genome-rb 0.1.4 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: ebe497996e7d2598a811469a808fa9998e0a6593
-  data.tar.gz: 8fe4e3d8de204dfa36f4c708c7b1b3906ad7886b
+SHA256:
+  metadata.gz: 82e81a4278f56a5ac9272fcbf7e46bbf1975b4f24c6a03a2a5bf717edc19878f
+  data.tar.gz: 9f830a3008836bcc3841babb8436b5231df84fee50f1b9f14937cb97842d0c29
 SHA512:
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-  data.tar.gz: 500afeca789a91b7f0644b2fa93d4882148fece885d83999214d240be026f7904ab28cc93bffa7ef26f6bcea0c5c70d5f317bfd53f9c6009318c3b383de3090d
+  metadata.gz: a22e8b43f9ee00ca751a0a50902b9d9d44c53df3bfc49654d6efdf3ff4a5cb35c39c3abd6b44916acd454dae5bacdb1a63d0f69797c24ac48134678b0ac1e184
+  data.tar.gz: 7ecc2890129173cfcb083a89de5be221caeec2373c9ffb1b1cab533c54cc564821bbbab38265be222ed0f2dc0c7ac7fcfe4401592308f0e2d6a53e887c926060

data/.travis.yml

@@ -6,7 +6,7 @@ rvm:
 - 2.4.6
 - 2.5.5
 - 2.6.3
-before_install: gem install bundler -v 2.0.1
+before_install: gem install bundler -v 2.0.2
 deploy:
   provider: rubygems
   api_key:

data/Gemfile.lock

@@ -0,0 +1,22 @@
+PATH
+  remote: .
+  specs:
+    genome-rb (0.2.0)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    minitest (5.11.3)
+    rake (10.5.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 2.0)
+  genome-rb!
+  minitest (~> 5.0)
+  rake (~> 10.0)
+
+BUNDLED WITH
+   2.0.2

data/lib/genome/errors.rb

@@ -0,0 +1,7 @@
+# frozen_string_literal: true
+
+class FileTypeError < StandardError
+  def initialize(message = 'FileTypeError')
+    super(message)
+  end
+end

data/lib/genome/reader.rb

@@ -0,0 +1,90 @@
+# frozen_string_literal: true
+
+require 'open-uri'
+
+class Reader
+  attr_reader :genome
+
+  def initialize(filename)
+    @filename = filename
+    @genome = GENOME::Genome.new @filename
+  end
+
+  def validate?(*)
+    raise NotImplementedError, 'Reader must define validate?.'
+  end
+
+  def parse(*)
+    raise NotImplementedError, 'Reader must parse validate?.'
+  end
+
+  def load
+    validate? @filename
+    open(@filename) do |f|
+      f.each_line do |line|
+        next if line.start_with?('#') || line.downcase.start_with?('rsid')
+
+        rsid, snp = parse line
+        @genome[rsid] = snp
+      end
+    end
+  end
+end
+
+module GENOME
+  class TwentyThreeAndMeReader < Reader
+    def validate?(filename)
+      magic_line = File.open(filename, &:readline)
+      unless magic_line.downcase.include? '23'.downcase
+        raise FileTypeError, 'format is not correct'
+      end
+    end
+
+    def parse(line)
+      rsid, chromosome, position, genotype = line.split
+      snp = SNP.new(chromosome = chromosome,
+                    position = position,
+                    genotype = Genotype.new(genotype))
+      [rsid, snp]
+    end
+  end
+end
+
+module GENOME
+  class AncestryReader < Reader
+    def validate?(filename)
+      magic_line = File.open(filename, &:readline)
+      unless magic_line.downcase.include? 'ancestry'.downcase
+        raise FileTypeError, 'format is not correct'
+      end
+    end
+
+    def parse(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
+  end
+end
+
+module GENOME
+  class MyHeritageReader < Reader
+    def validate?(filename)
+      magic_line = File.open(filename, &:readline)
+      unless magic_line.downcase.include? 'MyHeritage'.downcase
+        raise FileTypeError, 'format is not correct'
+      end
+    end
+
+    def parse(line)
+      rsid, chromosome, position, genotype = line.gsub(/"/, '').gsub("\n", '').split(',')
+      snp = SNP.new(chromosome = chromosome,
+                    position = position,
+                    genotype = Genotype.new(genotype))
+      [rsid, snp]
+    end
+  end
+end

data/lib/genome/version.rb

@@ -1,3 +1,3 @@
 module GENOME
-  VERSION = '0.1.4'.freeze
+  VERSION = '0.2.0'.freeze
 end

data/lib/genome.rb

@@ -1,68 +1,9 @@
 # frozen_string_literal: true
 
-require 'genome/version'
-require 'open-uri'
-
-class ProviderError < StandardError
-  def initialize(message = 'ProviderError')
-    super(message)
-  end
-end
-
-class FileTypeError < StandardError
-  def initialize(message = 'FileTypeError')
-    super(message)
-  end
-end
-
 module GENOME
-  # 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.validate?(_filename, _provider = '23andme')
-    raise ProviderError, "provider is not supported." unless %w[23andme ancestry].include? _provider
-
-    first_line = File.open(_filename, &:readline)
-    if _provider == '23andme'
-      raise FileTypeError, "format is not correct" unless first_line.downcase.include? '23'.downcase
-    elsif _provider == 'ancestry'
-      raise FileTypeError, "format is not correct" unless first_line.downcase.include? 'ancestry'.downcase
-    end
-  end
-
-  def self.load(_filename, _provider = '23andme')
-    genome = Genome.new(name = _filename)
-    reader = if _provider == '23andme'
-               :ttandme_reader
-             elsif _provider == 'ancestry'
-               :ancestry_reader
-             end
-    open(_filename) {|f|
-      f.each_line do |line|
-        next if line.start_with?('#') || line.start_with?('rsid')
-        rsid, snp = send reader, line
-        genome[rsid] = snp
-      end
-    }
-    genome
-  end
-end
+  require 'genome/genome'
+  require 'genome/snp'
+  require 'genome/genotype'
+  require 'genome/errors'
+  require 'genome/reader'
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: genome-rb
 version: !ruby/object:Gem::Version
-  version: 0.1.4
+  version: 0.2.0
 platform: ruby
 authors:
 - Gary Lai
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2019-06-29 00:00:00.000000000 Z
+date: 2019-07-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -65,6 +65,7 @@ files:
 - CHANGELOG.md
 - CODE_OF_CONDUCT.md
 - Gemfile
+- Gemfile.lock
 - LICENSE.txt
 - README.md
 - Rakefile
@@ -73,8 +74,10 @@ files:
 - exe/genome
 - genome-rb.gemspec
 - lib/genome.rb
+- lib/genome/errors.rb
 - lib/genome/genome.rb
 - lib/genome/genotype.rb
+- lib/genome/reader.rb
 - lib/genome/snp.rb
 - lib/genome/version.rb
 homepage: https://github.com/marigenhq/genome-rb
@@ -96,8 +99,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.5.2.3
+rubygems_version: 3.0.4
 signing_key: 
 specification_version: 4
 summary: ruby library to read genome data