cagnut_snpeff 0.3.0

checksums.yaml

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+---
+SHA1:
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+  data.tar.gz: 1e36fdf1efa937f926624d850b96305c38b65151
+SHA512:
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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_snpeff.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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+# CagnutSnpeff
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'cagnut_snpeff'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install cagnut_snpeff
+
+## 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_snpeff.
+
+
+## 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_snpeff"
+
+# 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_snpeff.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_snpeff/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "cagnut_snpeff"
+  spec.version       = CagnutSnpeff::VERSION
+  spec.authors       = ['Shi-Gang Wang', 'Tse-Ching Ho']
+  spec.email         = ['seanwang@goldenio.com', 'tsechingho@goldenio.com']
+
+  spec.summary       = %q{Cagnut Snpeff tools}
+  spec.description   = %q{Cagnut Snpeff tools}
+  spec.homepage      = "https://github.com/CAGNUT/cagnut_snpeff"
+  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/lib/cagnut_snpeff/base.rb

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+require 'cagnut_snpeff/functions/snp_annotation'
+
+module CagnutSnpeff
+  class Base
+    def snp_annotation dirs, order, previous_job_id, input = nil
+      opts = { input: input, dirs: dirs, order: order }
+      snp_annotation = CagnutSnpeff::SnpAnnotation.new opts
+      snp_annotation.run previous_job_id
+    end
+  end
+end

data/lib/cagnut_snpeff/check_tools.rb

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+module CagnutSnpeff
+  module CheckTools
+    def check_tool tools_path, ref=nil
+      super if defined?(super)
+      check_snpeff tools['snpeff'], refs['snpeff']['db'], refs['snpeff']['config'] if @java
+    end
+
+      def check_snpeff path, db_version, config_path
+        check_tool_ver 'snpEff' do
+          `#{@java} -jar #{path} -version 2>&1` if path
+        end
+
+        if db_version.nil?
+          @check_completed = false
+          puts "\tNot Set Snpeff DB in config.yml"
+        else
+          puts "\tSnpeff DB: #{db_version}"
+        end
+
+        if config_path
+          path = File.exist?(config_path) ? config_path : 'Not Found' if config_path
+          puts "\tSnpeff config file: #{path}"
+        else
+          puts "\tSnpeff config Not Found"
+        end
+      end
+  end
+end
+
+CagnutSnpeff.config::Checks::Tools.prepend CagnutSnpeff::CheckTools

data/lib/cagnut_snpeff/configuration.rb

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+require 'singleton'
+
+module CagnutSnpeff
+  class Configuration
+    include Singleton
+    attr_accessor :annotation_params
+
+    class << self
+      def load config, tools_config
+        instance.load config, tools_config
+      end
+    end
+
+    def load config, tools_config
+      @config = config
+      @tools_config = tools_config
+      attributes.each do |name, value|
+        send "#{name}=", value if respond_to? "#{name}="
+      end
+    end
+
+    def attributes
+      {
+        annotation_params: annotation_params_setup
+      }
+    end
+
+    private
+
+    def annotation_params_setup
+      {
+        'java' => add_java_params,
+        'params' => add_annotation_options
+      }
+    end
+
+    def add_java_params verbose=false
+      return if @tools_config['annotation'].blank?
+      array =  @tools_config['annotation']['java'].dup
+      array << "-verbose:sizes" if verbose
+      array << "-jar #{@config['tools']['snpeff']}"
+    end
+
+    def add_annotation_options
+      return if @tools_config['annotation'].blank?
+      array =  @tools_config['annotation']['params'].dup
+      array << @config['refs']['snpeff']['db']
+      array << snpeff_config_tag if snpeff_config_tag
+      array.uniq
+    end
+
+    def snpeff_config_tag
+      config = @config['refs']['snpeff']['config']
+      config.nil? ? nil : "-c #{config}"
+    end
+  end
+end

data/lib/cagnut_snpeff/functions/snp_annotation.rb

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+module CagnutSnpeff
+  class SnpAnnotation
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :jobs_dir, :java_path,
+                   :ref_fasta, :prefix_name, :dodebug
+    def_delegators :'CagnutSnpeff.config', :annotation_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}.vcf" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/#{sample_name}_snpeff.vcf"
+      @job_name = "#{prefix_name}_snpEff_#{sample_name}"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting snpAnnotation #{sample_name} Jobs"
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, cluster_options(previous_job_id)
+      @job_name
+    end
+
+    def cluster_options previous_job_id = nil
+      {
+        previous_job_id: previous_job_id,
+        adjust_memory: ['h_stack=256M', 'h_vmem=8G'],
+        tools: ['snpeff', 'annotation']
+      }
+    end
+
+    def annotation_options
+      array = annotation_params['params'].dup
+      array << "#{@input} > #{@output}"
+      array.uniq
+    end
+
+    def modified_java_array
+      array = annotation_params['java'].dup
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination_hash
+      @params_combination_hash ||= {
+        'java' => modified_java_array,
+        'params' => annotation_options
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_snpeff_snp_annotation"
+      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 $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+
+          #{params_combination_hash['java'].join("\s")} \\
+            #{params_combination_hash['params'].join(" \\\n            ")} \\
+            #{::Cagnut::JobManage.run_local}
+
+          EXITSTATUS=$?
+
+          #force error when missing output
+          if [ ! -s "#{@output}" ]; then exit 100;fi;
+          if [ $(grep -cv "^#" "#{@output}") -eq "0" ]
+          then
+            echo "No variants!"
+            exit 100;
+          fi
+
+          if [ $EXITSTATUS -eq 1 ];then
+            echo "Error in Java"
+            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)
+      script_name
+    end
+  end
+end

data/lib/cagnut_snpeff/util.rb

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+module CagnutSnpeff
+  class Util
+    attr_accessor :snpeff
+
+    def initialize
+      @snpeff = CagnutSnpeff::Base.new
+    end
+
+    def snp_annotation dirs, order=1, previous_job_id=nil, filename=nil
+      job_name = snpeff.snp_annotation dirs, order, previous_job_id, filename
+      [job_name, order]
+    end
+  end
+end

data/lib/cagnut_snpeff/version.rb

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+module CagnutSnpeff
+  VERSION = "0.3.0"
+end

data/lib/cagnut_snpeff.rb

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+require "cagnut_snpeff/version"
+
+module CagnutSnpeff
+  class << self
+    def config
+      @config ||= begin
+        CagnutSnpeff::Configuration.load(Cagnut::Configuration.config, Cagnut::Configuration.params['snpeff'])
+        CagnutSnpeff::Configuration.instance
+      end
+    end
+  end
+end
+
+require 'cagnut_snpeff/configuration'
+require 'cagnut_snpeff/base'
+require 'cagnut_snpeff/util'

metadata

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+--- !ruby/object:Gem::Specification
+name: cagnut_snpeff
+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 Snpeff tools
+email:
+- seanwang@goldenio.com
+- tsechingho@goldenio.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".ruby-version"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- cagnut_snpeff.gemspec
+- lib/cagnut_snpeff.rb
+- lib/cagnut_snpeff/base.rb
+- lib/cagnut_snpeff/check_tools.rb
+- lib/cagnut_snpeff/configuration.rb
+- lib/cagnut_snpeff/functions/snp_annotation.rb
+- lib/cagnut_snpeff/util.rb
+- lib/cagnut_snpeff/version.rb
+homepage: https://github.com/CAGNUT/cagnut_snpeff
+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 Snpeff tools
+test_files: []