cagnut_samtools 0.3.0

checksums.yaml

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+SHA1:
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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

@@ -0,0 +1 @@
+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_samtools.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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+# CagnutSamtools
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'cagnut_samtools'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install cagnut_samtools
+
+## 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_samtools.
+
+
+## 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_samtools"
+
+# 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_samtools.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_samtools/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "cagnut_samtools"
+  spec.version       = CagnutSamtools::VERSION
+  spec.authors       = ['Shi-Gang Wang', 'Tse-Ching Ho']
+  spec.email         = ['seanwang@goldenio.com', 'tsechingho@goldenio.com']
+
+  spec.summary       = %q{Cagnut Samtools tools}
+  spec.description   = %q{Cagnut Samtools tools}
+  spec.homepage      = "https://github.com/CAGNUT/cagnut_samtools"
+  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_samtools/base.rb

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+require 'cagnut_samtools/functions/merge_bam'
+require 'cagnut_samtools/functions/mg_bam_soft_link'
+require 'cagnut_samtools/functions/do_flag_stat'
+
+module CagnutSamtools
+  class Base
+
+    def merge_bam dirs, order, previous_job_id, input = nil
+      opts = { input: input, dirs: dirs, order: order }
+      CagnutSamtools::MergeBam.new(opts).run previous_job_id
+    end
+
+    def mg_bam_soft_link dirs, order, previous_job_id, input = nil
+      opts = { input: input, dirs: dirs, order: order  }
+      CagnutSamtools::MgBamSoftLink.new(opts).run previous_job_id
+    end
+
+    def do_flag_stat dirs, order, previous_job_id, input = nil
+      opts = { input: input, dirs: dirs, order: order  }
+      CagnutSamtools::DoFlagStat.new(opts).run previous_job_id
+    end
+  end
+end

data/lib/cagnut_samtools/check_tools.rb

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+module CagnutSamtools
+  module CheckTools
+    def check_tool tools_path, refs
+      super if defined?(super)
+      check_samtools tools_path['samtools']
+      check_samtools_index refs['ref_fasta']
+    end
+
+    def check_samtools path
+      check_tool_ver 'Samtools' do
+        `#{path} --version 2>&1| grep samtools | cut -f2 -d ' '` if path
+      end
+    end
+
+    def check_samtools_index ref_path
+      puts 'Checking Samtools Reference Index Files...'
+      tool = 'Samtools Index'
+      file = "#{ref_path}.fai"
+      command = "#{@config['tools']['samtools']} faidx #{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 CagnutSamtools::CheckTools

data/lib/cagnut_samtools/configuration.rb

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+require 'singleton'
+
+module CagnutSamtools
+  class Configuration
+
+    include Singleton
+    attr_accessor :samtools_path
+    attr_reader :config
+
+    class << self
+      def load config, params
+        instance.load config, params
+      end
+    end
+
+    def load config, params = nil
+      @config = config
+      attributes.each do |name, value|
+        send "#{name}=", value if respond_to? "#{name}="
+      end
+    end
+
+    def attributes
+      {
+        samtools_path: @config['tools']['samtools']
+      }
+    end
+  end
+end

data/lib/cagnut_samtools/functions/do_flag_stat.rb

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+module CagnutSamtools
+  class DoFlagStat
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :jobs_dir, :sample_name,
+                   :ref_fasta, :prefix_name, :dodebug
+    def_delegators :'CagnutSamtools.config', :samtools_path
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @job_name = "#{prefix_name}_doFlagStat_#{sample_name}"
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_markdup.bam" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/#{sample_name}_merged_markdup.flagstat"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting doFlagStat for #{sample_name}_markdup suffix"
+      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
+      {
+        previous_job_id: previous_job_id,
+        adjust_memory: ['h_vmem=500M'],
+        tools: ['samtools', 'do_flag_stat']
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_samtools_do_flag_stat"
+      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"
+          #{samtools_path} flagstat #{@input} > #{@output} \\
+            #{::Cagnut::JobManage.run_local}
+
+          if [ ! -s #{@output} ]
+          then
+            echo "Incomplete output file #{@output}"
+            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_samtools/functions/merge_bam.rb

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+module CagnutSamtools
+  class MergeBam
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :jobs_dir, :prefix_name,
+                   :magic28, :ref_fasta, :sample_name, :dodebug
+    def_delegators :'CagnutSamtools.config', :samtools_path
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @sam_dir = opts[:dirs][:input]
+      @bam_dir = opts[:dirs][:output]
+      @job_name = "#{prefix_name}_mgBam_#{sample_name}"
+      @input = opts[:input].nil? ? "#{@bam_dir}/*.bam" : opts[:input]
+      @output = "#{@bam_dir}/#{sample_name}_merged.bam"
+      @output_bai = "#{@bam_dir}/#{sample_name}_merged.bai"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting samtoolsMergeBam #{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,
+        adjust_memory: ['h_vmem=1G'],
+        tools: ['samtools', 'merge_bam']
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_samtools_merge_bam"
+      file = File.join jobs_dir, "#{script_name}.sh"
+      path = File.expand_path '../templates/merge_bam.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 job_params script_name
+      {
+        bam_dir: @bam_dir,
+        samtools_path: samtools_path,
+        magic28: magic28,
+        jobs_dir: jobs_dir,
+        input: @input,
+        output: @output,
+        output_bai: @output_bai,
+        sam_dir: @sam_dir,
+        script_name: script_name,
+        run_local: ::Cagnut::JobManage.run_local
+      }
+    end
+  end
+end

data/lib/cagnut_samtools/functions/mg_bam_soft_link.rb

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+module CagnutSamtools
+  class MgBamSoftLink
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :jobs_dir, :prefix_name, :dodebug,
+                   :magic28, :ref_fasta, :sample_name
+    def_delegators :'CagnutSamtools.config', :samtools_path
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @job_name = "#{prefix_name}_mgBam_#{sample_name}"
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_rg.bam" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/#{sample_name}_merged.bam"
+      @output_bai = "#{opts[:dirs][:output]}/#{sample_name}_merged.bai"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting mgBamSoftLink #{@input}"
+      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: ['samtools', 'mg_bam_soft_link']
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_samtools_mg_bam_soft_link"
+      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 $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+          rm -f #{@output} #{@output_bai}
+          ln -s #{@input}  #{@output}
+
+          # Check BAM EOF
+          BAM_28=$(tail -c 28 #{@output}|xxd -p)
+          if [ "#{magic28}" != "$BAM_28" ]
+          then
+            echo "Error with BAM EOF" 1>&2
+            exit 100
+          fi
+
+          #{samtools_path} index #{@output} \\
+            #{::Cagnut::JobManage.run_local}
+          mv #{output}.bai #{@output_bai}
+
+          if [ !  -s "#{@output_bai}" ]
+          then
+            echo "Incorrect Output!"
+            exit 100
+          fi
+          echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+
+          exit $EXITSTATUS
+        BASH
+      end
+      File.chmod(0700, file)
+      script_name
+    end
+  end
+end

data/lib/cagnut_samtools/functions/templates/merge_bam.sh

@@ -0,0 +1,50 @@
+#!/bin/bash
+
+cd "#{jobs_dir}/../"
+echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+rm -f #{output} #{output_bai}
+CORE_LIST=$(ls core.*)
+if [ -n "$CORE_LIST" ]
+then
+  echo "Found core dumps from bwa. Exiting with error."
+  exit 100
+fi
+
+arr=$(ls #{input})
+if [ ${#arr[@]} -eq 0 ]
+then
+  echo "Error: No BAM files found in BAM_DIR(#{bam_dir})"
+  exit 100
+elif [ ${#arr[@]} -eq 1 ]
+then
+  # bam1=$(ls #{bam_dir}/*.bam | head -1)
+  cp ${arr[0]} #{output} #{run_local}
+else
+  # create sam header for merged bam
+  # bam1=$(ls #{bam_dir}/*.bam | head -1)
+  #{samtools_path} view -H ${arr[0]} | grep -v RG > #{sam_dir}/header.sam #{run_local}
+  for i in `ls #{bam_dir}/*.bam`;do #{samtools_path} view -H $i | grep RG;done | sort | uniq >> #{sam_dir}/header.sam #{run_local}
+  #{samtools_path} merge -h #{sam_dir}/header.sam #{output} #{bam_dir}/*.bam #{run_local}
+fi
+
+EXITSTATUS=$?
+
+if [ ! -s "#{output}" ]
+then
+  echo "Incorrect Output!"
+  exit 100
+fi
+
+# Check BAM EOF
+BAM_28=$(tail -c 28 #{output}|xxd -p)
+if [ "#{magic28}" != "$BAM_28" ]
+then
+  echo "Error with BAM EOF" 1>&2
+  exit 100
+fi
+
+#{samtools_path} index #{output} #{run_local}
+mv #{bam_dir}/#{output}.bai #{output_bai}
+echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+
+exit $EXITSTATUS

data/lib/cagnut_samtools/util.rb

@@ -0,0 +1,25 @@
+module CagnutSamtools
+  class Util
+    attr_accessor :samtools, :config
+
+    def initialize config=nil
+      @config = config
+      @samtools = CagnutSamtools::Base.new
+    end
+
+    def merge_bam dirs, order=1, previous_job_id=nil, filename = nil
+      job_name, filename = samtools.merge_bam dirs, order, previous_job_id, filename
+      [job_name, filename, order+1]
+    end
+
+    def mg_bam_soft_link dirs, order=1, previous_job_id=nil, filename = nil
+      job_name, filename = samtools.mg_bam_soft_link dirs, order, previous_job_id, filename
+      [job_name, filename, order+1]
+    end
+
+    def do_flag_stat dirs, order=1, previous_job_id=nil, filename = nil
+      samtools.do_flag_stat dirs, order, previous_job_id, filename
+      order+1
+    end
+  end
+end

data/lib/cagnut_samtools/version.rb

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

data/lib/cagnut_samtools.rb

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

metadata

@@ -0,0 +1,123 @@
+--- !ruby/object:Gem::Specification
+name: cagnut_samtools
+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 Samtools 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_samtools.gemspec
+- lib/cagnut_samtools.rb
+- lib/cagnut_samtools/base.rb
+- lib/cagnut_samtools/check_tools.rb
+- lib/cagnut_samtools/configuration.rb
+- lib/cagnut_samtools/functions/do_flag_stat.rb
+- lib/cagnut_samtools/functions/merge_bam.rb
+- lib/cagnut_samtools/functions/mg_bam_soft_link.rb
+- lib/cagnut_samtools/functions/templates/merge_bam.sh
+- lib/cagnut_samtools/util.rb
+- lib/cagnut_samtools/version.rb
+homepage: https://github.com/CAGNUT/cagnut_samtools
+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 Samtools tools
+test_files: []