bio-kallisto 0.1.0
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- checksums.yaml +7 -0
- data/.document +5 -0
- data/.travis.yml +15 -0
- data/Gemfile +15 -0
- data/LICENSE.txt +20 -0
- data/README.md +47 -0
- data/README.rdoc +48 -0
- data/Rakefile +51 -0
- data/VERSION +1 -0
- data/bin/kallisto_index.rb +9 -0
- data/bin/kallisto_map.rb +9 -0
- data/ext/Rakefile +34 -0
- data/lib/bio-kallisto.rb +12 -0
- data/lib/bio-kallisto/kallisto.rb +49 -0
- data/test/helper.rb +34 -0
- data/test/test_bio-kallisto.rb +7 -0
- metadata +161 -0
checksums.yaml
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---
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SHA1:
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metadata.gz: 36048108c5b9813bf977518cf77b594d149b9082
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data.tar.gz: 14574c16217eb8cc0104e6dbe09e32e331af1fd2
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SHA512:
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metadata.gz: 038678b6cda9589385e8d9d5e3d10d2f9eda5d7c6149f252711c651a820b34db2dee47345fcfebb53f277486a5824a541a1c33e2b1e9b7087ab83272c3d4ada2
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data.tar.gz: a8d95291fcf1a1587a0776dc6f87fe62325df8c749331d9d9cdb6a3ef44ca47aabfe8e34f088bf9b1548c6db9d53bba46e732ccd8e0b33eee4cc62cdb10371c5
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data/.document
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data/.travis.yml
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language: ruby
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rvm:
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- 2.1.0
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- 2.2.0
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# - 1.9.2
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# - 1.9.3
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# - jruby-19mode # JRuby in 1.9 mode
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# - rbx-19mode
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# - 1.8.7
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# - jruby-18mode # JRuby in 1.8 mode
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# - rbx-18mode
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# uncomment this line if your project needs to run something other than `rake`:
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# script: bundle exec rspec spec
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data/Gemfile
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source "http://rubygems.org"
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# Add dependencies required to use your gem here.
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# Example:
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# gem "activesupport", ">= 2.3.5"
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gem "systemu", ">=2.5.2"
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# Add dependencies to develop your gem here.
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# Include everything needed to run rake, tests, features, etc.
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group :development do
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gem "shoulda", ">= 0"
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gem "rdoc", "~> 3.12"
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gem "simplecov", ">= 0"
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gem "jeweler", ">=2.0.1"
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gem "bundler", ">= 1.0.21"
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gem "bio", ">= 1.4.2"
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end
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data/LICENSE.txt
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Copyright (c) 2015 homonecloco
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.md
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# bio-kallisto
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[![Build Status](https://secure.travis-ci.org/homonecloco/bioruby-kallisto.png)](http://travis-ci.org/homonecloco/bioruby-kallisto)
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Full description goes here
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Note: this software is under active development!
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## Installation
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```sh
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gem install bio-kallisto
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```
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## Usage
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```ruby
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require 'bio-kallisto'
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```
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The API doc is online. For more code examples see the test files in
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the source tree.
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## Project home page
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Information on the source tree, documentation, examples, issues and
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how to contribute, see
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http://github.com/homonecloco/bioruby-kallisto
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The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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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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## Biogems.info
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This Biogem is published at (http://biogems.info/index.html#bio-kallisto)
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## Copyright
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Copyright (c) 2015 homonecloco. See LICENSE.txt for further details.
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data/README.rdoc
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= bio-kallisto
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{<img
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src="https://secure.travis-ci.org/homonecloco/bioruby-kallisto.png"
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/>}[http://travis-ci.org/#!/homonecloco/bioruby-kallisto]
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Full description goes here
|
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Note: this software is under active development!
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== Installation
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gem install bio-kallisto
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== Usage
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== Developers
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To use the library
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require 'bio-kallisto'
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The API doc is online. For more code examples see also the test files in
|
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the source tree.
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|
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== Project home page
|
27
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+
|
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Information on the source tree, documentation, issues and how to contribute, see
|
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|
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http://github.com/homonecloco/bioruby-kallisto
|
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The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
|
33
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+
|
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== Cite
|
35
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+
|
36
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+
If you use this software, please cite one of
|
37
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+
|
38
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+
* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
|
39
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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)
|
40
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+
|
41
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== Biogems.info
|
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|
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This Biogem is published at http://biogems.info/index.html#bio-kallisto
|
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|
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== Copyright
|
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|
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Copyright (c) 2015 homonecloco. See LICENSE.txt for further details.
|
48
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data/Rakefile
ADDED
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# encoding: utf-8
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require 'rubygems'
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require 'bundler'
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begin
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Bundler.setup(:default, :development)
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rescue Bundler::BundlerError => e
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$stderr.puts e.message
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9
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$stderr.puts "Run `bundle install` to install missing gems"
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exit e.status_code
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end
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require 'rake'
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require 'jeweler'
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Jeweler::Tasks.new do |gem|
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# gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
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gem.name = "bio-kallisto"
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gem.homepage = "http://github.com/homonecloco/bioruby-kallisto"
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gem.license = "MIT"
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gem.summary = %Q{Basic wrapper for the Kallistio Mapper}
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gem.description = %Q{Basic wrapper for the Kallistio Mapper}
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gem.email = "ricardo.ramirez-gonzalez@tgac.ac.uk"
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gem.authors = ["homonecloco"]
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# dependencies defined in Gemfile
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end
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Jeweler::RubygemsDotOrgTasks.new
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require 'rake/testtask'
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Rake::TestTask.new(:test) do |test|
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test.libs << 'lib' << 'test'
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test.pattern = 'test/**/test_*.rb'
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test.verbose = true
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end
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desc "Code coverage detail"
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task :simplecov do
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ENV['COVERAGE'] = "true"
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Rake::Task['test'].execute
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end
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task :default => :test
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require 'rdoc/task'
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Rake::RDocTask.new do |rdoc|
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version = File.exist?('VERSION') ? File.read('VERSION') : ""
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+
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rdoc.rdoc_dir = 'rdoc'
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rdoc.title = "bio-kallisto #{version}"
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rdoc.rdoc_files.include('README*')
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rdoc.rdoc_files.include('lib/**/*.rb')
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end
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data/VERSION
ADDED
@@ -0,0 +1 @@
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1
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0.1.0
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data/bin/kallisto_map.rb
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#!/bin/env ruby
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$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
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$: << File.expand_path('.')
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path= File.expand_path(File.dirname(__FILE__) + '/../lib/bio-kallisto.rb')
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require path
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Bio::Kallisto.map(index:ARGV[0], fastq:[ARGV[1], ARGV[2]], output_dir:ARGV[3] )
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data/ext/Rakefile
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require 'rbconfig'
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require 'open-uri'
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require 'fileutils'
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include FileUtils::Verbose
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require 'rake/clean'
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version="0.42.3"
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URL="https://github.com/pachterlab/kallisto/archive/v#{version}.tar.gz"
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path = File.expand_path(File.dirname(__FILE__))
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puts path
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#path_external = File.join ( path , "../lib/bio/external" )
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task :download do
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open(URL) do |uri|
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File.open("v#{version}.tar.gz",'wb') do |fout|
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fout.write(uri.read)
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end #fout
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end #uri
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end
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task :compile do
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sh "tar -xzf v#{version}.tar.gz"
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cd ("kallisto-#{version}") do
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mkdir "build"
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cd "build" do
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sh "cmake -DCMAKE_INSTALL_PREFIX:PATH=#{path}/../lib/bio/external .."
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sh "make"
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sh "make install"
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end
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end
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end
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#task :default => [:download, :compile, :clean]
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task :default => [:download, :compile]
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data/lib/bio-kallisto.rb
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# Please require your code below, respecting the naming conventions in the
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# bioruby directory tree.
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#
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# For example, say you have a plugin named bio-plugin, the only uncommented
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# line in this file would be
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#
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# require 'bio/bio-plugin/plugin'
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#
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# In this file only require other files. Avoid other source code.
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require 'bio-kallisto/kallisto.rb'
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require 'systemu'
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module Bio
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class Kallisto
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def self.index (reference:, output_index:nil, k:31 , unique: false )
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$stderr.put "reference undefined " unless reference
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output_index = "#{reference}.kallisto.k#{k}" unless output_index
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extra=""
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extra="--make-unique" if unique
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command = "kallisto index --kmer-size=#{k} --index=#{output_index} #{extra} #{reference}"
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status, stdout, stderr = systemu command
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if status.exitstatus != 0
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$stderr.puts "Failed to run wrapping command correctly, as non-zero exit status "+
|
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"#{status.exitstatus} detected. Command run was `#{command}'"
|
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return false
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else
|
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return true
|
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+
end
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end
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|
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def self.map(index:, fastq:, output_dir:, single:false, bias:false, fragment_length:0, pseudobam:false, bootstrap_samples:0, threads:1, seed:42)
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+
|
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extra = ""
|
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extra += " --single" if single
|
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extra += " --bias" if bias
|
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extra += " --fragment-length=#{fragment_length}" if fragment_length > 0
|
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extra += " --pseudobam" if pseudobam
|
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extra += " --bootstrap-samples=#{bootstrap-samples}" if bootstrap_samples > 0
|
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extra += " --threads=#{threads}" if threads > 1
|
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extra += " --seed=#{seed}" if seed != 42
|
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command = "kallisto quant --index=#{index} --output-dir=#{output_dir} #{extra} #{fastq.join(' ')}"
|
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|
+
|
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status, stdout, stderr = systemu command
|
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|
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if status.exitstatus != 0
|
40
|
+
$stderr.puts "Failed to run wrapping command correctly, as non-zero exit status "+
|
41
|
+
"#{status.exitstatus} detected. Command run was `#{command}'"
|
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return false
|
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+
else
|
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return true
|
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|
+
end
|
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|
+
|
47
|
+
end
|
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+
end
|
49
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+
end
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data/test/helper.rb
ADDED
@@ -0,0 +1,34 @@
|
|
1
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require 'simplecov'
|
2
|
+
|
3
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+
module SimpleCov::Configuration
|
4
|
+
def clean_filters
|
5
|
+
@filters = []
|
6
|
+
end
|
7
|
+
end
|
8
|
+
|
9
|
+
SimpleCov.configure do
|
10
|
+
clean_filters
|
11
|
+
load_adapter 'test_frameworks'
|
12
|
+
end
|
13
|
+
|
14
|
+
ENV["COVERAGE"] && SimpleCov.start do
|
15
|
+
add_filter "/.rvm/"
|
16
|
+
end
|
17
|
+
require 'rubygems'
|
18
|
+
require 'bundler'
|
19
|
+
begin
|
20
|
+
Bundler.setup(:default, :development)
|
21
|
+
rescue Bundler::BundlerError => e
|
22
|
+
$stderr.puts e.message
|
23
|
+
$stderr.puts "Run `bundle install` to install missing gems"
|
24
|
+
exit e.status_code
|
25
|
+
end
|
26
|
+
require 'test/unit'
|
27
|
+
require 'shoulda'
|
28
|
+
|
29
|
+
$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
|
30
|
+
$LOAD_PATH.unshift(File.dirname(__FILE__))
|
31
|
+
require 'bio-kallisto'
|
32
|
+
|
33
|
+
class Test::Unit::TestCase
|
34
|
+
end
|
metadata
ADDED
@@ -0,0 +1,161 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: bio-kallisto
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.1.0
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- homonecloco
|
8
|
+
autorequire:
|
9
|
+
bindir: bin
|
10
|
+
cert_chain: []
|
11
|
+
date: 2015-10-05 00:00:00.000000000 Z
|
12
|
+
dependencies:
|
13
|
+
- !ruby/object:Gem::Dependency
|
14
|
+
name: systemu
|
15
|
+
requirement: !ruby/object:Gem::Requirement
|
16
|
+
requirements:
|
17
|
+
- - ">="
|
18
|
+
- !ruby/object:Gem::Version
|
19
|
+
version: 2.5.2
|
20
|
+
type: :runtime
|
21
|
+
prerelease: false
|
22
|
+
version_requirements: !ruby/object:Gem::Requirement
|
23
|
+
requirements:
|
24
|
+
- - ">="
|
25
|
+
- !ruby/object:Gem::Version
|
26
|
+
version: 2.5.2
|
27
|
+
- !ruby/object:Gem::Dependency
|
28
|
+
name: shoulda
|
29
|
+
requirement: !ruby/object:Gem::Requirement
|
30
|
+
requirements:
|
31
|
+
- - ">="
|
32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: '0'
|
34
|
+
type: :development
|
35
|
+
prerelease: false
|
36
|
+
version_requirements: !ruby/object:Gem::Requirement
|
37
|
+
requirements:
|
38
|
+
- - ">="
|
39
|
+
- !ruby/object:Gem::Version
|
40
|
+
version: '0'
|
41
|
+
- !ruby/object:Gem::Dependency
|
42
|
+
name: rdoc
|
43
|
+
requirement: !ruby/object:Gem::Requirement
|
44
|
+
requirements:
|
45
|
+
- - "~>"
|
46
|
+
- !ruby/object:Gem::Version
|
47
|
+
version: '3.12'
|
48
|
+
type: :development
|
49
|
+
prerelease: false
|
50
|
+
version_requirements: !ruby/object:Gem::Requirement
|
51
|
+
requirements:
|
52
|
+
- - "~>"
|
53
|
+
- !ruby/object:Gem::Version
|
54
|
+
version: '3.12'
|
55
|
+
- !ruby/object:Gem::Dependency
|
56
|
+
name: simplecov
|
57
|
+
requirement: !ruby/object:Gem::Requirement
|
58
|
+
requirements:
|
59
|
+
- - ">="
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: '0'
|
62
|
+
type: :development
|
63
|
+
prerelease: false
|
64
|
+
version_requirements: !ruby/object:Gem::Requirement
|
65
|
+
requirements:
|
66
|
+
- - ">="
|
67
|
+
- !ruby/object:Gem::Version
|
68
|
+
version: '0'
|
69
|
+
- !ruby/object:Gem::Dependency
|
70
|
+
name: jeweler
|
71
|
+
requirement: !ruby/object:Gem::Requirement
|
72
|
+
requirements:
|
73
|
+
- - ">="
|
74
|
+
- !ruby/object:Gem::Version
|
75
|
+
version: 2.0.1
|
76
|
+
type: :development
|
77
|
+
prerelease: false
|
78
|
+
version_requirements: !ruby/object:Gem::Requirement
|
79
|
+
requirements:
|
80
|
+
- - ">="
|
81
|
+
- !ruby/object:Gem::Version
|
82
|
+
version: 2.0.1
|
83
|
+
- !ruby/object:Gem::Dependency
|
84
|
+
name: bundler
|
85
|
+
requirement: !ruby/object:Gem::Requirement
|
86
|
+
requirements:
|
87
|
+
- - ">="
|
88
|
+
- !ruby/object:Gem::Version
|
89
|
+
version: 1.0.21
|
90
|
+
type: :development
|
91
|
+
prerelease: false
|
92
|
+
version_requirements: !ruby/object:Gem::Requirement
|
93
|
+
requirements:
|
94
|
+
- - ">="
|
95
|
+
- !ruby/object:Gem::Version
|
96
|
+
version: 1.0.21
|
97
|
+
- !ruby/object:Gem::Dependency
|
98
|
+
name: bio
|
99
|
+
requirement: !ruby/object:Gem::Requirement
|
100
|
+
requirements:
|
101
|
+
- - ">="
|
102
|
+
- !ruby/object:Gem::Version
|
103
|
+
version: 1.4.2
|
104
|
+
type: :development
|
105
|
+
prerelease: false
|
106
|
+
version_requirements: !ruby/object:Gem::Requirement
|
107
|
+
requirements:
|
108
|
+
- - ">="
|
109
|
+
- !ruby/object:Gem::Version
|
110
|
+
version: 1.4.2
|
111
|
+
description: Basic wrapper for the Kallistio Mapper
|
112
|
+
email: ricardo.ramirez-gonzalez@tgac.ac.uk
|
113
|
+
executables:
|
114
|
+
- kallisto_index.rb
|
115
|
+
- kallisto_map.rb
|
116
|
+
extensions: []
|
117
|
+
extra_rdoc_files:
|
118
|
+
- LICENSE.txt
|
119
|
+
- README.md
|
120
|
+
- README.rdoc
|
121
|
+
files:
|
122
|
+
- ".document"
|
123
|
+
- ".travis.yml"
|
124
|
+
- Gemfile
|
125
|
+
- LICENSE.txt
|
126
|
+
- README.md
|
127
|
+
- README.rdoc
|
128
|
+
- Rakefile
|
129
|
+
- VERSION
|
130
|
+
- bin/kallisto_index.rb
|
131
|
+
- bin/kallisto_map.rb
|
132
|
+
- ext/Rakefile
|
133
|
+
- lib/bio-kallisto.rb
|
134
|
+
- lib/bio-kallisto/kallisto.rb
|
135
|
+
- test/helper.rb
|
136
|
+
- test/test_bio-kallisto.rb
|
137
|
+
homepage: http://github.com/homonecloco/bioruby-kallisto
|
138
|
+
licenses:
|
139
|
+
- MIT
|
140
|
+
metadata: {}
|
141
|
+
post_install_message:
|
142
|
+
rdoc_options: []
|
143
|
+
require_paths:
|
144
|
+
- lib
|
145
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
146
|
+
requirements:
|
147
|
+
- - ">="
|
148
|
+
- !ruby/object:Gem::Version
|
149
|
+
version: '0'
|
150
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
151
|
+
requirements:
|
152
|
+
- - ">="
|
153
|
+
- !ruby/object:Gem::Version
|
154
|
+
version: '0'
|
155
|
+
requirements: []
|
156
|
+
rubyforge_project:
|
157
|
+
rubygems_version: 2.4.7
|
158
|
+
signing_key:
|
159
|
+
specification_version: 4
|
160
|
+
summary: Basic wrapper for the Kallistio Mapper
|
161
|
+
test_files: []
|