--primary=UNIQUE set primary namespece to UNIQUE
|
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+
Default primary/secondary namespaces depend on
|
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each format of flatfiles.
|
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+
--secondary=KEY set secondary namespaces.
|
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You may use this option many times to specify
|
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more than one namespace.
|
38
|
+
--add-secondary=KEY add secondary namespaces to default specification.
|
39
|
+
You can use this option many times.
|
40
|
+
|
41
|
+
Options only valid for --create (or --update) --type flat:
|
42
|
+
--sort=/path/to/sort use external sort program (e.g. /usr/bin/sort)
|
43
|
+
--sort=BUILTIN use builtin sort routine
|
44
|
+
(default: /usr/bin/sort or BUILTIN)
|
45
|
+
--env=/path/to/env use env program to run sort (default: /usr/bin/env)
|
46
|
+
--env-arg=XXXXXX argument given to the env program (default: LC_ALL=C)
|
47
|
+
(multiple --env-arg=XXXXXX can be specified)
|
48
|
+
|
49
|
+
Options only valid for --update:
|
50
|
+
--renew re-read all flatfiles and update whole index
|
51
|
+
|
52
|
+
Backward compatibility:
|
53
|
+
--makeindex DIR/DBNAME
|
54
|
+
same as --create --type flat --location DIR --dbname DBNAME
|
55
|
+
--makeindexBDB DIR/DBNAME
|
56
|
+
same as --create --type bdb --location DIR --dbname DBNAME
|
57
|
+
--format=CLASS
|
58
|
+
instead of genbank|embl|fasta, specifing a class name is allowed
|
59
|
+
|
60
|
+
Show namespaces:
|
61
|
+
#{$0} --show-namespaces [--location DIR --dbname DBNAME] [DIR/DBNAME]
|
62
|
+
or
|
63
|
+
#{$0} --show-namespaces [--format=CLASS]
|
64
|
+
or
|
65
|
+
#{$0} --show-namespaces --files file
|
66
|
+
|
67
|
+
EOM
|
68
|
+
|
69
|
+
end
|
70
|
+
|
71
|
+
|
72
|
+
def do_index(mode = :create)
|
73
|
+
case ARGV[0]
|
74
|
+
when /^\-\-?make/
|
75
|
+
dbpath = ARGV[1]
|
76
|
+
args = ARGV[2..-1]
|
77
|
+
is_bdb = nil
|
78
|
+
when /^\-\-?make.*bdb/i
|
79
|
+
dbname = ARGV[1]
|
80
|
+
args = ARGV[2..-1]
|
81
|
+
is_bdb = Bio::FlatFileIndex::MAGIC_BDB
|
82
|
+
when /^\-\-create/, /^\-\-update/
|
83
|
+
args = ARGV[1..-1]
|
84
|
+
else
|
85
|
+
usage
|
86
|
+
end
|
87
|
+
|
88
|
+
options = {}
|
89
|
+
|
90
|
+
while args.first =~ /^\-/
|
91
|
+
case x = args.shift
|
92
|
+
|
93
|
+
# OBDA stuff
|
94
|
+
|
95
|
+
when /^\-\-?format$/
|
96
|
+
args.shift
|
97
|
+
format = nil # throw this f*ckin' mess for auto detect :)
|
98
|
+
when /^\-\-?location/
|
99
|
+
location = args.shift.chomp('/')
|
100
|
+
when /^\-\-?dbname/
|
101
|
+
dbname = args.shift
|
102
|
+
when /^\-\-?(index)?type/
|
103
|
+
indextype = args.shift
|
104
|
+
case indextype
|
105
|
+
when /bdb/
|
106
|
+
is_bdb = Bio::FlatFileIndex::MAGIC_BDB
|
107
|
+
when /flat/
|
108
|
+
is_bdb = nil
|
109
|
+
else
|
110
|
+
usage
|
111
|
+
end
|
112
|
+
|
113
|
+
# BioRuby extension
|
114
|
+
|
115
|
+
when /^\-\-?files/i
|
116
|
+
break
|
117
|
+
|
118
|
+
when /^\-\-?format\=(.*)/i
|
119
|
+
format = $1
|
120
|
+
|
121
|
+
when /^\-\-?sort\=(.*)/i
|
122
|
+
options['sort_program'] = $1
|
123
|
+
options['onmemory'] = nil
|
124
|
+
when /^\-\-?no\-?te?mp/i
|
125
|
+
options['onmemory'] = true
|
126
|
+
|
127
|
+
when /^\-\-?env\=(.*)/i
|
128
|
+
options['env_program'] = $1
|
129
|
+
|
130
|
+
when /^\-\-?env-arg(?:ument)?\=(.*)/i
|
131
|
+
options['env_program_arguments'] ||= []
|
132
|
+
options['env_program_arguments'].push $1
|
133
|
+
|
134
|
+
when /^\-\-?primary.*\=(.*)/i
|
135
|
+
options['primary_namespace'] = $1
|
136
|
+
|
137
|
+
when /^\-\-?add-secondary.*\=(.*)/i
|
138
|
+
unless options['additional_secondary_namespaces'] then
|
139
|
+
options['additional_secondary_namespaces'] = []
|
140
|
+
end
|
141
|
+
options['additional_secondary_namespaces'] << $1 if $1.length > 0
|
142
|
+
|
143
|
+
when /^\-\-?secondary.*\=(.*)/i
|
144
|
+
unless options['secondary_namespaces'] then
|
145
|
+
options['secondary_namespaces'] = []
|
146
|
+
end
|
147
|
+
options['secondary_namespaces'] << $1 if $1.length > 0
|
148
|
+
|
149
|
+
when /^\-\-?renew/
|
150
|
+
options['renew'] = true
|
151
|
+
|
152
|
+
else
|
153
|
+
$stderr.print "Warning: ignoring invalid option #{x.inspect}\n"
|
154
|
+
end
|
155
|
+
end
|
156
|
+
|
157
|
+
dbpath = File.join(location, dbname) unless dbpath
|
158
|
+
if mode == :update then
|
159
|
+
Bio::FlatFileIndex::update_index(dbpath, format, options, *args)
|
160
|
+
else
|
161
|
+
Bio::FlatFileIndex::makeindex(is_bdb, dbpath, format, options, *args)
|
162
|
+
end
|
163
|
+
end
|
164
|
+
|
165
|
+
|
166
|
+
def do_search
|
167
|
+
dbname = nil
|
168
|
+
location = nil
|
169
|
+
names = []
|
170
|
+
while x = ARGV.shift
|
171
|
+
case x
|
172
|
+
when /\A\-\-?search/i
|
173
|
+
#do nothing
|
174
|
+
when /\A\-\-?location/i
|
175
|
+
location = ARGV.shift.to_s.chomp('/')
|
176
|
+
when /\A\-\-?dbname/i
|
177
|
+
dbname = ARGV.shift
|
178
|
+
when /\A\-\-?name(?:space)?(?:\=(.+))?/i
|
179
|
+
if $1 then
|
180
|
+
names << $1
|
181
|
+
elsif x = ARGV.shift
|
182
|
+
names << x
|
183
|
+
end
|
184
|
+
else
|
185
|
+
ARGV.unshift x
|
186
|
+
break
|
187
|
+
end
|
188
|
+
end
|
189
|
+
dbname = ARGV.shift unless dbname
|
190
|
+
dbname = File.join(location, dbname) unless location.to_s.empty?
|
191
|
+
db = Bio::FlatFileIndex.open(dbname)
|
192
|
+
ARGV.each do |key|
|
193
|
+
$stderr.print "Searching for \'#{key}\'...\n"
|
194
|
+
#r = db.search(key)
|
195
|
+
#$stderr.print "OK, #{r.size} entry found\n"
|
196
|
+
#if r.size > 0 then
|
197
|
+
# print r
|
198
|
+
#end
|
199
|
+
begin
|
200
|
+
if names.empty? then
|
201
|
+
r = db.include?(key)
|
202
|
+
else
|
203
|
+
r = db.include_in_namespaces?(key, *names)
|
204
|
+
end
|
205
|
+
rescue RuntimeError
|
206
|
+
$stderr.print "ERROR: #{$!}\n"
|
207
|
+
next
|
208
|
+
end
|
209
|
+
r = [] unless r
|
210
|
+
$stderr.print "OK, #{r.size} entry found\n"
|
211
|
+
r.each do |i|
|
212
|
+
print db.search_primary(i)
|
213
|
+
end
|
214
|
+
end
|
215
|
+
db.close
|
216
|
+
end
|
217
|
+
|
218
|
+
|
219
|
+
def do_show_namespaces
|
220
|
+
dbname = nil
|
221
|
+
location = nil
|
222
|
+
files = nil
|
223
|
+
format = nil
|
224
|
+
names = []
|
225
|
+
while x = ARGV.shift
|
226
|
+
case x
|
227
|
+
when /\A\-\-?(show\-)?name(space)?s/i
|
228
|
+
#do nothing
|
229
|
+
when /\A\-\-?location/i
|
230
|
+
location = ARGV.shift.to_s.chomp('/')
|
231
|
+
when /\A\-\-?dbname/i
|
232
|
+
dbname = ARGV.shift
|
233
|
+
when /\A\-\-?format(?:\=(.+))?/i
|
234
|
+
if $1 then
|
235
|
+
format = $1
|
236
|
+
elsif x = ARGV.shift
|
237
|
+
format = x
|
238
|
+
end
|
239
|
+
when /\A\-\-?files/i
|
240
|
+
files = ARGV
|
241
|
+
break
|
242
|
+
else
|
243
|
+
ARGV.unshift x
|
244
|
+
break
|
245
|
+
end
|
246
|
+
end
|
247
|
+
if files then
|
248
|
+
k = nil
|
249
|
+
files.each do |x|
|
250
|
+
k = Bio::FlatFile.autodetect_file(x)
|
251
|
+
break if k
|
252
|
+
end
|
253
|
+
if k then
|
254
|
+
$stderr.print "Format: #{k.to_s}\n"
|
255
|
+
format = k
|
256
|
+
else
|
257
|
+
$stderr.print "ERROR: couldn't determine file format\n"
|
258
|
+
return
|
259
|
+
end
|
260
|
+
end
|
261
|
+
$stderr.print "Namespaces: (first line: primary namespace)\n"
|
262
|
+
if format then
|
263
|
+
parser = Bio::FlatFileIndex::Indexer::Parser.new(format)
|
264
|
+
print parser.primary.name, "\n"
|
265
|
+
puts parser.secondary.keys
|
266
|
+
else
|
267
|
+
dbname = ARGV.shift unless dbname
|
268
|
+
dbname = File.join(location, dbname) unless location.to_s.empty?
|
269
|
+
db = Bio::FlatFileIndex.open(dbname)
|
270
|
+
puts db.namespaces
|
271
|
+
db.close
|
272
|
+
end
|
273
|
+
end
|
274
|
+
|
275
|
+
if ARGV.size > 1
|
276
|
+
case ARGV[0]
|
277
|
+
when /--make/, /--create/
|
278
|
+
Bio::FlatFileIndex::DEBUG.out = true
|
279
|
+
do_index
|
280
|
+
when /--update/
|
281
|
+
Bio::FlatFileIndex::DEBUG.out = true
|
282
|
+
do_index(:update)
|
283
|
+
when /\A\-\-?(show\-)?name(space)?s/i
|
284
|
+
do_show_namespaces
|
285
|
+
when /--search/
|
286
|
+
do_search
|
287
|
+
else #default is search
|
288
|
+
do_search
|
289
|
+
end
|
290
|
+
else
|
291
|
+
usage
|
292
|
+
end
|
293
|
+
|
data/bin/br_biogetseq.rb
ADDED
@@ -0,0 +1,45 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
#
|
3
|
+
# = biogetseq - OBDA sequence data retrieval (executable)
|
4
|
+
#
|
5
|
+
# Copyright:: Copyright (C) 2003
|
6
|
+
# Toshiaki Katayama <k@bioruby.org>
|
7
|
+
# License:: The Ruby License
|
8
|
+
#
|
9
|
+
# $Id: br_biogetseq.rb,v 1.4 2007/04/05 23:35:39 trevor Exp $
|
10
|
+
#
|
11
|
+
|
12
|
+
require 'bio'
|
13
|
+
|
14
|
+
def usage
|
15
|
+
print <<END
|
16
|
+
#{$0} --dbname <dbname> [--namespace <namespace>] entry_id [entry_id]
|
17
|
+
END
|
18
|
+
exit 1
|
19
|
+
end
|
20
|
+
|
21
|
+
if ARGV.size < 3
|
22
|
+
usage
|
23
|
+
end
|
24
|
+
|
25
|
+
while ARGV.first =~ /^-/
|
26
|
+
case ARGV.shift
|
27
|
+
when /^\-\-format/
|
28
|
+
ARGV.shift
|
29
|
+
raise NotImplementedError
|
30
|
+
when /^\-\-dbname/
|
31
|
+
dbname = ARGV.shift
|
32
|
+
when /^\-\-namespace/
|
33
|
+
namespace = ARGV.shift
|
34
|
+
end
|
35
|
+
end
|
36
|
+
|
37
|
+
reg = Bio::Registry.new
|
38
|
+
db = reg.get_database(dbname)
|
39
|
+
if namespace
|
40
|
+
db['namespace'] = namespace
|
41
|
+
end
|
42
|
+
ARGV.each do |entry|
|
43
|
+
puts db.get_by_id(entry)
|
44
|
+
end
|
45
|
+
|
data/bin/br_pmfetch.rb
ADDED
@@ -0,0 +1,422 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
#
|
3
|
+
# = pmfetch - PubMed client
|
4
|
+
#
|
5
|
+
# Copyright:: Copyright (C) 2004, 2005
|
6
|
+
# Toshiaki Katayama <k@bioruby.org>
|
7
|
+
# License:: The Ruby License
|
8
|
+
#
|
9
|
+
# $Id:$
|
10
|
+
#
|
11
|
+
|
12
|
+
require 'bio'
|
13
|
+
|
14
|
+
PROG_VER = "Powered by BioRuby #{Bio::BIORUBY_VERSION_ID}"
|
15
|
+
PROG_NAME = File.basename($0)
|
16
|
+
|
17
|
+
|
18
|
+
require 'getoptlong'
|
19
|
+
|
20
|
+
|
21
|
+
### formatting
|
22
|
+
|
23
|
+
class String
|
24
|
+
def fill(fill_column = 80, prefix = '', separater = ' ')
|
25
|
+
prefix = ' ' * prefix if prefix.is_a?(Integer)
|
26
|
+
maxlen = fill_column - prefix.length
|
27
|
+
raise "prefix is longer than fill_column" if maxlen <= 0
|
28
|
+
|
29
|
+
cursor = pos = 0
|
30
|
+
lines = []
|
31
|
+
while cursor < self.length
|
32
|
+
line = self[cursor, maxlen]
|
33
|
+
pos = line.rindex(separater)
|
34
|
+
pos = nil if line.length < maxlen
|
35
|
+
if pos
|
36
|
+
len = pos + separater.length
|
37
|
+
lines << self[cursor, len]
|
38
|
+
cursor += len
|
39
|
+
else
|
40
|
+
lines << self[cursor, maxlen]
|
41
|
+
cursor += maxlen
|
42
|
+
end
|
43
|
+
end
|
44
|
+
return lines.join("\n#{prefix}")
|
45
|
+
end
|
46
|
+
end
|
47
|
+
|
48
|
+
|
49
|
+
module Bio
|
50
|
+
class Reference
|
51
|
+
def report
|
52
|
+
if (num = @authors.size) > 10
|
53
|
+
authors = "#{@authors[0]} et al. (#{num} authors)"
|
54
|
+
elsif num > 4
|
55
|
+
sep = ',' * (num - 1)
|
56
|
+
authors = "#{@authors[0]}#{sep} #{@authors[-1]}"
|
57
|
+
else
|
58
|
+
authors = authors_join(' & ')
|
59
|
+
end
|
60
|
+
journal = "#{@journal} #{@year} #{@volume}(#{@issue}):#{@pages}"
|
61
|
+
|
62
|
+
indent = 8
|
63
|
+
prefix = ' ' * indent
|
64
|
+
[
|
65
|
+
"#{@pages[/\d+/]}".ljust(indent) + "#{@title}".fill(78, indent),
|
66
|
+
authors,
|
67
|
+
"#{journal} [PMID:#{@pubmed}]",
|
68
|
+
].join("\n#{prefix}")
|
69
|
+
end
|
70
|
+
end
|
71
|
+
end
|
72
|
+
|
73
|
+
|
74
|
+
class PMFetch
|
75
|
+
|
76
|
+
class Examples < StandardError; end
|
77
|
+
class Version < StandardError; end
|
78
|
+
class Usage < StandardError; end
|
79
|
+
|
80
|
+
### default options
|
81
|
+
|
82
|
+
def initialize
|
83
|
+
@format = 'rd'
|
84
|
+
@search_opts = {
|
85
|
+
'retmax' => 20,
|
86
|
+
}
|
87
|
+
@query = nil
|
88
|
+
@query_opts = []
|
89
|
+
@pmid_list_only = false
|
90
|
+
|
91
|
+
pmfetch
|
92
|
+
end
|
93
|
+
|
94
|
+
|
95
|
+
### main
|
96
|
+
|
97
|
+
def pmfetch
|
98
|
+
begin
|
99
|
+
set_options
|
100
|
+
parse_options
|
101
|
+
check_query
|
102
|
+
rescue PMFetch::Examples
|
103
|
+
puts examples
|
104
|
+
exit
|
105
|
+
rescue PMFetch::Version
|
106
|
+
puts version
|
107
|
+
exit
|
108
|
+
rescue PMFetch::Usage
|
109
|
+
puts usage
|
110
|
+
exit
|
111
|
+
rescue GetoptLong::MissingArgument, GetoptLong::InvalidOption
|
112
|
+
puts usage
|
113
|
+
exit
|
114
|
+
end
|
115
|
+
|
116
|
+
list = pm_esearch
|
117
|
+
|
118
|
+
if list.empty?
|
119
|
+
;
|
120
|
+
elsif @pmid_list_only
|
121
|
+
puts list
|
122
|
+
else
|
123
|
+
pm_efetch(list)
|
124
|
+
end
|
125
|
+
end
|
126
|
+
|
127
|
+
|
128
|
+
### help
|
129
|
+
|
130
|
+
def usage
|
131
|
+
%Q[
|
132
|
+
Usage: #{PROG_NAME} [options...] "query string"
|
133
|
+
or #{PROG_NAME} --query "query string" [other options...]
|
134
|
+
|
135
|
+
Options:
|
136
|
+
-q --query "genome AND virus" Query string for PubMed search
|
137
|
+
-t --title "mobile elements" Title of the article to search
|
138
|
+
-j --journal "genome res" Journal title to search
|
139
|
+
-v --volume # Journal volume to search
|
140
|
+
-i --issue # Journal issue to search
|
141
|
+
-p --page # First page number of the article to search
|
142
|
+
-a --author "Altschul SF" Author name to search
|
143
|
+
-m --mesh "SARS virus" MeSH term to search
|
144
|
+
-f --format bibtex Summary output format
|
145
|
+
--pmidlist Output only a list of PubMed IDs
|
146
|
+
-n --retmax # Number of articles to retrieve at the maximum
|
147
|
+
-N --retstart # Starting number of the articles to retrieve
|
148
|
+
-s --sort pub+date Sort method for the summary output
|
149
|
+
--reldate # Search articles published within recent # days
|
150
|
+
--mindate YYYY/MM/DD Search articles published after the date
|
151
|
+
--maxdate YYYY/MM/DD Search articles published before the date
|
152
|
+
--help Output this help, then exit
|
153
|
+
--examples Output examples, then exit
|
154
|
+
--version Output version number, then exit
|
155
|
+
|
156
|
+
Formats:
|
157
|
+
endnote, medline, bibitem, bibtex, report, rd,
|
158
|
+
nature, science, genome_res, genome_biol, nar, current, trends, cell
|
159
|
+
|
160
|
+
Sort:
|
161
|
+
author, journal, pub+date, page
|
162
|
+
|
163
|
+
See the following pages for the PubMed search options:
|
164
|
+
http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
|
165
|
+
http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html
|
166
|
+
|
167
|
+
#{version}
|
168
|
+
|
169
|
+
]
|
170
|
+
end
|
171
|
+
|
172
|
+
def version
|
173
|
+
PROG_VER
|
174
|
+
end
|
175
|
+
|
176
|
+
def examples
|
177
|
+
DATA.read.gsub('PMFetch', PROG_NAME)
|
178
|
+
end
|
179
|
+
|
180
|
+
|
181
|
+
private
|
182
|
+
|
183
|
+
|
184
|
+
### options
|
185
|
+
|
186
|
+
def set_options
|
187
|
+
@parser = GetoptLong.new
|
188
|
+
|
189
|
+
@parser.set_options(
|
190
|
+
[ '--query', '-q', GetoptLong::REQUIRED_ARGUMENT ],
|
191
|
+
[ '--title', '-t', GetoptLong::REQUIRED_ARGUMENT ],
|
192
|
+
[ '--journal', '-j', GetoptLong::REQUIRED_ARGUMENT ],
|
193
|
+
[ '--volume', '-v', GetoptLong::REQUIRED_ARGUMENT ],
|
194
|
+
[ '--issue', '-i', GetoptLong::REQUIRED_ARGUMENT ],
|
195
|
+
[ '--page', '-p', GetoptLong::REQUIRED_ARGUMENT ],
|
196
|
+
[ '--author', '-a', GetoptLong::REQUIRED_ARGUMENT ],
|
197
|
+
[ '--mesh', '-m', GetoptLong::REQUIRED_ARGUMENT ],
|
198
|
+
[ '--format', '-f', GetoptLong::REQUIRED_ARGUMENT ],
|
199
|
+
[ '--pmidlist', GetoptLong::NO_ARGUMENT ],
|
200
|
+
[ '--retmax', '-n', GetoptLong::REQUIRED_ARGUMENT ],
|
201
|
+
[ '--retstart', '-N', GetoptLong::REQUIRED_ARGUMENT ],
|
202
|
+
[ '--sort', '-s', GetoptLong::REQUIRED_ARGUMENT ],
|
203
|
+
[ '--reldate', GetoptLong::REQUIRED_ARGUMENT ],
|
204
|
+
[ '--mindate', GetoptLong::REQUIRED_ARGUMENT ],
|
205
|
+
[ '--maxdate', GetoptLong::REQUIRED_ARGUMENT ],
|
206
|
+
[ '--examples', GetoptLong::NO_ARGUMENT ],
|
207
|
+
[ '--help', GetoptLong::NO_ARGUMENT ],
|
208
|
+
[ '--version', GetoptLong::NO_ARGUMENT ]
|
209
|
+
)
|
210
|
+
end
|
211
|
+
|
212
|
+
def parse_options
|
213
|
+
@parser.each_option do |optname, optarg|
|
214
|
+
case optname
|
215
|
+
when /--query/
|
216
|
+
@query = optarg
|
217
|
+
when /--title/
|
218
|
+
@query_opts << "#{optarg}[ti]"
|
219
|
+
when /--journal/
|
220
|
+
@query_opts << "#{optarg}[ta]"
|
221
|
+
when /--volume/
|
222
|
+
@query_opts << "#{optarg}[vi]"
|
223
|
+
when /--issue/
|
224
|
+
@query_opts << "#{optarg}[ip]"
|
225
|
+
when /--page/
|
226
|
+
@query_opts << "#{optarg}[pg]"
|
227
|
+
when /--author/
|
228
|
+
@query_opts << "#{optarg}[au]"
|
229
|
+
when /--mesh/
|
230
|
+
@query_opts << "#{optarg}[mh]"
|
231
|
+
when /--format/
|
232
|
+
@format = optarg
|
233
|
+
when /--pmidlist/
|
234
|
+
@pmid_list_only = true
|
235
|
+
when /--examples/
|
236
|
+
raise PMFetch::Examples
|
237
|
+
when /--help/
|
238
|
+
raise PMFetch::Usage
|
239
|
+
when /--version/
|
240
|
+
raise PMFetch::Version
|
241
|
+
when /--sort/
|
242
|
+
@sort = optarg
|
243
|
+
@search_opts["sort"] = @sort unless @sort == "page"
|
244
|
+
else
|
245
|
+
optname.delete!('-')
|
246
|
+
@search_opts[optname] = optarg
|
247
|
+
end
|
248
|
+
end
|
249
|
+
end
|
250
|
+
|
251
|
+
|
252
|
+
### check query
|
253
|
+
|
254
|
+
def check_query
|
255
|
+
p @query if $DEBUG
|
256
|
+
@query ||= ARGV.join(" ") unless ARGV.empty?
|
257
|
+
|
258
|
+
p @query if $DEBUG
|
259
|
+
@query_str = [ @query, @query_opts ].flatten.compact.join(" AND ")
|
260
|
+
|
261
|
+
p @query_str if $DEBUG
|
262
|
+
if @query_str.empty?
|
263
|
+
raise PMFetch::Usage
|
264
|
+
end
|
265
|
+
end
|
266
|
+
|
267
|
+
|
268
|
+
### search
|
269
|
+
|
270
|
+
def pm_esearch
|
271
|
+
return Bio::PubMed.esearch(@query_str, @search_opts)
|
272
|
+
end
|
273
|
+
|
274
|
+
def pm_efetch(list)
|
275
|
+
entries = Bio::PubMed.efetch(list)
|
276
|
+
|
277
|
+
if @format == 'medline'
|
278
|
+
medline_format(entries)
|
279
|
+
else
|
280
|
+
entries = parse_entries(entries)
|
281
|
+
if @sort == 'page'
|
282
|
+
entries = sort_entries(entries)
|
283
|
+
end
|
284
|
+
if @format == 'report'
|
285
|
+
report_format(entries)
|
286
|
+
else
|
287
|
+
other_format(entries)
|
288
|
+
end
|
289
|
+
end
|
290
|
+
end
|
291
|
+
|
292
|
+
|
293
|
+
### output
|
294
|
+
|
295
|
+
def medline_format(entries)
|
296
|
+
entries.each do |entry|
|
297
|
+
puts entry
|
298
|
+
puts '//'
|
299
|
+
end
|
300
|
+
end
|
301
|
+
|
302
|
+
def parse_entries(entries)
|
303
|
+
entries.map { |entry| Bio::MEDLINE.new(entry) }
|
304
|
+
end
|
305
|
+
|
306
|
+
def sort_entries(entries)
|
307
|
+
if RUBY_VERSION > "1.8.0"
|
308
|
+
entries.sort_by { |x|
|
309
|
+
[ x.journal, x.volume.to_i, x.issue.to_i, x.pages.to_i ]
|
310
|
+
}
|
311
|
+
else
|
312
|
+
entries.map { |x|
|
313
|
+
[ x.journal, x.volume.to_i, x.issue.to_i, x.pages.to_i, x ]
|
314
|
+
}.sort { |a, b|
|
315
|
+
a[0..3] <=> b[0..3]
|
316
|
+
}.map { |y|
|
317
|
+
y.pop
|
318
|
+
}
|
319
|
+
end
|
320
|
+
end
|
321
|
+
|
322
|
+
def report_format(entries)
|
323
|
+
entries.each do |entry|
|
324
|
+
puts entry.reference.report
|
325
|
+
puts
|
326
|
+
end
|
327
|
+
end
|
328
|
+
|
329
|
+
def other_format(entries)
|
330
|
+
entries.each do |entry|
|
331
|
+
puts entry.reference.format(@format)
|
332
|
+
puts
|
333
|
+
end
|
334
|
+
end
|
335
|
+
|
336
|
+
end
|
337
|
+
|
338
|
+
|
339
|
+
PMFetch.new
|
340
|
+
|
341
|
+
|
342
|
+
__END__
|
343
|
+
|
344
|
+
= Examples : PubMed search
|
345
|
+
|
346
|
+
These four lines will do the same job.
|
347
|
+
|
348
|
+
% PMFetch transcription factor
|
349
|
+
% PMFetch "transcription factor"
|
350
|
+
% PMFetch --query "transcription factor"
|
351
|
+
% PMFetch -q "transcription factor"
|
352
|
+
|
353
|
+
|
354
|
+
Retrieve max 100 artiecles (20 is a NCBI's default) at a time, use --retmax as
|
355
|
+
|
356
|
+
% PMFetch -q "transcription factor" --retmax 100
|
357
|
+
|
358
|
+
and, to retrieve next 100 articles, use --retstart as
|
359
|
+
|
360
|
+
% PMFetch -q "transcription factor" --retmax 100 --retstart 100
|
361
|
+
|
362
|
+
|
363
|
+
You can narrow the search target for an issue of the journal.
|
364
|
+
|
365
|
+
% PMFetch --journal development --volume 131 --issue 3 transcription factor
|
366
|
+
|
367
|
+
|
368
|
+
Short options are also available.
|
369
|
+
|
370
|
+
% PMFetch -j development -v 131 -i 3 transcription factor
|
371
|
+
|
372
|
+
|
373
|
+
Search articles indexed in PubMed within these 90 days.
|
374
|
+
|
375
|
+
% PMFetch -q "transcription factor" --reldate 90
|
376
|
+
|
377
|
+
|
378
|
+
Search articles indexed in PubMed during the period of 2001/04/01 to 2001/08/31
|
379
|
+
|
380
|
+
% PMFetch -q "transcription factor" --mindate 2001/04/01 --maxdate 2001/08/31
|
381
|
+
|
382
|
+
|
383
|
+
Output format can be changed by --format option.
|
384
|
+
|
385
|
+
% PMFetch -q "transcription factor" -j development -v 131 -i 3 -f report
|
386
|
+
% PMFetch -q "transcription factor" -j development -v 131 -i 3 -f rd
|
387
|
+
% PMFetch -q "transcription factor" -j development -v 131 -i 3 -f endnote
|
388
|
+
% PMFetch -q "transcription factor" -j development -v 131 -i 3 -f medline
|
389
|
+
% PMFetch -q "transcription factor" -j development -v 131 -i 3 -f bibitem
|
390
|
+
% PMFetch -q "transcription factor" -j development -v 131 -i 3 -f bibtex
|
391
|
+
% PMFetch -q "transcription factor" -j development -v 131 -i 3 -f nature
|
392
|
+
% PMFetch -q "transcription factor" -j development -v 131 -i 3 -f science
|
393
|
+
|
394
|
+
|
395
|
+
Generate title listings for the journal report meeting (don't forget
|
396
|
+
to inclease the number of --retmax for fetching all titles).
|
397
|
+
|
398
|
+
% PMFetch -f report -j development -v 131 -i 3 -n 100
|
399
|
+
|
400
|
+
|
401
|
+
Search by author name.
|
402
|
+
|
403
|
+
% PMFetch -a "Karlin S"
|
404
|
+
% PMFetch -a "Koonin EV"
|
405
|
+
|
406
|
+
|
407
|
+
Search by MeSH term.
|
408
|
+
|
409
|
+
% PMFetch -m "computational biology"
|
410
|
+
% PMFetch -m "SARS virus"
|
411
|
+
|
412
|
+
|
413
|
+
Search by PubMed ID (PMID).
|
414
|
+
|
415
|
+
% PMFetch 12345
|
416
|
+
|
417
|
+
|
418
|
+
Output PMID only.
|
419
|
+
|
420
|
+
% PMFetch --pmidlist tardigrada
|
421
|
+
|
422
|
+
|
@@ -0,0 +1,30 @@
|
|
1
|
+
# coding: utf-8
|
2
|
+
lib = File.expand_path("../lib", __FILE__)
|
3
|
+
$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
|
4
|
+
require "bio-executables/version"
|
5
|
+
|
6
|
+
Gem::Specification.new do |spec|
|
7
|
+
spec.name = "bio-executables"
|
8
|
+
spec.version = Bio::Executables::VERSION
|
9
|
+
spec.authors = ["BioRuby project"]
|
10
|
+
spec.email = ["staff@bioruby.org"]
|
11
|
+
|
12
|
+
spec.summary = %q{BioRuby executables: utilities bundled with BioRuby}
|
13
|
+
spec.description = %q{BioRuby executables is a collection of miscellaneous utilities for bioinformatics that were formerly part of the BioRuby core ("bio" gem). Because of reducing complexity, they were moved to this gem.}
|
14
|
+
spec.homepage = "https://github.com/bioruby/bioruby-executables"
|
15
|
+
|
16
|
+
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
|
+
spec.add_runtime_dependency "bio-old-biofetch-emulator", ">= 0.0.1"
|
25
|
+
|
26
|
+
spec.add_development_dependency "bundler", "~> 1.15"
|
27
|
+
spec.add_development_dependency "rake", "~> 10.0"
|
28
|
+
spec.add_development_dependency "rdoc", "~> 5"
|
29
|
+
spec.add_development_dependency "test-unit", "~> 3"
|
30
|
+
end
|
metadata
ADDED
@@ -0,0 +1,147 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: bio-executables
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.0.0
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- BioRuby project
|
8
|
+
autorequire:
|
9
|
+
bindir: bin
|
10
|
+
cert_chain: []
|
11
|
+
date: 2017-09-15 00:00:00.000000000 Z
|
12
|
+
dependencies:
|
13
|
+
- !ruby/object:Gem::Dependency
|
14
|
+
name: bio
|
15
|
+
requirement: !ruby/object:Gem::Requirement
|
16
|
+
requirements:
|
17
|
+
- - ">="
|
18
|
+
- !ruby/object:Gem::Version
|
19
|
+
version: 1.5.1
|
20
|
+
type: :runtime
|
21
|
+
prerelease: false
|
22
|
+
version_requirements: !ruby/object:Gem::Requirement
|
23
|
+
requirements:
|
24
|
+
- - ">="
|
25
|
+
- !ruby/object:Gem::Version
|
26
|
+
version: 1.5.1
|
27
|
+
- !ruby/object:Gem::Dependency
|
28
|
+
name: bio-old-biofetch-emulator
|
29
|
+
requirement: !ruby/object:Gem::Requirement
|
30
|
+
requirements:
|
31
|
+
- - ">="
|
32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: 0.0.1
|
34
|
+
type: :runtime
|
35
|
+
prerelease: false
|
36
|
+
version_requirements: !ruby/object:Gem::Requirement
|
37
|
+
requirements:
|
38
|
+
- - ">="
|
39
|
+
- !ruby/object:Gem::Version
|
40
|
+
version: 0.0.1
|
41
|
+
- !ruby/object:Gem::Dependency
|
42
|
+
name: bundler
|
43
|
+
requirement: !ruby/object:Gem::Requirement
|
44
|
+
requirements:
|
45
|
+
- - "~>"
|
46
|
+
- !ruby/object:Gem::Version
|
47
|
+
version: '1.15'
|
48
|
+
type: :development
|
49
|
+
prerelease: false
|
50
|
+
version_requirements: !ruby/object:Gem::Requirement
|
51
|
+
requirements:
|
52
|
+
- - "~>"
|
53
|
+
- !ruby/object:Gem::Version
|
54
|
+
version: '1.15'
|
55
|
+
- !ruby/object:Gem::Dependency
|
56
|
+
name: rake
|
57
|
+
requirement: !ruby/object:Gem::Requirement
|
58
|
+
requirements:
|
59
|
+
- - "~>"
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: '10.0'
|
62
|
+
type: :development
|
63
|
+
prerelease: false
|
64
|
+
version_requirements: !ruby/object:Gem::Requirement
|
65
|
+
requirements:
|
66
|
+
- - "~>"
|
67
|
+
- !ruby/object:Gem::Version
|
68
|
+
version: '10.0'
|
69
|
+
- !ruby/object:Gem::Dependency
|
70
|
+
name: rdoc
|
71
|
+
requirement: !ruby/object:Gem::Requirement
|
72
|
+
requirements:
|
73
|
+
- - "~>"
|
74
|
+
- !ruby/object:Gem::Version
|
75
|
+
version: '5'
|
76
|
+
type: :development
|
77
|
+
prerelease: false
|
78
|
+
version_requirements: !ruby/object:Gem::Requirement
|
79
|
+
requirements:
|
80
|
+
- - "~>"
|
81
|
+
- !ruby/object:Gem::Version
|
82
|
+
version: '5'
|
83
|
+
- !ruby/object:Gem::Dependency
|
84
|
+
name: test-unit
|
85
|
+
requirement: !ruby/object:Gem::Requirement
|
86
|
+
requirements:
|
87
|
+
- - "~>"
|
88
|
+
- !ruby/object:Gem::Version
|
89
|
+
version: '3'
|
90
|
+
type: :development
|
91
|
+
prerelease: false
|
92
|
+
version_requirements: !ruby/object:Gem::Requirement
|
93
|
+
requirements:
|
94
|
+
- - "~>"
|
95
|
+
- !ruby/object:Gem::Version
|
96
|
+
version: '3'
|
97
|
+
description: BioRuby executables is a collection of miscellaneous utilities for bioinformatics
|
98
|
+
that were formerly part of the BioRuby core ("bio" gem). Because of reducing complexity,
|
99
|
+
they were moved to this gem.
|
100
|
+
email:
|
101
|
+
- staff@bioruby.org
|
102
|
+
executables:
|
103
|
+
- br_biofetch.rb
|
104
|
+
- br_bioflat.rb
|
105
|
+
- br_biogetseq.rb
|
106
|
+
- br_pmfetch.rb
|
107
|
+
extensions: []
|
108
|
+
extra_rdoc_files: []
|
109
|
+
files:
|
110
|
+
- ".gitignore"
|
111
|
+
- BSDL
|
112
|
+
- COPYING
|
113
|
+
- COPYING.ja
|
114
|
+
- Gemfile
|
115
|
+
- LEGAL
|
116
|
+
- README.md
|
117
|
+
- Rakefile
|
118
|
+
- bin/br_biofetch.rb
|
119
|
+
- bin/br_bioflat.rb
|
120
|
+
- bin/br_biogetseq.rb
|
121
|
+
- bin/br_pmfetch.rb
|
122
|
+
- bio-executables.gemspec
|
123
|
+
- lib/bio-executables/version.rb
|
124
|
+
homepage: https://github.com/bioruby/bioruby-executables
|
125
|
+
licenses: []
|
126
|
+
metadata: {}
|
127
|
+
post_install_message:
|
128
|
+
rdoc_options: []
|
129
|
+
require_paths:
|
130
|
+
- lib
|
131
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
132
|
+
requirements:
|
133
|
+
- - ">="
|
134
|
+
- !ruby/object:Gem::Version
|
135
|
+
version: '0'
|
136
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
137
|
+
requirements:
|
138
|
+
- - ">="
|
139
|
+
- !ruby/object:Gem::Version
|
140
|
+
version: '0'
|
141
|
+
requirements: []
|
142
|
+
rubyforge_project:
|
143
|
+
rubygems_version: 2.6.11
|
144
|
+
signing_key:
|
145
|
+
specification_version: 4
|
146
|
+
summary: 'BioRuby executables: utilities bundled with BioRuby'
|
147
|
+
test_files: []
|