fix-trinity-output 1.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/.gitignore +48 -0
- data/Gemfile +3 -0
- data/README.md +11 -0
- data/Rakefile +8 -0
- data/bin/fix-trinity-output +42 -0
- data/fix-trinity-output.gemspec +21 -0
- data/lib/fix-trinity-output.rb +1 -0
- data/lib/fix-trinity-output/fix-trinity-output.rb +96 -0
- data/test/helper.rb +8 -0
- data/test/left.fq +888 -0
- data/test/right.fq +880 -0
- data/test/test_test.rb +37 -0
- metadata +150 -0
data/test/test_test.rb
ADDED
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@@ -0,0 +1,37 @@
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#!/usr/bin/env ruby
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require 'helper'
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require 'tmpdir'
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class TestFixer < Test::Unit::TestCase
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context 'fixer' do
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9
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setup do
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@fixer = Fixer.new
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@tmpdir = Dir.mktmpdir
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end
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teardown do
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cmd = "rm -rf #{@tmpdir}"
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`#{cmd}`
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end
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should 'fix pair of fastq files' do
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left = File.join(File.dirname(__FILE__), 'left.fq')
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right = File.join(File.dirname(__FILE__), 'right.fq')
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prefix = "#{@tmpdir}/test"
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@fixer.run left, right, prefix
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assert File.exist?("#{@tmpdir}/test-fixed.1.fastq")
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assert File.exist?("#{@tmpdir}/test-fixed.2.fastq")
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assert File.exist?("#{@tmpdir}/test-fixed.single.fastq")
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lines = `wc -l #{@tmpdir}/test-fixed.1.fastq`
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assert_equal 876, lines.split(/\s+/).first.to_i
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lines = `wc -l #{@tmpdir}/test-fixed.2.fastq`
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assert_equal 876, lines.split(/\s+/).first.to_i
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assert_equal 762, File.size("#{@tmpdir}/test-fixed.single.fastq")
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end
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end
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end
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metadata
ADDED
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--- !ruby/object:Gem::Specification
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name: fix-trinity-output
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version: !ruby/object:Gem::Version
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version: 1.0.0
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platform: ruby
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authors:
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- Chris Boursnell
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2014-10-23 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: trollop
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '2.0'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '2.0'
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- !ruby/object:Gem::Dependency
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name: rake
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '10.3'
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- - ">="
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- !ruby/object:Gem::Version
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version: 10.3.2
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '10.3'
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- - ">="
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- !ruby/object:Gem::Version
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version: 10.3.2
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- !ruby/object:Gem::Dependency
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name: turn
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '0.9'
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- - ">="
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- !ruby/object:Gem::Version
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version: 0.9.7
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '0.9'
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- - ">="
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- !ruby/object:Gem::Version
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version: 0.9.7
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- !ruby/object:Gem::Dependency
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name: simplecov
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '0.8'
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- - ">="
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- !ruby/object:Gem::Version
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version: 0.8.2
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '0.8'
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- - ">="
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- !ruby/object:Gem::Version
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version: 0.8.2
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- !ruby/object:Gem::Dependency
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name: shoulda-context
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '1.2'
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- - ">="
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- !ruby/object:Gem::Version
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version: 1.2.1
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '1.2'
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- - ">="
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- !ruby/object:Gem::Version
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version: 1.2.1
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description: See readme
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email: cmb211@cam.ac.uk
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executables:
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- fix-trinity-output
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extensions: []
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extra_rdoc_files: []
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files:
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- ".gitignore"
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- Gemfile
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- README.md
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- Rakefile
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- bin/fix-trinity-output
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- fix-trinity-output.gemspec
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- lib/fix-trinity-output.rb
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- lib/fix-trinity-output/fix-trinity-output.rb
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- test/helper.rb
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- test/left.fq
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- test/right.fq
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- test/test_test.rb
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homepage: http://rubygems.org/gems/fix-trinity-output
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licenses:
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- MIT
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metadata: {}
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post_install_message:
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rdoc_options: []
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require_paths:
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- lib
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required_ruby_version: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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required_rubygems_version: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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rubyforge_project:
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rubygems_version: 2.2.2
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signing_key:
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specification_version: 4
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summary: Fix output fastq files from Trinity
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test_files: []
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