genome-rb 0.1.0

Sign up to get free protection for your applications and to get access to all the features.
checksums.yaml ADDED
@@ -0,0 +1,7 @@
1
+ ---
2
+ SHA256:
3
+ metadata.gz: 720d3f90b716800b67257c44ccacec7d8e2f06d79c19047a2d0a0df51c68c97c
4
+ data.tar.gz: 03bb58c453382af625ed4e85bbd11efcfbec4e7c4f36ff5c1e47e64cb41408cb
5
+ SHA512:
6
+ metadata.gz: 59e51076ee77934ffe20cb6a5d5b0a78eef008c5d64a3126880716821ef6397ac4020a974470fade6abf128fe3003e480ffaff1800e60bfc4f4a69e8190e68b0
7
+ data.tar.gz: 6841cfc17e64cf6ecf671b68d07a5c892cf962dba3a77f59f3f04ef2138838a1503a887e94eded214e0aae6465f1d5560e1ba9297e5f1ed1ac4f20d52af7a273
data/.gitignore ADDED
@@ -0,0 +1,9 @@
1
+ /.bundle/
2
+ /.yardoc
3
+ /_yardoc/
4
+ /coverage/
5
+ /doc/
6
+ /pkg/
7
+ /spec/reports/
8
+ /tmp/
9
+ .idea
data/.travis.yml ADDED
@@ -0,0 +1,16 @@
1
+ sudo: false
2
+ language: ruby
3
+ cache: bundler
4
+ rvm:
5
+ - 2.3.4
6
+ - 2.4.6
7
+ - 2.5.5
8
+ - 2.6.3
9
+ before_install: gem install bundler -v 2.0.1
10
+ deploy:
11
+ provider: rubygems
12
+ api_key:
13
+ secure: 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
14
+ gem: genome-rb
15
+ on:
16
+ repo: marigenhq/genome-rb
data/CHANGELOG.md ADDED
File without changes
@@ -0,0 +1,74 @@
1
+ # Contributor Covenant Code of Conduct
2
+
3
+ ## Our Pledge
4
+
5
+ In the interest of fostering an open and welcoming environment, we as
6
+ contributors and maintainers pledge to making participation in our project and
7
+ our community a harassment-free experience for everyone, regardless of age, body
8
+ size, disability, ethnicity, gender identity and expression, level of experience,
9
+ nationality, personal appearance, race, religion, or sexual identity and
10
+ orientation.
11
+
12
+ ## Our Standards
13
+
14
+ Examples of behavior that contributes to creating a positive environment
15
+ include:
16
+
17
+ * Using welcoming and inclusive language
18
+ * Being respectful of differing viewpoints and experiences
19
+ * Gracefully accepting constructive criticism
20
+ * Focusing on what is best for the community
21
+ * Showing empathy towards other community members
22
+
23
+ Examples of unacceptable behavior by participants include:
24
+
25
+ * The use of sexualized language or imagery and unwelcome sexual attention or
26
+ advances
27
+ * Trolling, insulting/derogatory comments, and personal or political attacks
28
+ * Public or private harassment
29
+ * Publishing others' private information, such as a physical or electronic
30
+ address, without explicit permission
31
+ * Other conduct which could reasonably be considered inappropriate in a
32
+ professional setting
33
+
34
+ ## Our Responsibilities
35
+
36
+ Project maintainers are responsible for clarifying the standards of acceptable
37
+ behavior and are expected to take appropriate and fair corrective action in
38
+ response to any instances of unacceptable behavior.
39
+
40
+ Project maintainers have the right and responsibility to remove, edit, or
41
+ reject comments, commits, code, wiki edits, issues, and other contributions
42
+ that are not aligned to this Code of Conduct, or to ban temporarily or
43
+ permanently any contributor for other behaviors that they deem inappropriate,
44
+ threatening, offensive, or harmful.
45
+
46
+ ## Scope
47
+
48
+ This Code of Conduct applies both within project spaces and in public spaces
49
+ when an individual is representing the project or its community. Examples of
50
+ representing a project or community include using an official project e-mail
51
+ address, posting via an official social media account, or acting as an appointed
52
+ representative at an online or offline event. Representation of a project may be
53
+ further defined and clarified by project maintainers.
54
+
55
+ ## Enforcement
56
+
57
+ Instances of abusive, harassing, or otherwise unacceptable behavior may be
58
+ reported by contacting the project team at garylai1990@gmail.com. All
59
+ complaints will be reviewed and investigated and will result in a response that
60
+ is deemed necessary and appropriate to the circumstances. The project team is
61
+ obligated to maintain confidentiality with regard to the reporter of an incident.
62
+ Further details of specific enforcement policies may be posted separately.
63
+
64
+ Project maintainers who do not follow or enforce the Code of Conduct in good
65
+ faith may face temporary or permanent repercussions as determined by other
66
+ members of the project's leadership.
67
+
68
+ ## Attribution
69
+
70
+ This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
71
+ available at [http://contributor-covenant.org/version/1/4][version]
72
+
73
+ [homepage]: http://contributor-covenant.org
74
+ [version]: http://contributor-covenant.org/version/1/4/
data/Gemfile ADDED
@@ -0,0 +1,4 @@
1
+ source 'https://rubygems.org'
2
+
3
+ # Specify your gem's dependencies in genome.gemspec
4
+ gemspec
data/LICENSE.txt ADDED
@@ -0,0 +1,21 @@
1
+ The MIT License (MIT)
2
+
3
+ Copyright (c) 2019 Gary Lai
4
+
5
+ Permission is hereby granted, free of charge, to any person obtaining a copy
6
+ of this software and associated documentation files (the "Software"), to deal
7
+ in the Software without restriction, including without limitation the rights
8
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9
+ copies of the Software, and to permit persons to whom the Software is
10
+ furnished to do so, subject to the following conditions:
11
+
12
+ The above copyright notice and this permission notice shall be included in
13
+ all copies or substantial portions of the Software.
14
+
15
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
21
+ THE SOFTWARE.
data/README.md ADDED
@@ -0,0 +1,43 @@
1
+ # Genome
2
+
3
+ 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.
4
+
5
+ TODO: Delete this and the text above, and describe your gem
6
+
7
+ ## Installation
8
+
9
+ Add this line to your application's Gemfile:
10
+
11
+ ```ruby
12
+ gem 'genome-rb'
13
+ ```
14
+
15
+ And then execute:
16
+
17
+ $ bundle
18
+
19
+ Or install it yourself as:
20
+
21
+ $ gem install genome-rb
22
+
23
+ ## Usage
24
+
25
+ TODO: Write usage instructions here
26
+
27
+ ## Development
28
+
29
+ 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.
30
+
31
+ 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).
32
+
33
+ ## Contributing
34
+
35
+ 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.
36
+
37
+ ## License
38
+
39
+ The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
40
+
41
+ ## Code of Conduct
42
+
43
+ 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 ADDED
@@ -0,0 +1,10 @@
1
+ require "bundler/gem_tasks"
2
+ require "rake/testtask"
3
+
4
+ Rake::TestTask.new(:test) do |t|
5
+ t.libs << "test"
6
+ t.libs << "lib"
7
+ t.test_files = FileList["test/**/*_test.rb"]
8
+ end
9
+
10
+ task :default => :test
data/bin/console ADDED
@@ -0,0 +1,14 @@
1
+ #!/usr/bin/env ruby
2
+
3
+ require "bundler/setup"
4
+ require "genome"
5
+
6
+ # You can add fixtures and/or initialization code here to make experimenting
7
+ # with your gem easier. You can also use a different console, if you like.
8
+
9
+ # (If you use this, don't forget to add pry to your Gemfile!)
10
+ # require "pry"
11
+ # Pry.start
12
+
13
+ require "irb"
14
+ IRB.start(__FILE__)
data/bin/setup ADDED
@@ -0,0 +1,8 @@
1
+ #!/usr/bin/env bash
2
+ set -euo pipefail
3
+ IFS=$'\n\t'
4
+ set -vx
5
+
6
+ bundle install
7
+
8
+ # Do any other automated setup that you need to do here
data/exe/genome ADDED
@@ -0,0 +1,3 @@
1
+ #!/usr/bin/env ruby
2
+
3
+ require "genome"
data/genome-rb.gemspec ADDED
@@ -0,0 +1,28 @@
1
+ lib = File.expand_path('lib', __dir__)
2
+ $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
3
+ require 'genome/version'
4
+
5
+ Gem::Specification.new do |spec|
6
+ spec.name = 'genome-rb'
7
+ spec.version = GENOME::VERSION
8
+ spec.authors = ['Gary Lai']
9
+ spec.email = ['gary.lai@marigen.us']
10
+
11
+ spec.summary = 'ruby library to read genome data'
12
+ spec.description = 'ruby library to read genome data'
13
+ spec.homepage = 'https://github.com/marigenhq/genome-rb'
14
+ spec.license = 'MIT'
15
+
16
+ # Specify which files should be added to the gem when it is released.
17
+ # The `git ls-files -z` loads the files in the RubyGem that have been added into git.
18
+ spec.files = Dir.chdir(File.expand_path(__dir__)) do
19
+ `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
20
+ end
21
+ spec.bindir = 'exe'
22
+ spec.executables = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
23
+ spec.require_paths = ['lib']
24
+
25
+ spec.add_development_dependency 'bundler', '~> 2.0'
26
+ spec.add_development_dependency 'minitest', '~> 5.0'
27
+ spec.add_development_dependency 'rake', '~> 10.0'
28
+ end
@@ -0,0 +1,13 @@
1
+ module GENOME
2
+ class Genome < Hash
3
+ attr_accessor :name
4
+
5
+ def initialize(name)
6
+ @name = name
7
+ end
8
+
9
+ def to_s
10
+ "<Genome: SNPs=#{length}, name=#{@name}>"
11
+ end
12
+ end
13
+ end
@@ -0,0 +1,16 @@
1
+ module GENOME
2
+ class Genotype
3
+ attr_accessor :genotype
4
+ def initialize(genotype)
5
+ @genotype = genotype
6
+ end
7
+
8
+ def to_s
9
+ genotype
10
+ end
11
+
12
+ def ==(other)
13
+ @genotype == other.genotype
14
+ end
15
+ end
16
+ end
data/lib/genome/snp.rb ADDED
@@ -0,0 +1,20 @@
1
+ module GENOME
2
+ class SNP
3
+ attr_accessor :chromosome, :position, :genotype
4
+ def initialize(chromosome, position, genotype)
5
+ @chromosome = chromosome
6
+ @position = position
7
+ @genotype = genotype
8
+ end
9
+
10
+ def to_s
11
+ "<SNP: chromosome=#{chromosome} position=#{position} genotype=#{genotype}>"
12
+ end
13
+
14
+ def ==(other)
15
+ chromosome == other.chromosome &&
16
+ @position == other.position &&
17
+ @genotype == other.genotype
18
+ end
19
+ end
20
+ end
@@ -0,0 +1,3 @@
1
+ module GENOME
2
+ VERSION = '0.1.0'.freeze
3
+ end
data/lib/genome.rb ADDED
@@ -0,0 +1,41 @@
1
+ require 'genome/version'
2
+
3
+ module GENOME
4
+ class Error < StandardError; end
5
+ # Your code goes here...
6
+ autoload :Genome, 'genome/genome'
7
+ autoload :SNP, 'genome/snp'
8
+ autoload :Genotype, 'genome/genotype'
9
+
10
+ def self.ttandme_reader(line)
11
+ rsid, chromosome, position, genotype = line.split
12
+ snp = SNP.new(chromosome = chromosome,
13
+ position = position,
14
+ genotype = Genotype.new(genotype))
15
+ [rsid, snp]
16
+ end
17
+
18
+ def self.ancestry_reader(line)
19
+ rsid, chromosome, position, allele1, allele2 = line.split
20
+ genotype = allele1 + allele2
21
+ snp = SNP.new(chromosome = chromosome,
22
+ position = position,
23
+ genotype = Genotype.new(genotype))
24
+ [rsid, snp]
25
+ end
26
+
27
+ def self.load(_filename, _provider = '23andme')
28
+ genome = Genome.new(name = _filename)
29
+ File.open(_filename).each do |line|
30
+ next if line.start_with?('#') || line.start_with?('rsid')
31
+
32
+ if _provider.casecmp? '23andme'
33
+ rsid, snp = ttandme_reader line
34
+ else
35
+ rsid, snp = ancestry_reader line
36
+ end
37
+ genome[rsid] = snp
38
+ end
39
+ genome
40
+ end
41
+ end
metadata ADDED
@@ -0,0 +1,103 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: genome-rb
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.1.0
5
+ platform: ruby
6
+ authors:
7
+ - Gary Lai
8
+ autorequire:
9
+ bindir: exe
10
+ cert_chain: []
11
+ date: 2019-05-27 00:00:00.000000000 Z
12
+ dependencies:
13
+ - !ruby/object:Gem::Dependency
14
+ name: bundler
15
+ requirement: !ruby/object:Gem::Requirement
16
+ requirements:
17
+ - - "~>"
18
+ - !ruby/object:Gem::Version
19
+ version: '2.0'
20
+ type: :development
21
+ prerelease: false
22
+ version_requirements: !ruby/object:Gem::Requirement
23
+ requirements:
24
+ - - "~>"
25
+ - !ruby/object:Gem::Version
26
+ version: '2.0'
27
+ - !ruby/object:Gem::Dependency
28
+ name: minitest
29
+ requirement: !ruby/object:Gem::Requirement
30
+ requirements:
31
+ - - "~>"
32
+ - !ruby/object:Gem::Version
33
+ version: '5.0'
34
+ type: :development
35
+ prerelease: false
36
+ version_requirements: !ruby/object:Gem::Requirement
37
+ requirements:
38
+ - - "~>"
39
+ - !ruby/object:Gem::Version
40
+ version: '5.0'
41
+ - !ruby/object:Gem::Dependency
42
+ name: rake
43
+ requirement: !ruby/object:Gem::Requirement
44
+ requirements:
45
+ - - "~>"
46
+ - !ruby/object:Gem::Version
47
+ version: '10.0'
48
+ type: :development
49
+ prerelease: false
50
+ version_requirements: !ruby/object:Gem::Requirement
51
+ requirements:
52
+ - - "~>"
53
+ - !ruby/object:Gem::Version
54
+ version: '10.0'
55
+ description: ruby library to read genome data
56
+ email:
57
+ - gary.lai@marigen.us
58
+ executables:
59
+ - genome
60
+ extensions: []
61
+ extra_rdoc_files: []
62
+ files:
63
+ - ".gitignore"
64
+ - ".travis.yml"
65
+ - CHANGELOG.md
66
+ - CODE_OF_CONDUCT.md
67
+ - Gemfile
68
+ - LICENSE.txt
69
+ - README.md
70
+ - Rakefile
71
+ - bin/console
72
+ - bin/setup
73
+ - exe/genome
74
+ - genome-rb.gemspec
75
+ - lib/genome.rb
76
+ - lib/genome/genome.rb
77
+ - lib/genome/genotype.rb
78
+ - lib/genome/snp.rb
79
+ - lib/genome/version.rb
80
+ homepage: https://github.com/marigenhq/genome-rb
81
+ licenses:
82
+ - MIT
83
+ metadata: {}
84
+ post_install_message:
85
+ rdoc_options: []
86
+ require_paths:
87
+ - lib
88
+ required_ruby_version: !ruby/object:Gem::Requirement
89
+ requirements:
90
+ - - ">="
91
+ - !ruby/object:Gem::Version
92
+ version: '0'
93
+ required_rubygems_version: !ruby/object:Gem::Requirement
94
+ requirements:
95
+ - - ">="
96
+ - !ruby/object:Gem::Version
97
+ version: '0'
98
+ requirements: []
99
+ rubygems_version: 3.0.3
100
+ signing_key:
101
+ specification_version: 4
102
+ summary: ruby library to read genome data
103
+ test_files: []