cagnut_toolbox 0.3.0

checksums.yaml

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data/.gitignore

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

data/.rspec

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+--format documentation
+--color

data/.ruby-version

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+ruby-2.3.1

data/.travis.yml

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+sudo: false
+language: ruby
+rvm:
+  - 2.3.1
+before_install: gem install bundler -v 1.12.5

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in cagnut_toolbox.gemspec
+gemspec

data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2016 Goldenio Technology
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.md

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+# CagnutToolbox
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'cagnut_toolbox'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install cagnut_toolbox
+
+## Usage
+
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/cagnut_toolbox.
+
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](http://opensource.org/licenses/MIT).
+

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "cagnut_toolbox"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start

data/bin/setup

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/cagnut_toolbox.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'cagnut_toolbox/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "cagnut_toolbox"
+  spec.version       = CagnutToolbox::VERSION
+  spec.authors       = ['Shi-Gang Wang', 'Tse-Ching Ho']
+  spec.email         = ['seanwang@goldenio.com', 'tsechingho@goldenio.com']
+
+  spec.summary       = %q{Cagnut Toolbox tools}
+  spec.description   = %q{Cagnut Toolbox tools}
+  spec.homepage      = "https://github.com/CAGNUT/cagnut_toolbox"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_dependency 'cagnut_core'
+
+  spec.add_development_dependency "bundler", "~> 1.12"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+end

data/exe/qseq_to_fastq.rb

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+#!/usr/bin/env ruby
+require 'zlib'
+
+File.open(ARGV[0], 'w') do |f|
+  STDIN.each_line do |line|
+    part = line.gsub!(/\n/, '').split(/\t/)
+    f.puts "@#{part[2..7].join(':')}\n"
+    f.puts "#{part[8]}\n"
+    f.puts "+\n"
+    f.puts "#{part[9]}\n"
+  end
+end

data/lib/cagnut_toolbox.rb

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+require "cagnut_toolbox/version"
+
+module CagnutToolbox
+  class << self
+    def config
+      @config ||= begin
+        CagnutToolbox::Configuration.load(Cagnut::Configuration.config, Cagnut::Configuration.params['toolbox'])
+        CagnutToolbox::Configuration.instance
+      end
+    end
+
+    def root
+      ::Pathname.new File.expand_path '../..', __FILE__
+    end
+  end
+end
+
+require 'cagnut_toolbox/configuration'
+require 'cagnut_toolbox/base'
+require 'cagnut_toolbox/util'

data/lib/cagnut_toolbox/base.rb

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+require 'cagnut_toolbox/functions/qseq_to_fastq'
+
+module CagnutToolbox
+  class Base
+    def qseq2fastq dirs
+      opts = { dirs: dirs, order: order }
+      qseq2fastq = CagnutToolbox::QseqToFastq.new opts
+      qseq2fastq.run
+    end
+  end
+end

data/lib/cagnut_toolbox/configuration.rb

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+require 'singleton'
+
+module CagnutToolbox
+class Configuration
+    include Singleton
+    attr_accessor :exe_path
+
+    class << self
+      def load config, params
+        instance.load config, params
+      end
+    end
+
+    def load config, params
+      @config = config
+      attributes.each do |name, value|
+        send "#{name}=", value if respond_to? "#{name}="
+      end
+    end
+
+    def attributes
+      {
+        exe_path: exe_path
+      }
+    end
+
+    def exe_path
+      CagnutToolbox.root.join('exe')
+    end
+  end
+end

data/lib/cagnut_toolbox/functions/qseq_to_fastq.rb

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+module CagnutToolbox
+  class QseqToFastq
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :dodebug,
+                   :jobs_dir, :ref_fasta, :seqs_path, :prefix_name
+    def_delegators :'CagnutToolbox.config', :exe_path
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @input = opts[:input].nil? ? "#{seqs_path}" : opts[:input]
+      @input.gsub! '.gz', ''
+      @input2 = File.expand_path fetch_filename, File.dirname(@input)
+      abort('Cant recognized sequence files') if @input2.nil?
+      @output = "#{opts[:dirs][output]}/#{sample_name}_1_qtf.fastq"
+      @output2 = "#{opts[:dirs][output]}/s_#{sample_name}_2_qtf.fastq"
+      @job_name = "#{prefix_name}_qseq_to_fastq_#{sample_name}"
+    end
+
+    def fetch_filename
+      filename = File.basename(@input)
+      if filename.match '_R1_'
+        filename.gsub '_R1_', '_R2_'
+      elsif filename.match '_1_'
+        filename.gsub '_1_', '_2_'
+      end
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting #{sample_name} qseqToFastq"
+      script_name = generate_script task
+      ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id)
+      [@job_name, @output]
+    end
+
+    def queuing_options previous_job_id = nil
+      {
+        previous_job_id: previous_job_id,
+        tools: ['toolbox', 'qseq_to_fastq']
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_toolbox_qseq2fastq"
+      exe_qseq_to_fastq = "ruby #{exe_path}/qseq_to_fastq.rb"
+      file = File.join jobs_dir, "#{script_name}.sh"
+      File.open(file, 'w') do |f|
+        f.puts <<-BASH.strip_heredoc
+          #!/bin/bash
+
+          cd "#{jobs_dir}/../"
+          echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+          if [ -s "#{@input}.gz" ]
+          then
+            gunzip -c #{@input}.gz | #{exe_qseq_to_fastq} #{@output} \\
+              #{::Cagnut::JobManage.run_local}
+            gunzip -c #{@input2}.gz | #{exe_qseq_to_fastq} #{@output2} \\
+              #{::Cagnut::JobManage.run_local}
+          else
+            cat #{@input} | #{exe_qseq_to_fastq} #{@output} \\
+              #{::Cagnut::JobManage.run_local}
+            cat #{@input2} | #{exe_qseq_to_fastq} #{@output2} \\
+              #{::Cagnut::JobManage.run_local}
+          fi
+
+          #force error when missing/empty fastq . Would prevent continutation of pipeline
+          if [ ! -s "#{@output2}" ]
+          then
+            echo "Missing FASTQ: #{@output2} file!"
+            exit 100
+          fi
+          echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+
+        BASH
+      end
+      File.chmod(0700, file)
+    end
+  end
+end

data/lib/cagnut_toolbox/util.rb

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+module CagnutToolbox
+  class Util
+    attr_accessor :toolbox, :config
+
+    def initialize configure
+      @config = configure
+      @toolbox = CagnutToolbox::Base.new
+    end
+
+    def qseq2fastq dirs, order=1
+      if check_files
+        job_name, filename = toolbox.qseq2fastq dirs, order
+        [job_name, filename, order+1]
+      else
+        [nil, nil, order]
+      end
+    end
+
+    private
+
+    def check_files
+      tilesqseq? && check_incomplete_fastq
+    end
+
+    def tilesqseq?
+      @config['data_type'] == 'TILESQSEQ'
+    end
+
+    def check_incomplete_fastq
+      file = fetch_filename @config['seqs_path'][sample]
+      !File.size? file
+    end
+
+    def fetch_filename file
+      filename = File.basename(@file)
+      if filename.match '_R1_'
+        filename.gsub '_R1_', '_R2_'
+      elsif filename.match '_1_'
+        filename.gsub '_1_', '_2_'
+      end
+    end
+  end
+end

data/lib/cagnut_toolbox/version.rb

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+module CagnutToolbox
+  VERSION = "0.3.0"
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: cagnut_toolbox
+version: !ruby/object:Gem::Version
+  version: 0.3.0
+platform: ruby
+authors:
+- Shi-Gang Wang
+- Tse-Ching Ho
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2016-11-01 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: cagnut_core
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.12'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+description: Cagnut Toolbox tools
+email:
+- seanwang@goldenio.com
+- tsechingho@goldenio.com
+executables:
+- qseq_to_fastq.rb
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".ruby-version"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- cagnut_toolbox.gemspec
+- exe/qseq_to_fastq.rb
+- lib/cagnut_toolbox.rb
+- lib/cagnut_toolbox/base.rb
+- lib/cagnut_toolbox/configuration.rb
+- lib/cagnut_toolbox/functions/qseq_to_fastq.rb
+- lib/cagnut_toolbox/util.rb
+- lib/cagnut_toolbox/version.rb
+homepage: https://github.com/CAGNUT/cagnut_toolbox
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.5.1
+signing_key: 
+specification_version: 4
+summary: Cagnut Toolbox tools
+test_files: []