genome-rb 0.1.0

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data/.gitignore

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

data/.travis.yml

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+sudo: false
+language: ruby
+cache: bundler
+rvm:
+- 2.3.4
+- 2.4.6
+- 2.5.5
+- 2.6.3
+before_install: gem install bundler -v 2.0.1
+deploy:
+  provider: rubygems
+  api_key:
+    secure: 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
+  gem: genome-rb
+  on:
+    repo: marigenhq/genome-rb

data/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+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, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at garylai1990@gmail.com. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

data/Gemfile

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

data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2019 Gary Lai
+
+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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+# Genome
+
+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/genome/rb`. 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 'genome-rb'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install genome-rb
+
+## 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]/genome-rb. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
+
+## Code of Conduct
+
+Everyone interacting in the Genome::Rb project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/[USERNAME]/genome-rb/blob/master/CODE_OF_CONDUCT.md).

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 "genome"
+
+# 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(__FILE__)

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/exe/genome

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+#!/usr/bin/env ruby
+
+require "genome"

data/genome-rb.gemspec

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+lib = File.expand_path('lib', __dir__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'genome/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = 'genome-rb'
+  spec.version       = GENOME::VERSION
+  spec.authors       = ['Gary Lai']
+  spec.email         = ['gary.lai@marigen.us']
+
+  spec.summary       = 'ruby library to read genome data'
+  spec.description   = 'ruby library to read genome data'
+  spec.homepage      = 'https://github.com/marigenhq/genome-rb'
+  spec.license       = 'MIT'
+
+  # Specify which files should be added to the gem when it is released.
+  # The `git ls-files -z` loads the files in the RubyGem that have been added into git.
+  spec.files         = Dir.chdir(File.expand_path(__dir__)) do
+    `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  end
+  spec.bindir        = 'exe'
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ['lib']
+
+  spec.add_development_dependency 'bundler', '~> 2.0'
+  spec.add_development_dependency 'minitest', '~> 5.0'
+  spec.add_development_dependency 'rake', '~> 10.0'
+end

data/lib/genome/genome.rb

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+module GENOME
+  class Genome < Hash
+    attr_accessor :name
+
+    def initialize(name)
+      @name = name
+    end
+
+    def to_s
+      "<Genome: SNPs=#{length}, name=#{@name}>"
+    end
+  end
+end

data/lib/genome/genotype.rb

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+module GENOME
+  class Genotype
+    attr_accessor :genotype
+    def initialize(genotype)
+      @genotype = genotype
+    end
+
+    def to_s
+      genotype
+    end
+
+    def ==(other)
+      @genotype == other.genotype
+    end
+  end
+end

data/lib/genome/snp.rb

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+module GENOME
+  class SNP
+    attr_accessor :chromosome, :position, :genotype
+    def initialize(chromosome, position, genotype)
+      @chromosome = chromosome
+      @position = position
+      @genotype = genotype
+    end
+
+    def to_s
+      "<SNP: chromosome=#{chromosome} position=#{position} genotype=#{genotype}>"
+    end
+
+    def ==(other)
+      chromosome == other.chromosome &&
+        @position == other.position &&
+        @genotype == other.genotype
+    end
+  end
+end

data/lib/genome/version.rb

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+module GENOME
+  VERSION = '0.1.0'.freeze
+end

data/lib/genome.rb

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+require 'genome/version'
+
+module GENOME
+  class Error < StandardError; end
+  # Your code goes here...
+  autoload :Genome, 'genome/genome'
+  autoload :SNP, 'genome/snp'
+  autoload :Genotype, 'genome/genotype'
+
+  def self.ttandme_reader(line)
+    rsid, chromosome, position, genotype = line.split
+    snp = SNP.new(chromosome = chromosome,
+                  position = position,
+                  genotype = Genotype.new(genotype))
+    [rsid, snp]
+  end
+
+  def self.ancestry_reader(line)
+    rsid, chromosome, position, allele1, allele2 = line.split
+    genotype = allele1 + allele2
+    snp = SNP.new(chromosome = chromosome,
+                  position = position,
+                  genotype = Genotype.new(genotype))
+    [rsid, snp]
+  end
+
+  def self.load(_filename, _provider = '23andme')
+    genome = Genome.new(name = _filename)
+    File.open(_filename).each do |line|
+      next if line.start_with?('#') || line.start_with?('rsid')
+
+      if _provider.casecmp? '23andme'
+        rsid, snp = ttandme_reader line
+      else
+        rsid, snp = ancestry_reader line
+      end
+      genome[rsid] = snp
+    end
+    genome
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: genome-rb
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Gary Lai
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2019-05-27 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+- !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'
+description: ruby library to read genome data
+email:
+- gary.lai@marigen.us
+executables:
+- genome
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".travis.yml"
+- CHANGELOG.md
+- CODE_OF_CONDUCT.md
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- exe/genome
+- genome-rb.gemspec
+- lib/genome.rb
+- lib/genome/genome.rb
+- lib/genome/genotype.rb
+- lib/genome/snp.rb
+- lib/genome/version.rb
+homepage: https://github.com/marigenhq/genome-rb
+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: []
+rubygems_version: 3.0.3
+signing_key: 
+specification_version: 4
+summary: ruby library to read genome data
+test_files: []