cagnut_bwa 0.3.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 212201476cdd487c7d175275b4b2dda5064794a8
+  data.tar.gz: e1b5fb5113d105b8ba7782c3b34e100fb05f6820
+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_bwa.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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+# CagnutBwa
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'cagnut_bwa'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install cagnut_bwa
+
+## 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_bwa.
+
+
+## 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_bwa"
+
+# 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_bwa.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_bwa/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "cagnut_bwa"
+  spec.version       = CagnutBwa::VERSION
+  spec.authors       = ['Shi-Gang Wang', 'Tse-Ching Ho']
+  spec.email         = ['seanwang@goldenio.com', 'tsechingho@goldenio.com']
+
+  spec.summary       = %q{Cagnut BWA tools}
+  spec.description   = %q{Cagnut BWA tools}
+  spec.homepage      = "https://github.com/CAGNUT/cagnut_bwa"
+  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_bwa/base.rb

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+require 'cagnut_bwa/functions/aln'
+require 'cagnut_bwa/functions/samp'
+require 'cagnut_bwa/functions/aln_one_fastq'
+require 'cagnut_bwa/functions/samp_one_fastq'
+require 'cagnut_bwa/functions/mem'
+
+module CagnutBwa
+  class Base
+    def aln dirs, order, previous_job_id, input = nil
+      opts = { input: input, dirs: dirs, order: order  }
+      CagnutBwa::Aln.new(opts).run previous_job_id
+    end
+
+    def samp dirs, order, previous_job_id = nil, input = nil
+      opts = { input: input, dirs: dirs, order: order  }
+      CagnutBwa::Samp.new(opts).run previous_job_id
+    end
+
+    def aln_one_fastq dirs, order, input = nil
+      opts = { input: input, dirs: dirs, order: order  }
+      CagnutBwa::AlnOneFastq.new(opts).run
+    end
+
+    def samp_one_fastq dirs, order, previous_job_id = nil, input = nil
+      opts = { input: input, dirs: dirs, order: order  }
+      CagnutBwa::SampOneFastq.new(opts).run previous_job_id
+    end
+
+    def mem dirs, order, input = nil
+      opts = { input: input, dirs: dirs, order: order }
+      CagnutBwa::Mem.new(opts).run
+    end
+  end
+end

data/lib/cagnut_bwa/check_tools.rb

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+module CagnutBwa
+  module CheckTools
+    def check_tool tools_path
+      super if defined?(super)
+      check_bwa tools_path['bwa']
+      check_bwa_index refs['ref_fasta']
+    end
+
+    def check_bwa path
+      check_tool_ver 'BWA' do
+        `#{path} 2>&1 | grep Version | cut -f2 -d ' '` if path
+        check_bwa_index
+      end
+    end
+
+    def check_bwa_index ref_path
+      tool = 'Bwa Index'
+      file = "#{ref_path}.ann"
+      command = "#{@config['tools']['bwa']} index #{ref_path}"
+      check_ref_related file, tool, command
+    end
+
+
+    def check_ref_related file, tool, command
+      if File.exist?(file)
+        puts "\t#{tool}: Done"
+      else
+        puts "\t#{tool}: Not Found!"
+        puts "\tPlease execute command:"
+        puts "\t\t#{command}"
+        @check_completed = false
+      end
+    end
+  end
+end
+
+Cagnut::Configuration::Checks::Tools.prepend CagnutBwa::CheckTools

data/lib/cagnut_bwa/configuration.rb

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+require 'singleton'
+
+module CagnutBwa
+  class Configuration
+    include Singleton
+    attr_accessor :rg_str, :mem_params, :aln_params, :samp_params
+
+    class << self
+      def load config, params
+        instance.load config, params
+      end
+    end
+
+    def load config, params
+      @config = config
+      @params = params
+      generate_rg_str
+      attributes.each do |name, value|
+        send "#{name}=", value if respond_to? "#{name}="
+      end
+    end
+
+    def attributes
+      {
+        rg_str: @config['sample']['rg_str'],
+        mem_params: add_bwa_path_in_params(@params['mem']),
+        aln_params: add_bwa_path_in_params(@params['aln']),
+        samp_params: add_bwa_path_in_params(@params['samp'])
+      }
+    end
+
+    def add_bwa_path_in_params method_params
+      return if method_params.blank?
+      array = method_params['params'].dup
+      array.unshift "#{@config['tools']['bwa']}"
+    end
+
+    def generate_rg_str
+      @config['samples'].each do |sample|
+        arg = %W(
+          @RG
+          ID:#{sample['rgid']}
+          SM:#{sample['name']}
+          PL:#{@config['info']['pl']}
+          PU:#{sample['pu']}
+          LB:#{@config['info']['lb']}
+          DS:#{@config['info']['ds']}
+          CN:#{@config['info']['cn']}
+          DT:#{@config['info']['dt']}
+        )
+        rg_str = { 'rg_str' => arg.join('\t') }
+        sample.merge! rg_str
+      end
+    end
+  end
+end

data/lib/cagnut_bwa/functions/aln.rb

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+module CagnutBwa
+  class Aln
+    extend Forwardable
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :dodebug, :seqs_path,
+                   :ref_fasta, :jobs_dir, :prefix_name, :pipeline_name
+    def_delegators :'CagnutBwa.config', :aln_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @input = opts[:input].nil? ? "#{seqs_path}" : opts[:input]
+      @input2 = File.expand_path fetch_filename, File.dirname(@input)
+      abort('Cant recognized sequence files') if @input2.nil?
+      @output = "#{opts[:dirs][:output]}/#{File.basename(@input)}.sai"
+      @output2 = "#{opts[:dirs][:output]}/#{fetch_filename}.sai"
+      @job_name = "#{prefix_name}_#{sample_name}_Aln"
+    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 bwaAln #{sample_name}"
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id)
+      @job_name
+    end
+
+    def queuing_options previous_job_id = nil
+      threads = 2
+      {
+        previous_job_id: previous_job_id,
+        var_env: [ref_fasta],
+        adjust_memory: ["h_vmem=adjustWorkingMem 5G #{threads}"],
+        parallel_env: [threads],
+        tools: ['bwa', 'aln']
+      }
+    end
+
+    def aln_params_for_r1
+      array = aln_params.dup
+      array.insert 1, 'aln'
+      array << "#{ref_fasta}"
+      array << "-f #{@output}"
+      array << "#{@input}"
+      array.uniq
+    end
+
+    def aln_params_for_r2
+      array = aln_params.dup
+      array.insert 1, 'aln'
+      array << "#{ref_fasta}"
+      array << "-f #{@output2}"
+      array << "#{@input2}"
+      array.uniq
+    end
+
+    def generate_script
+      script_name = "#{@order}_bwa_aln"
+      file = File.join jobs_dir, "#{script_name}.sh"
+      template = Tilt.new(File.expand_path '../templates/aln.sh', __FILE__)
+      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 job_params script_name
+      {
+        jobs_dir: jobs_dir,
+        script_name: script_name,
+        input: @input,
+        input2: @input2,
+        output: @output,
+        output2: @output2,
+        aln_params_for_r1: aln_params_for_r1,
+        aln_params_for_r2: aln_params_for_r2,
+        run_local: ::Cagnut::JobManage.run_local
+      }
+    end
+  end
+end

data/lib/cagnut_bwa/functions/aln_one_fastq.rb

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+module CagnutBwa
+  class AlnOneFastq
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :prefix_name, :dodebug,
+                   :ref_fasta, :jobs_dir, :data_type
+    def_delegators :'CagnutBwa.config', :aln_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @input = opts[:input].nil? ? "#{seqs_path}" : opts[:input]
+      abort('Cant recognized sequence files') if @input.nil?
+      @input2 = File.expand_path fetch_filename(@input), File.dirname(@input) if @input.match '_1_'
+      @output = "#{opts[:dirs][:output]}/#{File.basename(@input).gsub('.gz', '').gsub('.txt','.sai')}"
+      @output2 = "#{opts[:dirs][:output]}/#{fetch_filename(@output)}" if @input.match '_1_'
+      @job_name = "#{prefix_name}_#{sample_name}_Aln_one_fastq"
+    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
+
+    def run previous_job_id = nil
+      puts "Submitting bwa_aln_one_fastq #{sample_name}"
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id)
+      @job_name
+    end
+
+    def queuing_options previous_job_id = nil
+      threads = 2
+      {
+        previous_job_id: previous_job_id,
+        var_env: [fastq_dir, sai_dir, threads],
+        adjust_memory: ['h_vmem=3.4G'],
+        parallel_env: [threads],
+        tools: ['bwa', 'aln']
+      }
+    end
+
+    def aln_params_for_r1
+      array = aln_params.dup
+      array.insert 1, 'aln'
+      array << "#{ref_fasta}"
+      array << "-f #{@output}"
+      array << "#{@input}"
+      array.uniq
+    end
+
+    def aln_params_for_r2
+      array = aln_params.dup
+      array.insert 1, 'aln'
+      array << "#{ref_fasta}"
+      array << "-f #{@output2}"
+      array << "#{@input2}"
+      array.uniq
+    end
+
+    def generate_script
+      script_name = "#{@order}_bwa_aln_one_fastq"
+      file = File.join jobs_dir, "#{script_name}.sh"
+      File.open(file, 'w') do |f|
+        f.puts <<-BASH.strip_heredoc
+          #!/bin/bash
+          echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+          if [[ #{@input} =~ _1_ ]]
+          then
+            #{aln_params_for_r2.join(" \\\n            ")} \\
+              #{::Cagnut::JobManage.run_local}
+          else
+          fi
+
+          #{aln_params_for_r1.join(" \\\n            ")} \\
+            #{::Cagnut::JobManage.run_local}
+
+          if [ ! -s "#{@output}" ]
+          then
+            echo "Missing SAI:#{@output} 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)
+      script_name
+    end
+  end
+end

data/lib/cagnut_bwa/functions/mem.rb

@@ -0,0 +1,74 @@
+module CagnutBwa
+  class Mem
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :seqs_path,
+                   :ref_fasta, :jobs_dir, :prefix_name
+    def_delegators :'CagnutBwa.config', :rg_str, :mem_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @input = opts[:input].nil? ? "#{seqs_path}" : opts[:input]
+      @input2 = File.expand_path fetch_filename, File.dirname(@input)
+      abort('Cant recognized sequence files') if @input2.nil?
+      @output = "#{opts[:dirs][:output]}/#{sample_name}_mem.sam"
+      @job_name = "#{prefix_name}_#{sample_name}_mem*"
+    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 bwaMem #{sample_name}"
+      script_name = generate_script
+      ::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: ['bwa', 'mem']
+      }
+    end
+
+    def mem_options
+      array = mem_params.dup
+      array.insert 1, 'mem'
+      array << "-M"
+      array << "-R \"#{rg_str}\""
+      array << "#{ref_fasta}"
+      array << "#{@input}"
+      array << "#{@input2}"
+      array << "> #{@output}"
+      array.uniq
+    end
+
+    def generate_script
+      script_name = "#{@order}_bwa_mem"
+      file = File.join jobs_dir, "#{script_name}.sh"
+      template = Tilt.new(File.expand_path '../templates/mem.sh', __FILE__)
+      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 job_params script_name
+      {
+        jobs_dir: jobs_dir,
+        script_name: script_name,
+        output: @output,
+        mem_params: mem_options,
+        run_local: ::Cagnut::JobManage.run_local
+      }
+    end
+  end
+end

data/lib/cagnut_bwa/functions/samp.rb

@@ -0,0 +1,81 @@
+module CagnutBwa
+  class Samp
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :seqs_path,
+                   :ref_fasta, :jobs_dir, :dodebug, :prefix_name
+    def_delegators :'CagnutBwa.config', :rg_str,:samp_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @fastq = opts[:input].nil? ? "#{seqs_path}" : opts[:input]
+      @fastq2 = File.expand_path fetch_filename(@fastq), File.dirname(@fastq)
+      @input = "#{opts[:dirs][:input]}/#{File.basename(@fastq)}.sai"
+      @input2 = File.expand_path fetch_filename(@input), File.dirname(@input)
+      abort('Cant recognized sequence files') if @input2.nil?
+      @output = "#{opts[:dirs][:output]}/#{sample_name}_aligned.sam.gz"
+      @job_name = "#{prefix_name}_#{sample_name}_Samp"
+    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
+
+    def run previous_job_id = nil
+      puts "Submitting bwaSamp #{sample_name} RG_STR= #{rg_str}"
+      script_name = generate_script
+      ::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,
+        adjust_memory: ['h_vmem=5G'],
+        tools: ['bwa', 'samp']
+      }
+    end
+
+    def samp_options
+      array = samp_params.dup
+      array.insert 1, 'sampe'
+      array << "-r \"#{rg_str}\""
+      array << "#{ref_fasta}"
+      array << "#{@input}"
+      array << "#{@input2}"
+      array << "#{@fastq}"
+      array << "#{@fastq2} | gzip > #{@output}"
+      array.uniq.compact
+    end
+
+    def generate_script
+      script_name = "#{@order}_bwa_samp"
+      file = File.join jobs_dir, "#{script_name}.sh"
+      template = Tilt.new(File.expand_path '../templates/samp.sh', __FILE__)
+      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 job_params script_name
+      {
+        jobs_dir: jobs_dir,
+        script_name: script_name,
+        input: @input,
+        input2: @input2,
+        fastq: @fastq,
+        fastq2: @fastq2,
+        output: @output,
+        samp_options: samp_options,
+        run_local: ::Cagnut::JobManage.run_local
+      }
+    end
+  end
+end

data/lib/cagnut_bwa/functions/samp_one_fastq.rb

@@ -0,0 +1,95 @@
+module CagnutBwa
+  class SampOneFastq
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :prefix_name,
+                   :ref_fasta, :jobs_dir, :data_type, :dodebug
+    def_delegators :'CagnutBwa.config', :rg_str, :samp_params
+
+    def initizaline opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @job_name = "#{prefix_name}_#{sample_name}_Samp"
+      @seq = opts[:input].nil? ? "#{seqs_path}" : opts[:input]
+      abort('Cant recognized sequence files') if @seq.nil?
+      @sai = "#{opts[:dirs][:input]}/#{File.basename(@seq).gsub('.gz', '').gsub('.txt','.sai')}"
+      @seq2 = @seq.match('_1_') ? "#{File.expand_path(fetch_filename(@seq), File.dirname(@seq))}" : ''
+      @sai2 = @sai.match('_1_') ? "#{opts[:dirs][:input]}/#{fetch_filename(@sai)}" : ''
+      @output = "#{opts[:dirs][:output]}/#{sample_name}_sequence.aligned.sam.gz"
+    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
+
+    def run previous_job_id = nil
+      puts "Submitting bwaSampOneFastq #{sample_name} RG_STR= #{rg_str}"
+      script_name = generate_script
+      ::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,
+        adjust_memory: ['h_vmem=5G'],
+        parallel_env: ['30'],
+        tools: ['bwa', 'samp']
+      }
+    end
+
+    def generate_script
+      script_name = data_type == 'ONEFASTQ' ? 'bwa_samp_one_fastq' : 'bwa_samse_one_fastq'
+      bwa_samp_one_fastq script_name
+      script_name
+    end
+
+    def samp_one_fastq_options
+      array = samp_params.dup
+      array.insert 1, 'sampe'
+      array << "-r \"#{rg_str}\""
+      array << "#{ref_fasta}"
+      array << "#{@sai}"
+      array << "#{@sai2}"
+      array << "#{@seq}"
+      array << "#{@seq2} | gzip > #{@output}"
+      array.uniq.compact
+    end
+
+    def samse_one_fastq_options
+      array = samp_params.dup
+      array.insert 1, 'sampe'
+      array << "-r \"#{rg_str}\""
+      array << "#{ref_fasta}"
+      array << "#{@sai}"
+      array << "#{@seq} | gzip > #{@output}"
+      array.uniq.compact
+    end
+
+    def bwa_samp_one_fastq script_name
+      file = File.join jobs_dir, "#{@order}_#{script_name}.sh"
+      path = File.expand_path "../templates/#{script_name}.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)
+    end
+
+    def job_params script_name
+      {
+        jobs_dir: jobs_dir,
+        script_name: script_name,
+        output: @output,
+        seq: @seq,
+        seq2: @seq2,
+        samp_options: (data_type == 'ONEFASTQ' ? 'samp_one_fastq_options' : 'samse_one_fastq_options'),
+        run_local: ::Cagnut::JobManage.run_local
+      }
+    end
+  end
+end

data/lib/cagnut_bwa/functions/templates/aln.sh

@@ -0,0 +1,104 @@
+#!/bin/bash
+
+cd "#{jobs_dir}/../"
+echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+echo #{aln_params_for_r1.join("\s")}
+#{aln_params_for_r1.join(" \\\n  ")} \\
+  #{run_local}
+
+#force error when missing/empty sai . Would prevent continutation of pipeline
+if [ ! -s "#{output}" ]
+then
+  echo "Missing SAI:#{output} file!"
+  exit 100
+fi
+
+# check STDOUT has correct termination string
+HASENDING=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed.")
+
+if [ -n "$HASENDING" ]
+then
+  OK=1
+else
+  #echo " empty variable"
+  echo "Improper stdout termination"
+  exit 100
+fi
+
+#check for correct number of sequences processed, based on fastq records
+PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o -P " \\d+ ")
+
+echo "checking stdout file: " #{jobs_dir}/#{script_name}.err
+echo "bwa processed" $PROCESSED
+
+if [[ "#{input}" =~ gz$ ]]
+then
+  LINESFASTQ1=$(zcat "#{input}" | wc -l)
+else
+# non gz files
+  LINESFASTQ1=$(wc -l "#{input}" | cut -d" " -f1 )
+fi
+  echo "Fastq1 number lines:= " $LINESFASTQ1
+  SEQLINES=$[ $LINESFASTQ1 / 4 ]
+  echo "Estimated Minimum Sequences:= " $SEQLINES
+  if (( "$PROCESSED" >= "$SEQLINES" ))
+    then
+      echo "Complete."
+    else
+      echo "Error, incorrect number of processed sequences"
+      exit 100
+  fi
+
+####################################################################
+# PAIR _2_
+# run and check pair _2_
+#
+#
+####################################################################
+
+#{aln_params_for_r2.join(" \\\n  ")} \\
+  #{run_local}
+
+#force error when missing/empty sai . Would prevent continutation of pipeline
+if [ ! -s "#{output2}" ]
+then
+  echo "Missing SAI:#{output2} file!"
+  exit 100
+fi
+
+# check STDOUT has correct termination string
+HASENDING=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed.")
+
+if [ -n "$HASENDING" ]
+then
+  OK=1
+else
+  #echo " empty variable"
+  echo "Improper stdout termination"
+  exit 100
+fi
+
+#check for correct number of sequences processed, based on fastq records
+PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o -P " \\d+ ")
+echo "checking stdout file: " #{jobs_dir}/#{script_name}.err
+echo "bwa processed" $PROCESSED
+
+if [[ "#{input2}" =~ gz$ ]]
+then
+  LINESFASTQ2=$(zcat "#{input2}" | wc -l)
+else
+# non gz files
+  LINESFASTQ2=$(wc -l "#{input2}" | cut -d" " -f1 )
+fi
+  echo "Fastq2 number lines:= " $LINESFASTQ2
+  SEQLINES=$[ $LINESFASTQ2 / 4 ]
+  echo "Estimated Minimum Sequences:= " $SEQLINES
+  if (( "$PROCESSED" >= "$SEQLINES" ))
+    then
+      echo "Complete."
+    else
+      echo "Error, incorrect number of processed sequences"
+      exit 100
+  fi
+
+echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"

data/lib/cagnut_bwa/functions/templates/bwa_samp_one_fastq.sh

@@ -0,0 +1,67 @@
+#!/bin/bash
+
+cd "#{jobs_dir}/../"
+echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+#{samp_options.join(" \\\n  ")} \\
+  #{run_local}
+
+# check file size less than 1MB
+#
+# if [ $(stat --printf="%s" "#{sam_dir}/#{line}_sequence.aligned.sam.gz") -le 1024000 ]
+# then
+#  echo "Error with output."
+#  exit 100
+# fi
+
+#check STDOUT has correct termination string
+HASENDING=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed.")
+
+if [ -n "$HASENDING" ]
+then
+  echo "OUTPUT ok."
+else
+  #echo " empty variable"
+  echo "Improper stdout termination"
+  exit 100
+fi
+
+#check for correct number of sequences processed, based on fastq records
+PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o -P " \\d+ ")
+
+echo "checking stdout file: " #{jobs_dir}/#{script_name}.err
+echo "bwa processed" $PROCESSED
+
+if [[ "#{seq}" =~ gz$ ]]
+then
+
+  LINESFASTQ1=$(zcat "#{seq}" | wc -l)
+  LINESFASTQ2=$(zcat "#{seq2}" | wc -l)
+
+else
+# non gz files
+  LINESFASTQ1=$(wc -l "#{seq}" )
+  LINESFASTQ2=$(wc -l "#{seq2}" )
+fi
+
+echo "Fastq1 number lines:= " $LINESFASTQ1
+echo "Fastq2 number lines:= " $LINESFASTQ2
+
+if (( "$LINESFASTQ1" >= "$LINESFASTQ2" ))
+then
+  SEQLINES=$[ $LINESFASTQ2 / 4 ]
+else
+  SEQLINES=$[ $LINESFASTQ1 / 4 ]
+fi
+
+echo "Estimated Minimum Sequences:= " $SEQLINES
+
+if (( "$PROCESSED" >= "$SEQLINES" ))
+then
+  echo "Complete."
+else
+  echo "Error, incorrect number of processed sequences"
+  exit 100
+fi
+
+echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+

data/lib/cagnut_bwa/functions/templates/bwa_samse_one_fastq.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+
+cd "#{jobs_dir}/../"
+echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+#{samp_options.join(" \\\n  ")} \\
+  #{run_local}
+
+# check file size less than 1MB
+
+if [ $(stat --printf="%s" "#{output}") -le 1024000 ]
+then
+  echo "Error with output."
+  exit 100
+fi
+
+#check STDOUT has correct termination string
+HASENDING=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed.")
+
+if [ -n "$HASENDING" ]
+then
+  echo "OUTPUT ok."
+else
+  #echo " empty variable"
+  echo "Improper stdout termination"
+  exit 100
+fi
+
+#check for correct number of sequences processed, based on fastq records
+
+PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o -P " \\d+ ")
+
+echo "checking stdout file: " #{jobs_dir}/#{script_name}.err
+echo "bwa processed" $PROCESSED
+echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"

data/lib/cagnut_bwa/functions/templates/mem.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+
+cd "#{jobs_dir}/../"
+echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+echo #{mem_params.join("\s")}
+#{mem_params.join(" \\\n  ")} \\
+  #{run_local}
+
+#force error when missing/empty sam . Would prevent continutation of pipeline
+if [ ! -s #{output} ]
+then
+  echo "Missing SAM:#{output} file!"
+  exit 100
+fi
+
+# check STDOUT has correct termination string
+HASENDING=$(tail -5 #{jobs_dir}/#{script_name}.err  | grep " Processed")
+
+if [ -n "$HASENDING" ]
+then
+  OK=1
+else
+  #echo " empty variable"
+  echo "Error: Improper stdout termination"
+  echo $EXITSTATUS
+  echo "bwa (mem) has likely crashed. Exiting"
+  exit 100
+fi
+echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"

data/lib/cagnut_bwa/functions/templates/samp.sh

@@ -0,0 +1,73 @@
+#!/bin/bash
+
+cd "#{jobs_dir}/../"
+echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+# File Checking
+if [ ! -s "#{input}" ];then
+  echo "Error: Missing " #{input}
+  exit 100
+fi
+if [ ! -s "#{input2}" ];then
+  echo "Error: Missing " #{input2}
+  exit 100
+fi
+
+#{samp_options.join(" \\\n  ")} \\
+  #{run_local}
+
+# check if file size less than 1MB
+if [ $(stat --printf="%s" "#{output}") -le 1024000 ]
+then
+  echo "Error with output."
+  exit 100
+fi
+
+# check STDOUT has correct termination string
+HASENDING=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed.")
+
+if [ -n "$HASENDING" ]
+then
+  OK=1
+else
+  #echo " empty variable"
+  echo "Improper stdout termination"
+  exit 100
+fi
+
+#check for correct number of sequences processed, based on fastq records
+PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o -P " \\d+ ")
+
+echo "checking stdout file: " #{jobs_dir}/#{script_name}.err
+echo "bwa processed" $PROCESSED
+
+if [[ "#{fastq}" =~ gz$ ]]
+then
+  LINESFASTQ1=$(zcat "#{fastq}" | wc -l)
+  LINESFASTQ2=$(zcat "#{fastq2}.gz" | wc -l)
+else
+# non gz files
+  LINESFASTQ1=$(wc -l "#{fastq}" | cut -d" " -f1 )
+  LINESFASTQ2=$(wc -l "#{fastq2}" | cut -d" " -f1 )
+fi
+
+echo "Fastq1 number lines:= " $LINESFASTQ1
+echo "Fastq2 number lines:= " $LINESFASTQ2
+
+if (( "$LINESFASTQ1" >= "$LINESFASTQ2" ))
+then
+  SEQLINES=$[ $LINESFASTQ2 / 4 ]
+else
+  SEQLINES=$[ $LINESFASTQ1 / 4 ]
+fi
+
+echo "Estimated Minimum Sequences:= " $SEQLINES
+
+if (( "$PROCESSED" >= "$SEQLINES" ))
+then
+  echo "Complete."
+else
+  echo "Error, incorrect number of processed sequences"
+  exit 100
+fi
+echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+

data/lib/cagnut_bwa/util.rb

@@ -0,0 +1,35 @@
+module CagnutBwa
+  class Util
+    attr_accessor :bwa, :config
+
+    def initialize config
+      @config = config
+      @bwa = CagnutBwa::Base.new
+    end
+
+    def aln_one_fastq dirs, order=1, filename=nil
+      job_name = bwa.aln_one_fastq dirs, order, filename
+      [job_name, order+1]
+    end
+
+    def samp_one_fastq dirs, order=1, previous_job_id=nil, filename=nil
+      job_name, filename = bwa.samp_one_fastq dirs, order, previous_job_id, filename
+      [job_name, filename, order+1]
+    end
+
+    def aln dirs, order=1, previous_job_id = nil, filename=nil
+      job_name = bwa.aln dirs, order, previous_job_id, filename
+      [job_name, order+1]
+    end
+
+    def samp dirs, order=1, previous_job_id=nil, filename=nil
+      job_name, filename = bwa.samp dirs, order, previous_job_id, filename
+      [job_name, filename, order+1]
+    end
+
+    def mem dirs, order=1, filename = nil
+      job_name, filename = bwa.mem dirs, order, filename
+      [job_name, filename, order+1]
+    end
+  end
+end

data/lib/cagnut_bwa/version.rb

@@ -0,0 +1,3 @@
+module CagnutBwa
+  VERSION = "0.3.0"
+end

data/lib/cagnut_bwa.rb

@@ -0,0 +1,16 @@
+require "cagnut_bwa/version"
+
+module CagnutBwa
+  class << self
+    def config
+      @config ||= begin
+        CagnutBwa::Configuration.load(Cagnut::Configuration.config, Cagnut::Configuration.params['bwa'])
+        CagnutBwa::Configuration.instance
+      end
+    end
+  end
+end
+
+require 'cagnut_bwa/configuration'
+require 'cagnut_bwa/base'
+require 'cagnut_bwa/util'

metadata

@@ -0,0 +1,129 @@
+--- !ruby/object:Gem::Specification
+name: cagnut_bwa
+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 BWA 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_bwa.gemspec
+- lib/cagnut_bwa.rb
+- lib/cagnut_bwa/base.rb
+- lib/cagnut_bwa/check_tools.rb
+- lib/cagnut_bwa/configuration.rb
+- lib/cagnut_bwa/functions/aln.rb
+- lib/cagnut_bwa/functions/aln_one_fastq.rb
+- lib/cagnut_bwa/functions/mem.rb
+- lib/cagnut_bwa/functions/samp.rb
+- lib/cagnut_bwa/functions/samp_one_fastq.rb
+- lib/cagnut_bwa/functions/templates/aln.sh
+- lib/cagnut_bwa/functions/templates/bwa_samp_one_fastq.sh
+- lib/cagnut_bwa/functions/templates/bwa_samse_one_fastq.sh
+- lib/cagnut_bwa/functions/templates/mem.sh
+- lib/cagnut_bwa/functions/templates/samp.sh
+- lib/cagnut_bwa/util.rb
+- lib/cagnut_bwa/version.rb
+homepage: https://github.com/CAGNUT/cagnut_bwa
+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 BWA tools
+test_files: []