cheripic 0.1.0

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data/.gitignore

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

data/.travis.yml

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+language: ruby
+rvm:
+  - 2.2.1
+before_install: gem install bundler -v 1.10.6

data/CODE_OF_CONDUCT.md

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+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or contacting one or more of the project maintainers.
+
+This Code of Conduct is adapted from the [Contributor Covenant](http://contributor-covenant.org), version 1.0.0, available at [http://contributor-covenant.org/version/1/0/0/](http://contributor-covenant.org/version/1/0/0/)

data/Gemfile

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

data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2016 Shyam Rallapalli
+
+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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+# Cheripic
+
+[![Build Status](https://travis-ci.org/shyamrallapalli/cheripic.svg?branch=master)](https://travis-ci.org/shyamrallapalli/cheripic)
+[![Coverage Status](https://coveralls.io/repos/github/shyamrallapalli/cheripic/badge.svg?branch=master)](https://coveralls.io/github/shyamrallapalli/cheripic?branch=master)
+
+
+Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/cheripic`. To experiment with that code, run `bin/console` for an interactive prompt.
+
+TODO: Delete this and the text above, and describe your gem
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'cheripic'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install cheripic
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake test` 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]/cheripic. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](contributor-covenant.org) code of conduct.
+
+
+## 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 "rake/testtask"
+
+Rake::TestTask.new(:test) do |t|
+  t.libs << "test"
+  t.libs << "lib"
+  t.test_files = FileList['test/**/*_test.rb']
+end
+
+task :default => :test

data/bin/console

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

data/cheripic.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'cheripic/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = 'cheripic'
+  spec.version       = Cheripic::VERSION
+  spec.authors       = ['Shyam Rallapalli']
+  spec.email         = ['ghanasyam.rallapalli@tsl.ac.uk']
+
+  spec.summary       = %q{picks causative mutation from bulks segregant sequencing}
+  spec.description   = %q{a library and commandline tool to pick causative mutation from bulks segregant sequencing}
+  spec.homepage      = 'https://github.com/shyamrallapalli/cheripic'
+  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 'yell', '~> 2.0.5'
+  spec.add_dependency 'trollop', '~> 2.1.2'
+  spec.add_dependency 'bio', '~> 1.5.0'
+  # spec.add_dependency 'bio-samtools', '~> 2.3.3'
+  # spec.add_dependency 'bio-gngm', '~> 0.2.1'
+  spec.add_dependency 'rinruby', '~> 2.0.3'
+
+  spec.add_development_dependency 'bundler', '~> 1.10'
+  spec.add_development_dependency 'rake', '~> 10.0'
+  spec.add_development_dependency 'minitest'
+  spec.add_development_dependency 'minitest-reporters', '>= 1.0.17'
+  spec.add_development_dependency 'simplecov', '>= 0.8.2'
+  spec.add_development_dependency 'shoulda', '>= 3.5.0'
+  spec.add_development_dependency 'coveralls', '>= 0.7.2'
+end

data/lib/cheripic/cmd.rb

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+#!/usr/bin/env ruby
+
+module Cheripic
+
+  class Cmd
+
+    require 'trollop'
+    require 'pathname'
+    require 'ostruct'
+
+    def initialize (args)
+      @options = OpenStruct.new
+      @options = parse_arguments (args)
+      check_arguments
+    end
+
+    def parse_arguments (args)
+      Trollop::with_standard_exception_handling argument_parser do
+        if args.empty? || args.include?('-h') || args.include?('--help')
+          raise Trollop::HelpNeeded
+        elsif args.include?('--examples')
+          print_examples
+        end
+        argument_parser.parse args
+      end
+    end
+
+    def argument_parser
+      cmds = self
+      Trollop::Parser.new do
+        banner cmds.help_message
+        opt :assembly, 'Assembly file in FASTA format',
+            :short => '-f',
+            :type => String
+        opt :input_format, 'bulk and parent alignment file format types - set either pileup or bam',
+            :short => '-F',
+            :type => String,
+            :default => 'pileup'
+        opt :mut_bulk, 'Pileup or sorted BAM file alignments from mutant/trait of interest bulk 1',
+            :short => '-a',
+            :type => String
+        opt :bg_bulk, 'Pileup or sorted BAM file alignments from background/wildtype bulk 2',
+            :short => '-b',
+            :type => String
+        opt :output, 'Directory to store results, will be created if not existing',
+            :default => 'cheripic_results'
+        opt :loglevel, 'Choose any one of "info / warn / debug" level for logs generated',
+            :default => 'info'
+        opt :hmes_adjust, 'factor added to snp count of each contig to adjust for hme score calculations',
+            :type => Float,
+            :default => 0.5
+        opt :htlow, 'lower level for categorizing heterozygosity',
+            :type => Float,
+            :default => 0.2
+        opt :hthigh, 'high level for categorizing heterozygosity',
+            :type => Float,
+            :default => 0.9
+        opt :mindepth, 'minimum read depth to conisder a position for variant calls',
+            :type => Integer,
+            :default => 6
+        opt :min_non_ref_count, 'minimum read depth supporting non reference base at each position',
+            :type => Integer,
+            :default => 3
+        opt :min_indel_count_support, 'minimum read depth supporting an indel at each position',
+            :type => Integer,
+            :default => 3
+        opt :ignore_reference_n, 'ignore variant calls at N (completely ambigous) bases in the reference',
+            :type => FalseClass,
+            :default => true
+        opt :mapping_quality, 'minimum mapping quality of read covering the position',
+            :short => '-q',
+            :type => Integer,
+            :default => 20
+        opt :base_quality, 'minimum base quality of bases covering the position',
+            :short => '-Q',
+            :type => Integer,
+            :default => 15
+        opt :noise, 'praportion of reads for a variant to conisder as noise',
+            :type => Float,
+            :default => 0.1
+        opt :cross_type, 'type of cross used to generated mapping population - back or out',
+            :type => String,
+            :default => 'back'
+        opt :only_frag_with_vars, 'select only contigs containing variants for analysis',
+            :type => FalseClass,
+            :default => true
+        opt :filter_out_low_hmes, 'ignore variants from contigs with low hmescore or bfr to list in the final output',
+            :type => FalseClass,
+            :default => true
+        opt :polyploidy, 'Set if the data input is from polyploids',
+            :type => FalseClass,
+            :default => false
+        opt :mut_parent, 'Pileup or sorted BAM file alignments from mutant/trait of interest parent',
+            :short => '-p',
+            :type => String,
+            :default => ''
+        opt :bg_parent, 'Pileup or sorted BAM file alignments from background/wildtype parent',
+            :short => '-r',
+            :type => String,
+            :default => ''
+        opt :br_adjust, 'factor added to hemi snp frequency of each parent to adjust for bfr calculations',
+            :type => Float,
+            :default => 0.05
+        opt :examples, 'shows some example commands with explanation'
+      end
+    end
+
+    def help_message
+      <<-EOS
+
+Cheripic v#{Cheripic::VERSION.dup}
+Authors: Shyam Rallapalli and Dan MacLean
+
+Description: Candidate mutation and closely linked marker selection for non reference genomes
+Uses bulk segregant data from non-reference sequence genomes
+
+Inputs:
+1. Needs a reference fasta file of asssembly use for variant analysis
+2. Pileup files for mutant (phenotype of interest) bulks and background (wildtype phenotype) bulks
+3. If polyploid species, include of pileup from one or both parents
+
+USAGE:
+cheripic <options>
+
+OPTIONS:
+
+      EOS
+    end
+
+    def print_examples
+      msg = <<-EOS
+
+    Cheripic v#{Cheripic::VERSION.dup}
+
+    EXAMPLE COMMANDS:
+
+      EOS
+      puts msg.split("\n").map{ |line| line.lstrip }.join("\n")
+      exit(0)
+    end
+
+    def check_arguments
+      check_output
+      check_loglevel
+      check_inputfiles
+    end
+
+    # def check_input_types
+    #   if @options.input_format == 'vcf'
+    #
+    #   end
+    # end
+
+    def check_inputfiles
+      if @options.polyploidy
+        inputfiles = %i{assembly mut_bulk bg_bulk mut_parent bg_parent}
+      else
+        inputfiles = %i{assembly mut_bulk bg_bulk}
+      end
+      inputfiles.each do | symbol |
+        if @options[symbol]
+          file = @options[symbol]
+          @options[symbol] = File.expand_path(file)
+          unless File.exist?(file)
+            raise CheripicIOError.new "#{symbol} file, #{file} does not exist: "
+          end
+        else
+          raise CheripicArgError.new "Options #{inputfiles}, all must be specified. " +
+                                            'Try --help for help.'
+        end
+      end
+    end
+
+    def check_output
+      if Dir.exist?(@options.output)
+        raise CheripicArgError.new "#{@options.output} directory exists" +
+                                       'please choose a different output directory name'
+      end
+    end
+
+    def check_loglevel
+      unless %w(error info warn debug).include?(@options.loglevel)
+        raise CheripicArgError.new "Loglevel #{@options.loglevel} is not valid. " +
+                                       'It must be one of: error, info, warn, debug.'
+      end
+      logger.level = Yell::Level.new @options.loglevel.to_sym
+    end
+
+    # def run
+    #   @options.output = File.expand_path @options.output
+    #   FileUtils.mkdir_p @options.output
+    #   Dir.chdir @options.output
+    #   analyse_bulks
+    # end
+    #
+    # def analyse_bulks
+    #   assembly = @options.assembly
+    #   logger.info "Loading assembly: #{assembly}"
+    #   # a = Assembly.new assembly
+    #   logger.info "Analysing assembly: #{assembly}"
+    #
+    # end
+
+  end # Cmd
+
+end # Cheripic

data/lib/cheripic/version.rb

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+module Cheripic
+  VERSION = '0.1.0'
+end

data/lib/cheripic.rb

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+require 'cheripic/cmd'
+require 'cheripic/version'
+
+# set up a golbal logger object to access across module
+require 'yell'
+module Cheripic
+
+  # custom error handling
+  class CheripicError < StandardError; end
+  class CheripicIOError < CheripicError; end
+  class CheripicArgError < CheripicError; end
+
+  # Define a logger and pass `Object` as name.
+  # Yell adds this logger to the repository where you can access it later on.
+  format = Yell::Formatter.new('[%5L] %d : %m', '%Y-%m-%d %H:%M:%S')
+  Yell.new(:format => format) do |l|
+    l.level = :info
+    l.name = Object
+    l.adapter STDOUT, level: [:debug, :info, :warn]
+    l.adapter STDERR, level: [:error, :fatal]
+  end
+  # Enable logging for the class that (almost) every Ruby class inherits from
+  Object.send :include, Yell::Loggable
+
+end # Cheripic

metadata

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+--- !ruby/object:Gem::Specification
+name: cheripic
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Shyam Rallapalli
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2016-05-01 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: yell
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.5
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.5
+- !ruby/object:Gem::Dependency
+  name: trollop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.1.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.1.2
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.5.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.5.0
+- !ruby/object:Gem::Dependency
+  name: rinruby
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.3
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+- !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: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: minitest-reporters
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.17
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.17
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.8.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.8.2
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.5.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.5.0
+- !ruby/object:Gem::Dependency
+  name: coveralls
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.7.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.7.2
+description: a library and commandline tool to pick causative mutation from bulks
+  segregant sequencing
+email:
+- ghanasyam.rallapalli@tsl.ac.uk
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".travis.yml"
+- CODE_OF_CONDUCT.md
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- cheripic.gemspec
+- lib/cheripic.rb
+- lib/cheripic/cmd.rb
+- lib/cheripic/version.rb
+homepage: https://github.com/shyamrallapalli/cheripic
+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: 2.4.6
+signing_key: 
+specification_version: 4
+summary: picks causative mutation from bulks segregant sequencing
+test_files: []