mgnu 2.1.1

data/spec/mgnu/parser/fasta_parser_spec.rb

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+require 'spec_helper'
+
+describe MgNu::Parser::Fasta do
+  before do
+    @ff = MgNu::Parser::Fasta.new('data/test.fasta')
+  end
+
+  it 'should be know about attributes' do
+    expect(@ff).to be_a(MgNu::Parser::Fasta)
+    expect(@ff).to respond_to(:filename)
+    expect(@ff).to respond_to(:each)
+  end
+
+  it 'should yield MgNu::Sequence::Fasta objects' do
+    count = 0
+    @ff.each do |f|
+      expect(f).to be_a(MgNu::Sequence::Fasta)
+      expect(f.sequence).not_to be_nil
+      expect(f.header).not_to be_nil
+      count += 1
+    end
+    expect(count).to eq(2)
+  end
+
+  it 'should concatenate multiline seqeunces' do
+    @ff.each do |f|
+      expect(f.sequence).not_to match(/\n/)
+    end
+  end
+end
+
+describe 'MgNu::Parser::Fasta with a fasta quality file' do
+  before do
+    @ff = MgNu::Parser::Fasta.new('data/testqual.fasta.qual', true)
+  end
+
+  it 'should correctly format quality strings' do
+    @ff.each do |f|
+      expect(f).to be_a(MgNu::Sequence::Fasta)
+      expect(f).to respond_to(:header)
+      expect(f).to respond_to(:sequence)
+      expect(f.sequence).not_to be_nil
+      expect(f.header).not_to be_nil
+      str = f.to_s
+      temp = str.split(/\n/)
+      temp.shift # drop header line
+
+      temp.each do |qline|
+        expect(qline.split(/\s+/).length).to eq(17)
+      end
+    end
+  end
+end

data/spec/mgnu/parser_spec.rb

@@ -0,0 +1,22 @@
+require 'spec_helper'
+
+describe MgNu::Parser do
+  class DummyClass
+    include MgNu::Loggable
+    include MgNu::Parser
+  end
+
+  before(:each) do
+    @dummy_class = DummyClass.new
+    @dummy_class.extend(MgNu::Parser)
+  end
+
+  it 'can be included' do
+    expect(@dummy_class).to respond_to(:parse_until)
+    expect(@dummy_class).to respond_to(:strip_quotes)
+  end
+
+  it 'can strip quotes' do
+    expect(@dummy_class.strip_quotes('"ABC"')).to eq('ABC')
+  end
+end

data/spec/mgnu/sequence/fasta_spec.rb

@@ -0,0 +1,60 @@
+require 'spec_helper'
+
+describe MgNu::Sequence::Fasta do
+  before do
+    @fs = MgNu::Sequence::Fasta.new(:header => 'test', :sequence => 'atgcatgcatgcatgcaaaa')
+  end
+
+  it 'knows about attributes' do
+    expect(@fs).to be_a(MgNu::Sequence::Fasta)
+    expect(@fs).to respond_to(:value)
+    expect(@fs).to respond_to(:sequence)
+    expect(@fs).to respond_to(:type)
+    expect(@fs).to respond_to(:reverse_complement)
+    expect(@fs).to respond_to(:translate)
+    expect(@fs).to respond_to(:levenshtein_distance)
+    expect(@fs).to respond_to(:distance)
+    expect(@fs).to respond_to(:percent_identity)
+    expect(@fs).to respond_to(:identity)
+  end
+
+  it 'can represent itself as a string' do
+    expect(@fs.to_s).to eq(">test\natgcatgcatgcatgcaaaa")
+
+    # create a long sequence
+    @fs.sequence << 'atgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaaatgcatgatgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaa'
+
+    # fasta entry with 60 (the default) chars/row
+    result = ">test\n"
+    result << "atgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaa\n"
+    result << "atgcatgcatgcatgcaaaaatgcatgatgcatgcatgcatgcaaaaatgcatgcatgca\n"
+    result << "tgcaaaaatgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaa\n"
+    expect(@fs.to_s).to eq(result)
+
+    # create a fasta entry with 50 chars/row
+    result = ">test\n"
+    result << "atgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaaatgcatgcat\n"
+    result << "gcatgcaaaaatgcatgcatgcatgcaaaaatgcatgatgcatgcatgca\n"
+    result << "tgcaaaaatgcatgcatgcatgcaaaaatgcatgcatgcatgcaaaaatg\n"
+    result << "catgcatgcatgcaaaa\n"
+    expect(@fs.to_s(50)).to eq(result)
+  end
+
+  it 'can revcomp' do
+    expect(@fs.reverse_complement).to eq('ttttgcatgcatgcatgcat')
+  end
+
+  it 'cat split on N' do
+    fs = MgNu::Sequence::Fasta.new(
+      :header => 'test',
+      :sequence   => 'atgcatgcatgcatgcaaaaNNNNNNNNNNNNNNNNNNNNNNatgcatgcatgcatgcaaaa'
+    )
+    expect(fs.split_on_n.split("\n>").length).to eq(2)
+
+    fs = MgNu::Sequence::Fasta.new(
+      :header => 'test',
+      :sequence   => 'atgcatgcatgcatgcaaaannnnnnnnnnnnnnnnnnnnnnatgcatgcatgcatgcaaaa'
+    )
+    expect(fs.split_on_n.split("\n>").length).to eq(2)
+  end
+end

data/spec/mgnu/sequence/fastq_spec.rb

@@ -0,0 +1,31 @@
+require 'spec_helper'
+describe MgNu::Sequence::Fastq do
+  before do
+    @fs = MgNu::Sequence::Fastq.new(
+      :header => 'HWI-EAS385_0092_FC:5:1:2510:1094#0/1',
+      :sequence => 'CAAAGGTGATTCATTTAACTGGCAATCNNNNNNNCGACCGTCGTTTTTTGTGCCT',
+      :quality  => 'eWddWa`cbeffff__afff_ggggWWBBBBBBBUXW\YZcffbef_fbcZZa^^'
+    )
+  end
+
+  it 'knows about attributes' do
+    expect(@fs).to be_a(MgNu::Sequence::Fastq)
+    expect(@fs).to respond_to(:value)
+    expect(@fs).to respond_to(:value=)
+    expect(@fs).to respond_to(:sequence)
+    expect(@fs).to respond_to(:sequence=)
+    expect(@fs).to respond_to(:qualhdr)
+    expect(@fs).to respond_to(:quality)
+    expect(@fs).to respond_to(:unpack_quality)
+  end
+
+  it 'can represent itself as a string' do
+    result = <<EOT
+@HWI-EAS385_0092_FC:5:1:2510:1094#0/1
+CAAAGGTGATTCATTTAACTGGCAATCNNNNNNNCGACCGTCGTTTTTTGTGCCT
++
+eWddWa`cbeffff__afff_ggggWWBBBBBBBUXW\\YZcffbef_fbcZZa^^
+EOT
+    expect(@fs.to_s).to eq(result)
+  end
+end

data/spec/mgnu/sequence_spec.rb

@@ -0,0 +1,81 @@
+require 'spec_helper'
+describe MgNu::Sequence do
+  before do
+    @s = MgNu::Sequence.new(:type => 'dna', :sequence => 'atgcatgcatgcatgcaaaa')
+  end
+
+  it 'knows about attributes' do
+    expect(@s).to be_a(MgNu::Sequence)
+    expect(@s).to respond_to(:value)
+    expect(@s).to respond_to(:value=)
+    expect(@s).to respond_to(:sequence)
+    expect(@s).to respond_to(:sequence=)
+    expect(@s).to respond_to(:type)
+    expect(@s).to respond_to(:reverse_complement)
+    expect(@s).to respond_to(:translate)
+    expect(@s).to respond_to(:levenshtein_distance)
+    expect(@s).to respond_to(:distance)
+    expect(@s).to respond_to(:percent_identity)
+    expect(@s).to respond_to(:identity)
+  end
+
+  it 'can determine dna/rna/protein' do
+    expect(@s.dna?).to be(true)
+    expect(@s.rna?).to be(false)
+    expect(@s.aa?).to be(false)
+    expect(@s.aminoacid?).to be(false)
+    expect(@s.protein?).to be(false)
+  end
+
+  it 'can reverse complement' do
+    expect(@s.reverse_complement).to eq('ttttgcatgcatgcatgcat')
+  end
+
+  it 'sequence unchanged after reverse complement' do
+    @s.reverse_complement
+    expect(@s.sequence).to eq('atgcatgcatgcatgcaaaa')
+  end
+
+  it 'sequence changed after reverse complement!' do
+    @s.reverse_complement!
+    expect(@s.sequence).to eq('ttttgcatgcatgcatgcat')
+  end
+
+  it 'can be changed' do
+    @s.value = 'atgc'
+    expect(@s.value).to eq('atgc')
+    @s.sequence = 'tacg'
+    expect(@s.sequence).to eq('tacg')
+  end
+
+  it 'can be translated' do
+    expect(@s.translate).to eq('MHACMQ')
+    expect(@s.translate(1)).to eq('MHACMQ')
+    expect(@s.translate(2)).to eq('CMHACK')
+    expect(@s.translate(3)).to eq('ACMHAK')
+    expect(@s.translate(-1)).to eq('FCMHAC')
+  end
+
+  it 'can compute a levenshtein distance' do
+    @s.sequence = 'kitten'
+    other = MgNu::Sequence.new(:value => 'knitting')
+    expect(@s.distance('knitting')).to eq(3)
+    expect(@s.distance(other)).to eq(3)
+  end
+
+  it 'can determine percent identity' do
+    @s.sequence = 'acgt'
+    other = MgNu::Sequence.new(:value => 'acgg')
+    expect(@s.identity('acgt')).to eq(1.0)
+    expect(@s.identity('acgg')).to eq(0.75)
+    expect(@s.identity(other)).to eq(0.75)
+  end
+
+  it 'can find blocks of N characters' do
+    sequence_with_nblocks = MgNu::Sequence.new(:type     => 'dna',
+                                             :sequence => 'atgnnnncatgnnnnnnnncatgcnnnnnnnatgcnnnnaaaa')
+    pieces = sequence_with_nblocks.nblocks(3)
+    expect(pieces.length).to eq(5)
+    expect(pieces).to eq([1..3, 8..11, 20..24, 32..35, 40..43])
+  end
+end

data/spec/mgnu_spec.rb

@@ -0,0 +1,7 @@
+require 'spec_helper'
+
+describe MgNu do
+  it 'has a version number' do
+    expect(MgNu::Version).not_to be nil
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,53 @@
+$LOAD_PATH.unshift File.expand_path('../../lib', __FILE__)
+require 'rspec'
+require 'timecop'
+
+require 'mgnu'
+
+# set up configure for RSpec
+RSpec.configure do |config|
+  # config.before { MgNu::XXXXXX.reset_configuration }
+  config.expect_with :rspec do |c|
+    c.syntax = :expect
+  end
+end
+
+# base fixture path
+#
+# @return [String] load path for fixtures
+def fixture_path
+  File.expand_path('../fixtures', __FILE__)
+end
+
+# return json given a fixture file name
+#
+# @param [String] file name
+# @return [Hash] json hash
+def fixture(file)
+  File.read(fixture_path + '/' + file)
+end
+
+# return multiple fixtures given multiple file names
+#
+# @param [Array] file names
+# @return [Array] array of json hashes
+def fixtures(files)
+  all = []
+  files.each do |file|
+    all << Yajl::Parser.parse(File.read(fixture_path + '/' + file))
+  end
+  Yajl::Encoder.encode(all)
+end
+
+# return a group of fixtures repeated count times
+#
+# @param [String,Fixnum] file name and integer count
+# @return [Array] array of json hashes
+def fixture_set(file, count)
+  all = []
+  content = Yajl::Parser.parse(fixture(file))
+  (1 .. count).each do
+    all << content
+  end
+  Yajl::Encoder.encode(all)
+end

metadata

@@ -0,0 +1,376 @@
+--- !ruby/object:Gem::Specification
+name: mgnu
+version: !ruby/object:Gem::Version
+  version: 2.1.1
+platform: ruby
+authors:
+- Brian C. Thomas
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2018-10-18 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: naught
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+- !ruby/object:Gem::Dependency
+  name: moneta
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+- !ruby/object:Gem::Dependency
+  name: tokyocabinet
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.29'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.29.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.29'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.29.1
+- !ruby/object:Gem::Dependency
+  name: ox
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.8'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.8.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.8'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.8.2
+- !ruby/object:Gem::Dependency
+  name: memoizable
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.9'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.9.11
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.9'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.9.11
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '12.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 12.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '12.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 12.0.0
+- !ruby/object:Gem::Dependency
+  name: mime-types
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">"
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">"
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">"
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">"
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+- !ruby/object:Gem::Dependency
+  name: rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.49'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.49.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.49'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.49.0
+- !ruby/object:Gem::Dependency
+  name: timecop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">"
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">"
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+- !ruby/object:Gem::Dependency
+  name: yardstick
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">"
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">"
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">"
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
+    - - ">"
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+description: Lightweight ruby bioinformatics library
+email:
+- bct.x42@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".yardopts"
+- README.md
+- Rakefile
+- lib/mgnu.rb
+- lib/mgnu/alignment.rb
+- lib/mgnu/common.rb
+- lib/mgnu/genbank.rb
+- lib/mgnu/genbank/feature.rb
+- lib/mgnu/genbank/location.rb
+- lib/mgnu/genbank/qualifier.rb
+- lib/mgnu/genbank/reference.rb
+- lib/mgnu/genbank/source.rb
+- lib/mgnu/loggable.rb
+- lib/mgnu/parser.rb
+- lib/mgnu/parser/blast.rb
+- lib/mgnu/parser/blast/format0.rb
+- lib/mgnu/parser/blast/format7.rb
+- lib/mgnu/parser/blast/format8.rb
+- lib/mgnu/parser/blast/hsp.rb
+- lib/mgnu/parser/blast/query.rb
+- lib/mgnu/parser/blast/sbjct.rb
+- lib/mgnu/parser/clustalw.rb
+- lib/mgnu/parser/fasta.rb
+- lib/mgnu/parser/fasta_header_index.rb
+- lib/mgnu/parser/fasta_index.rb
+- lib/mgnu/parser/fastq.rb
+- lib/mgnu/parser/genbank.rb
+- lib/mgnu/parser/gff.rb
+- lib/mgnu/parser/iprscan/hit.rb
+- lib/mgnu/parser/iprscan_file.rb
+- lib/mgnu/parser/kegg_ontology_index.rb
+- lib/mgnu/parser/pilercr.rb
+- lib/mgnu/parser/prodigal.rb
+- lib/mgnu/parser/sam.rb
+- lib/mgnu/parser/sam/alignment.rb
+- lib/mgnu/parser/sam/header.rb
+- lib/mgnu/parser/sam/pair.rb
+- lib/mgnu/sequence.rb
+- lib/mgnu/sequence/fasta.rb
+- lib/mgnu/sequence/fastq.rb
+- lib/mgnu/version.rb
+- mgnu.gemspec
+- spec/mgnu/parser/blast_format0_spec.rb
+- spec/mgnu/parser/blast_format7_spec.rb
+- spec/mgnu/parser/blast_format8_spec.rb
+- spec/mgnu/parser/blast_multihsp_spec.rb
+- spec/mgnu/parser/blast_oof_spec.rb
+- spec/mgnu/parser/clustalw_spec.rb
+- spec/mgnu/parser/fasta_header_index_tc_parser_spec.rb
+- spec/mgnu/parser/fasta_index_tc_parser_spec.rb
+- spec/mgnu/parser/fasta_parser_spec.rb
+- spec/mgnu/parser_spec.rb
+- spec/mgnu/sequence/fasta_spec.rb
+- spec/mgnu/sequence/fastq_spec.rb
+- spec/mgnu/sequence_spec.rb
+- spec/mgnu_spec.rb
+- spec/spec_helper.rb
+homepage: http://www.metagenomi.co
+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: 2.7.6
+signing_key: 
+specification_version: 4
+summary: MgNu Ruby Bioinformatics Library
+test_files:
+- spec/mgnu/parser/blast_format0_spec.rb
+- spec/mgnu/parser/blast_format7_spec.rb
+- spec/mgnu/parser/blast_format8_spec.rb
+- spec/mgnu/parser/blast_multihsp_spec.rb
+- spec/mgnu/parser/blast_oof_spec.rb
+- spec/mgnu/parser/clustalw_spec.rb
+- spec/mgnu/parser/fasta_header_index_tc_parser_spec.rb
+- spec/mgnu/parser/fasta_index_tc_parser_spec.rb
+- spec/mgnu/parser/fasta_parser_spec.rb
+- spec/mgnu/parser_spec.rb
+- spec/mgnu/sequence/fasta_spec.rb
+- spec/mgnu/sequence/fastq_spec.rb
+- spec/mgnu/sequence_spec.rb
+- spec/mgnu_spec.rb
+- spec/spec_helper.rb