PRbed 0.1.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA256:
+  metadata.gz: 46d90436d24fa45018d5edf825ba7f686fd1be4b658810790ed4228a4efad27a
+  data.tar.gz: d7b280dc3a680d456bbb379da04c372f969b4620302ed5a37cd099a7c4ed58c4
+SHA512:
+  metadata.gz: 70feca0fe8180d84c7ada8e44bcaf1be6a6d3b4744533c240a796376ee8387d04b97d30983ecb630c73e872336b4224de617e2610e5b23966903938e9fd23a5e
+  data.tar.gz: a69beb9d167cb621531eeff54cd3d9b025c65e4e61c236ab0721f9c87ec69ece61fb8bfcd7449dba3bb13576ac7169b950ebca08a586fdfefc9ace1a1ecf9d34

data/.gitignore

@@ -0,0 +1,9 @@
+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+Gemfile.lock

data/.travis.yml

@@ -0,0 +1,6 @@
+---
+language: ruby
+cache: bundler
+rvm:
+  - 2.7.1
+before_install: gem install bundler -v 2.1.4

data/Gemfile

@@ -0,0 +1,7 @@
+source "https://rubygems.org"
+
+# Specify your gem's dependencies in PRbed.gemspec
+gemspec
+
+gem "rake", "~> 12.0"
+gem "minitest", "~> 5.0"

data/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 holrock <ispeporez@gmail.com>
+
+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/PRbed.gemspec

@@ -0,0 +1,23 @@
+require_relative 'lib/PRbed/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "PRbed"
+  spec.version       = PRbed::VERSION
+  spec.authors       = ["holrock"]
+  spec.email         = ["ispeporez@gmail.com"]
+
+  spec.summary       = %q{PLINK bed file reader}
+  spec.description   = %q{pure ruby implementation of PLINK bed file stream reader}
+  spec.homepage      = "https://github.com/holrock/PRbed"
+  spec.required_ruby_version = Gem::Requirement.new(">= 2.3.0")
+  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('..', __FILE__)) 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"]
+end

data/README.md

@@ -0,0 +1,40 @@
+# PRbed
+
+pure ruby implementation of PLINK bed file stream reader
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'PRbed'
+```
+
+And then execute:
+
+    $ bundle install
+
+Or install it yourself as:
+
+    $ gem install PRbed
+
+## Usage
+
+```ruby
+require "PRbed"
+r = PRbed::Reader.new("test/test") # bfile prefix
+r.each_variants do |variant, fam, genotypes|
+  p [variant, fam, genotypes]
+end
+```
+
+## 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/holrock/PRbed.
+

data/Rakefile

@@ -0,0 +1,10 @@
+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

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "PRbed"
+
+# 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

@@ -0,0 +1,8 @@
+#!/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/lib/PRbed.rb

@@ -0,0 +1,94 @@
+require "PRbed/version"
+
+module PRbed
+  class PRBedError < StandardError; end
+
+  HOMO_A1 = 0
+  MISSING = 1
+  HETERO = 2
+  HOMO_A2 = 3
+
+  SAMPLES_PER_BYTE = 4
+
+  Fam = Struct.new(:fid, :iid, :sex, :phenotype)
+  Bim = Struct.new(:chr, :vid, :bp, :a1, :a2)
+
+  class BytesParser
+    def initialize(nsamples)
+      @nsamples = nsamples
+      @bufsize = (@nsamples + 3) & ~3
+    end
+
+    def parse(bs)
+      a = Array.new(@bufsize, MISSING)
+      i = 0
+      bs.each_byte do |c|
+        a[i    ] =  c & 0b00000011
+        a[i + 1] = (c & 0b00001100) >> 2
+        a[i + 2] = (c & 0b00110000) >> 4
+        a[i + 3] = (c & 0b11000000) >> 6
+        i += SAMPLES_PER_BYTE
+      end
+      a.pop(@bufsize - @nsamples)
+      a
+    end
+  end
+
+  class Reader
+    attr_reader :fam, :bim
+
+    def initialize(bfile)
+      @bfile = bfile
+      @fam = load_fam("#{bfile}.fam")
+      @bim = load_bim("#{bfile}.bim")
+    end
+
+    def each_variants
+      nsamples = @fam.size
+      mod = nsamples % SAMPLES_PER_BYTE
+      nread_bytes = nsamples / SAMPLES_PER_BYTE
+      nread_bytes += 1 unless mod ==0
+
+      File.open("#{@bfile}.bed", "rb") do |f|
+        raise PRBedError.new("not plink bed file") unless f.read(3) == "\x6c\x1b\x01"
+        parser = BytesParser.new(nsamples)
+        buf = '\x0' * nsamples
+        @bim.each do |v|
+          b = f.read(nread_bytes, buf)
+          raise PRBedError.new("unpxpected file end") unless b
+          a = parser.parse(b)
+          yield(v, @fam, a)
+        end
+      end
+      self
+    end
+
+    alias_method :each, :each_variants
+
+    private
+
+    def load_fam(fam)
+      fs = []
+      File.open(fam) do |f|
+        while s = f.gets
+          s.chomp!
+          fid, iid, _, _, sex, pheno = s.split(/\s/)
+          fs.push(Fam.new(fid, iid, Integer(sex, 10), Integer(pheno, 10)))
+        end
+      end
+      fs
+    end
+
+    def load_bim(bim)
+      bs = []
+      File.open(bim) do |f|
+        while s = f.gets
+          s.chomp!
+          chr, vid, _, bp, a1, a2 = s.split(/\s/)
+          bs.push(Bim.new(Integer(chr, 10), vid, Integer(bp, 10), a1, a2))
+        end
+      end
+      bs
+    end
+  end
+end

data/lib/PRbed/version.rb

@@ -0,0 +1,3 @@
+module PRbed
+  VERSION = "0.1.0"
+end

metadata

@@ -0,0 +1,54 @@
+--- !ruby/object:Gem::Specification
+name: PRbed
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- holrock
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2020-07-24 00:00:00.000000000 Z
+dependencies: []
+description: pure ruby implementation of PLINK bed file stream reader
+email:
+- ispeporez@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".travis.yml"
+- Gemfile
+- LICENSE
+- PRbed.gemspec
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- lib/PRbed.rb
+- lib/PRbed/version.rb
+homepage: https://github.com/holrock/PRbed
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.3.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.1.2
+signing_key: 
+specification_version: 4
+summary: PLINK bed file reader
+test_files: []