cagnut_gatk 0.3.0

checksums.yaml

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+---
+SHA1:
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+  data.tar.gz: 0b74a7f00a8a7ecc9f9a4be0cf3f88a87de2fc57
+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_gatk.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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+# CagnutGatk
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'cagnut_gatk'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install cagnut_gatk
+
+## 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_gatk.
+
+
+## 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_gatk"
+
+# 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_gatk.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_gatk/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "cagnut_gatk"
+  spec.version       = CagnutGatk::VERSION
+  spec.authors       = ['Shi-Gang Wang', 'Tse-Ching Ho']
+  spec.email         = ['seanwang@goldenio.com', 'tsechingho@goldenio.com']
+
+  spec.summary       = %q{Cagnut Gatk tools}
+  spec.description   = %q{Cagnut Gatk tools}
+  spec.homepage      = "https://github.com/CAGNUT/cagnut_gatk"
+  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_gatk/base.rb

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+require 'cagnut_gatk/functions/count_read'
+require 'cagnut_gatk/functions/realigner_target_creator'
+require 'cagnut_gatk/functions/indel_realigner'
+require 'cagnut_gatk/functions/base_recalibrator'
+require 'cagnut_gatk/functions/analyze_covariates'
+require 'cagnut_gatk/functions/print_reads'
+require 'cagnut_gatk/functions/depth_of_coverage'
+require 'cagnut_gatk/functions/unified_genotyper'
+require 'cagnut_gatk/functions/haplotype_caller'
+require 'cagnut_gatk/functions/variant_filtration'
+require 'cagnut_gatk/functions/variant_eval'
+
+module CagnutGatk
+  class Base
+
+    def count_read dirs, order, previous_job_id, opts = {}
+      opts = { dirs: dirs, order: order }.merge opts
+      count_read = CagnutGatk::CountRead.new opts
+      count_read.run previous_job_id
+    end
+
+    def realigner_target_creator dirs, order, previous_job_id, input = nil
+      opts = { input: input, dirs: dirs, order: order }
+      realigner_target_creator = CagnutGatk::RealignerTargetCreator.new opts
+      realigner_target_creator.run previous_job_id
+    end
+
+    def indel_realigner dirs, order, previous_job_id, input, interval_list
+      opts = { input: input, interval_list: interval_list, dirs: dirs, order: order }
+      indel_realigner = CagnutGatk::IndelRealigner.new opts
+      indel_realigner.run previous_job_id
+    end
+
+    def base_recalibrator dirs, order, previous_job_id, input, opts
+      opts = { input: input, dirs: dirs, order: order }.merge opts
+      base_recalibrator = CagnutGatk::BaseRecalibrator.new opts
+      base_recalibrator.run previous_job_id
+    end
+
+    def analyze_covariates dirs, order, previous_job_id, input
+      opts = { input: input, dirs: dirs, order: order }
+      analyze_covariates = CagnutGatk::AnalyzeCovariates.new opts
+      analyze_covariates.run previous_job_id
+    end
+
+    def print_reads dirs, order, previous_job_id, input
+      opts = { input: input, dirs: dirs, order: order}
+      print_reads = CagnutGatk::PrintReads.new opts
+      print_reads.run previous_job_id
+    end
+
+    def depth_of_coverage dirs, order, previous_job_id, input, opts
+      opts = { input: input, dirs: dirs, order: order }.merge opts
+      depth_of_coverage = CagnutGatk::DepthOfCoverage.new opts
+      depth_of_coverage.run previous_job_id
+    end
+
+    def haplotype_caller dirs, order, previous_job_id, input
+      opts = { input: input, dirs: dirs, order: order }
+      haplotype_caller = CagnutGatk::HaplotypeCaller.new opts
+      haplotype_caller.run previous_job_id
+    end
+
+    def unified_genotyper dirs, order, previous_job_id, input
+      opts = { input: input, dirs: dirs, order: order }
+      unifiedgenotyper = CagnutGatk::UnifiedGenotyper.new opts
+      unifiedgenotyper.run previous_job_id
+    end
+
+    def variant_filtration dirs, order, previous_job_id, input
+      opts = { input: input, dirs: dirs, order: order }
+      variant_filtration = CagnutGatk::VariantFiltration.new opts
+      variant_filtration.run previous_job_id
+    end
+
+    def variant_eval dirs, order, previous_job_id, input
+      opts = { input: input, dirs: dirs, order: order }
+      variant_eval = CagnutGatk::VariantEval.new opts
+      variant_eval.run previous_job_id
+    end
+  end
+end

data/lib/cagnut_gatk/check_tools.rb

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+module CagnutGatk
+  module CheckTools
+    def check_tool tools_path
+      super if defined?(super)
+      check_gatk tools_path['gatk'] if @java
+    end
+
+    def check_gatk path
+      check_tool_ver 'GATK' do
+        `#{@java} -jar #{path} --version` if path
+      end
+    end
+  end
+end
+
+Cagnut::Configuration::Checks::Tools.prepend CagnutGatk::CheckTools

data/lib/cagnut_gatk/configuration.rb

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+require 'singleton'
+
+module CagnutGatk
+  class Configuration
+
+    include Singleton
+    attr_accessor :analyze_covariates_params, :base_recalibrator_params,
+                  :count_reads_params, :depth_of_coverage_params,
+                  :haplotype_caller_params, :indel_realigner_params,
+                  :print_reads_params, :realigner_target_creator_params,
+                  :unified_genotyper_params, :variant_eval_params,
+                  :variant_filtration_params
+
+    class << self
+      def load config, params
+        instance.load config, params
+      end
+    end
+
+    def load config, params
+      @config = config
+      @params = params
+      attributes.each do |name, value|
+        send "#{name}=", value if respond_to? "#{name}="
+      end
+    end
+
+    def attributes
+      {
+        analyze_covariates_params: add_java_params(@params['analyze_covariates']),
+        base_recalibrator_params: add_java_params(@params['base_recalibrator']),
+        count_reads_params: add_java_params(@params['count_reads']),
+        depth_of_coverage_params: add_java_params(@params['depth_of_coverage'], true),
+        haplotype_caller_params: add_java_params(@params['haplotype_caller']),
+        indel_realigner_params: add_java_params(@params['indel_realigner']),
+        print_reads_params: add_java_params(@params['print_reads']),
+        realigner_target_creator_params: add_java_params(@params['realigner_target_creator']),
+        unified_genotyper_params: add_java_params(@params['unified_genotyper']),
+        variant_eval_params: add_java_params(@params['variant_eval']),
+        variant_filtration_params: add_java_params(@params['variant_filtration'])
+      }
+    end
+
+    def add_java_params method_params, verbose=false
+      return if method_params.blank?
+      array = method_params['java'].dup
+      array << "-verbose:sizes" if verbose
+      array << "-jar #{@config['tools']['gatk']}"
+      {
+        'java' => array,
+        'params' => method_params['params']
+      }
+    end
+
+  end
+end

data/lib/cagnut_gatk/functions/analyze_covariates.rb

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+module CagnutGatk
+  class AnalyzeCovariates
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :jobs_dir, :prefix_name,
+                   :ref_fasta, :dodebug, :java_path, :magic28
+    def_delegators :'CagnutGatk.config', :analyze_covariates_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @job_name = "#{prefix_name}_AnalyzeCovariates_#{sample_name}"
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_realn.bam" : opts[:input]
+      @recal_csv = "#{opts[:dirs][:contrast]}/#{replace_filename('_recal.csv')}"
+      @recal_bqsr_csv = "#{opts[:dirs][:contrast]}/#{replace_filename('_recal_post.csv')}"
+      @output = "#{opts[:dirs][:output]}/#{output_file}"
+    end
+
+    def file_basename
+      @basename ||= File.basename @input
+    end
+
+    def replace_filename target_name
+      file_basename.gsub '_realn.bam', target_name
+    end
+
+    def output_file
+      output = replace_filename '_recalibration_plots.pdf'
+      return output unless output == file_basename
+      abort 'Input file is not correctly'
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting AnalyzeCovariates #{sample_name}"
+      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
+      core_num = 6
+      {
+        previous_job_id: previous_job_id,
+        var_env: ["#{core_num}"],
+        adjust_memory: ["h_vmem=adjustWorkingMem 7G #{core_num}"],
+        tools: ['gatk', 'analyze_covariates']
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_gatk_analyze_covariates"
+      file = File.join jobs_dir, "#{script_name}.sh"
+      path = File.expand_path '../templates/analyze_covariates.sh', __FILE__
+      template = Tilt.new path
+      File.open(file, 'w') do |f|
+        f.puts template.render Object.new, job_params(script_name)
+      end
+      File.chmod(0700, file)
+      script_name
+    end
+
+    def params_combination
+      {
+        'java' => modified_java_array,
+        'params' => analyze_covariates_options
+      }
+    end
+
+    def analyze_covariates_options
+      array = analyze_covariates_params['params'].dup
+      array << "-T AnalyzeCovariates"
+      array << "-R #{ref_fasta}"
+      array << "-before #{@recal_csv}"
+      array << "-after #{@recal_bqsr_csv}"
+      array << "-plots #{@output}"
+      array.uniq
+    end
+
+    def modified_java_array
+      array = analyze_covariates_params['java'].dup
+      array.unshift(java_path).uniq
+    end
+
+    def job_params script_name
+      {
+        jobs_dir: jobs_dir,
+        script_name: script_name,
+        after: @after,
+        output: @output,
+        analyze_covariates_params: params_combination,
+        run_local: "#{::Cagnut::JobManage.run_local}"
+      }
+    end
+  end
+end

data/lib/cagnut_gatk/functions/base_recalibrator.rb

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+module CagnutGatk
+  class BaseRecalibrator
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :jobs_dir, :prefix_name,
+                   :ref_fasta, :snpdb, :target_flanks_file, :dodebug,
+                   :magic28, :java_path
+    def_delegators :'CagnutGatk.config', :base_recalibrator_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @csv_dir = opts[:dirs][:output]
+      @has_bqsr_file = opts[:has_bqsr_file]
+      @input = opts[:file_name].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_realn.bam" : opts[:input]
+      setup_output_and_bqsr_file
+    end
+
+    def setup_output_and_bqsr_file
+      file_name = File.basename @input
+      if @has_bqsr_file
+        output = file_name.gsub '_realn.bam', '_recal_post.csv'
+        bqsr_file = file_name.gsub '_realn.bam', '_recal.csv'
+      else
+        output = file_name.gsub '_realn.bam', '_recal.csv'
+      end
+      @output = "#{@csv_dir}/#{output}"
+      @bqsr_file = "#{@csv_dir}/#{bqsr_file}" if @has_bqsr_file
+    end
+
+    def run previous_job_id = nil
+      message = @has_bqsr_file ? 'with BQSR' : ''
+      puts "Submitting BaseRecalibrator #{sample_name} #{message}"
+      script_name = generate_script
+      job_name = "#{prefix_name}_#{script_name}"
+      ::Cagnut::JobManage.submit script_name, job_name, cluster_options(previous_job_id)
+      job_name
+    end
+
+    def cluster_options previous_job_id = nil
+      core_num = 6
+      {
+        previous_job_id: previous_job_id,
+        var_env: [core_num],
+        adjust_memory: ["h_vmem=adjustWorkingMem 7G #{core_num}"],
+        parallel_env: [core_num],
+        tools: ['gatk', 'base_recalibrator']
+      }
+    end
+
+    def generate_script
+      script_name = @has_bqsr_file ? "#{@order}_gatk_base_recalibrator_post" : "#{@order}_gatk_base_recalibrator"
+      file = File.join jobs_dir, "#{script_name}.sh"
+      path = File.expand_path "../templates/base_recalibrator.sh", __FILE__
+      template = Tilt.new path
+      File.open(file, 'w') do |f|
+        f.puts template.render Object.new, job_params(script_name)
+      end
+      File.chmod(0700, file)
+      script_name
+    end
+
+    def base_recalibrator_options
+      dtag = snpdb.nil? ? "--run_without_dbsnp_potentially_ruining_quality" : "-knownSites #{snpdb}"
+      array = base_recalibrator_params['params'].dup
+      array << "-T BaseRecalibrator"
+      array << "-R #{ref_fasta}"
+      array << "-I #{@input}"
+      array << "-o #{@output}"
+      array << "#{dtag}"
+      array << "-BQSR #{@bqsr_file}" if @has_bqsr_file
+      array << "-L #{target_flanks_file}" if target_flanks_file
+      array.uniq
+    end
+
+    def modified_java_array
+      array = base_recalibrator_params['java'].dup
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination
+      {
+        'java' => modified_java_array,
+        'params' => base_recalibrator_options
+      }
+    end
+
+    def job_params script_name
+      {
+        jobs_dir: jobs_dir,
+        script_name: script_name,
+        magic28: magic28,
+        input: @input,
+        output: @output,
+        base_recalibrator_params: params_combination,
+        run_local: ::Cagnut::JobManage.run_local
+      }
+    end
+  end
+end

data/lib/cagnut_gatk/functions/count_read.rb

@@ -0,0 +1,77 @@
+module CagnutGatk
+  class CountRead
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :jobs_dir, :java_path,
+                   :ref_fasta, :prefix_name, :dodebug
+    def_delegators :'CagnutGatk.config', :count_reads_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @target = opts[:target]
+      @suffix = @target.nil? ? 'genome.readct' : 'target.readct'
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_markdup.bam" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/#{sample_name}_markdup_#{@suffix}"
+      @job_name = "#{prefix_name}_countRead_#{sample_name}_#{@suffix}"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting countRead #{@suffix}"
+      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,
+        var_env: [ref_fasta],
+        adjust_memory: ['h_vmem=5G'],
+        tools: ['gatk', 'count_reads']
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_gatk_count_reads_#{@suffix}"
+      file = File.join jobs_dir, "#{script_name}.sh"
+      path = File.expand_path '../templates/count_read.sh', __FILE__
+      template = Tilt.new path
+      File.open(file, 'w') do |f|
+        f.puts template.render Object.new, job_params(script_name)
+      end
+      File.chmod(0700, file)
+      script_name
+    end
+
+    def count_reads_options
+      array = count_reads_params['params'].dup
+      array << "-T CountReads"
+      array << "-R #{ref_fasta}"
+      array << "-I #{@input} > #{@output}"
+      array << "-L #{@target}" if @target
+      array.uniq
+    end
+
+    def modified_java_array
+      array = count_reads_params['java'].dup
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination
+      {
+        'java' => modified_java_array,
+        'params' => count_reads_options
+      }
+    end
+
+    def job_params script_name
+      {
+        jobs_dir: jobs_dir,
+        script_name: script_name,
+        output: @output,
+        count_reads_params: params_combination,
+        run_local: ::Cagnut::JobManage.run_local
+      }
+    end
+  end
+end

data/lib/cagnut_gatk/functions/depth_of_coverage.rb

@@ -0,0 +1,81 @@
+module CagnutGatk
+  class DepthOfCoverage
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :jobs_dir, :java_path,
+                   :ref_fasta, :prefix_name, :dodebug
+    def_delegators :'CagnutGatk.config', :depth_of_coverage_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @suffix = opts[:suffix]
+      @target_file = opts[:target]
+      @job_name = "#{prefix_name}_#{sample_name}_#{@suffix}_depthofcoverage"
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_recal.bam" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/#{sample_name}_#{@suffix}_depthofcoverage"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting #{sample_name} #{@suffix} depth of coverage Jobs"
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, cluster_options(previous_job_id)
+      [@job_name, @output]
+    end
+
+    def cluster_options previous_job_id = nil
+      core_num = 6
+      {
+        previous_job_id: previous_job_id,
+        var_env: [core_num],
+        adjust_memory: ['h_stack=256M', 'h_vmem=8G'],
+        parallel_env: [core_num],
+        tools: ['gatk', 'depth_of_coverage']
+      }
+    end
+
+    def generate_script
+      file_name = "#{@order}_gatk_depth_of_coverage_#{@suffix}"
+      file = File.join jobs_dir, "#{file_name}.sh"
+      path = File.expand_path '../templates/depth_of_coverage.sh', __FILE__
+      template = Tilt.new path
+      File.open(file, 'w') do |f|
+        f.puts template.render Object.new, job_params(file_name)
+      end
+      File.chmod(0700, file)
+      file_name
+    end
+
+    def depth_of_coverage_options
+      target = @target_file.blank? ? '-omitIntervals' : "-L #{@target_file}"
+      array = depth_of_coverage_params['params'].dup
+      array << "-T DepthOfCoverage"
+      array << "-R #{ref_fasta}"
+      array << "-I #{@input}"
+      array << "-o #{@output}"
+      array << target
+      array.uniq
+    end
+
+    def modified_java_array
+      array = depth_of_coverage_params['java'].dup
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination_hash
+      {
+        'java' => modified_java_array,
+        'params' => depth_of_coverage_options
+      }
+    end
+
+    def job_params script_name
+      {
+        jobs_dir: jobs_dir,
+        script_name: script_name,
+        output: @output,
+        depth_of_coverage_params: params_combination_hash,
+        run_local: ::Cagnut::JobManage.run_local
+      }
+    end
+  end
+end