mgnu 2.1.1

data/spec/mgnu/parser/blast_format0_spec.rb

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+require 'spec_helper'
+
+describe 'MgNu::Parser::Blast format0' do
+  before do
+    @report = MgNu::Parser::Blast.new('data/test.blast', 0)
+  end
+
+  it 'knows about attributes' do
+    expect(@report).to be_a(MgNu::Parser::Blast)
+    expect(@report).to respond_to(:parse)
+  end
+
+  describe 'after calling parse' do
+    before do
+      @queries = @report.parse
+    end
+    
+    it 'should have the correct number of queries' do
+      expect(@queries.length).to eq(3)
+    end
+
+    it 'should contain the correct first query' do
+      expect(@queries[0].query_id).to eq('test')
+    end
+
+    it 'should have the correct number of sbjcts for query 1' do
+      expect(@queries[0].sbjcts.length).to eq(10)
+    end
+
+    it 'should have the correct number of sbjcts for query 2' do
+      expect(@queries[1].sbjcts.length).to eq(10)
+    end
+
+    describe 'the third query' do
+      before do
+        @query = @queries[2]
+      end
+
+      it 'should have a correct database name' do
+        expect(@query.database).to eq('NCBI Protein Reference Sequences')
+      end
+
+      it 'should respond to sbjcts' do
+        expect(@query).to respond_to(:sbjcts)
+        expect(@query.sbjcts).to be_a(Array)
+        expect(@query.sbjcts.length).to eq(10)
+      end
+      
+      describe 'the first sbjct of the third query' do
+        before do
+          @sbjct = @query.sbjcts[0]
+        end
+
+        it 'should have number 1' do
+          expect(@sbjct.number).to eq(1)
+        end
+
+        it 'should have the correct sbjct name' do
+          expect(@sbjct.sbjct_id).to eq('ref|ZP_02544218.1|')
+        end
+
+        it 'should have the correct length' do
+          expect(@sbjct.length).to eq(121)
+        end
+
+        it 'should have a non-empty array of Hsps' do
+          expect(@sbjct.hsps.length).to be > 0
+        end
+
+        it 'should respond to best_hsp and return an Hsp object' do
+          expect(@query.sbjcts[0]).to respond_to(:best_hsp)
+          expect(@sbjct.best_hsp).to be_a(MgNu::Parser::Blast::Hsp)
+        end
+
+        describe 'the first hsp of the first sbjct of the third query' do
+          before do
+            @hsp = @sbjct.hsps[0]
+          end
+
+          it 'should have a known query sequence' do
+            str = 'MKKIL-ATIXSAALYGLP----AXVMAQGITDDLSNLGLNXFGNETNLGTNIALIGTIARIINILLGFLGVLAVILVLWGGFKWMTAAGDEAKIGEAKKLMGAGVIGLVIILAAFAIASFVVNQL'
+            expect(@hsp.query_sequence).to eq(str)
+          end
+
+          it 'should have a known midline' do
+            str = 'MKK L A + S  +   P    A V A   ++  S +     GN T+L +       I  I+NILL   G +AVI+++ GG +++ ++GD  ++  AK  +   VIGL++++ A+AI +FVV  +'
+            expect(@hsp.midline).to eq(str)
+          end
+
+          it 'should have a known sbjct sequence' do
+            str = 'MKKFLIAALVSLGIVVTPLAMDAPVFANAKSEVTSGVSSVNDGNSTDLPS------FITNIVNILLFLAGAVAVIVIIIGGIRYVMSSGDAGQVQSAKNTILYAVIGLIVVIMAYAIVNFVVTNV'
+            expect(@hsp.sbjct_sequence).to eq(str)
+          end
+
+          it 'should have the correct bit score and raw score' do
+            expect(@hsp.bit_score).to eq(62.0)
+            expect(@hsp.score).to eq(149)
+          end
+
+          it 'should have a correct evalue' do
+            expect(@hsp.evalue).to eq(1e-10)
+          end
+
+          it 'should have a non-nil query|sbjct_from and _to values' do
+            expect(@hsp.query_from).not_to be_nil
+            expect(@hsp.query_to).not_to be_nil
+            expect(@hsp.sbjct_from).not_to be_nil
+            expect(@hsp.sbjct_to).not_to be_nil
+          end
+        end
+      end
+    end
+  end
+end

data/spec/mgnu/parser/blast_format7_spec.rb

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+require 'spec_helper'
+
+describe 'MgNu::Parser::Blast format7' do
+  before do
+    @report = MgNu::Parser::Blast.new('data/test.blast.xml')
+    @queries = @report.parse
+  end
+
+  it 'should correctly parse' do
+    expect(@queries.length).to eq(8)
+  end
+
+  it 'should report the correct information for queries' do
+    query_10 = @queries.select{|x| x.number == 10}[0]
+    expect(query_10).to be_a(MgNu::Parser::Blast::Query)
+    expect(query_10.number).to eq(10)
+    expect(query_10.sbjcts.length).to eq(7)
+
+    sbjct_6 = query_10.sbjcts.select{|x| x.number == 6}[0]
+    expect(sbjct_6.sbjct_id).to eq('gi|31376410|gb|AC096051.7|')
+    expect(sbjct_6.hsps.length).to eq(1)
+    expect(sbjct_6.hsps[0].evalue).to eq(2.97608)
+  end
+end

data/spec/mgnu/parser/blast_format8_spec.rb

@@ -0,0 +1,26 @@
+require 'spec_helper'
+
+describe 'MgNu::Parser::Blast format8' do
+  before do
+    @report = MgNu::Parser::Blast.new('./data/test.blast.m8', 8)
+    @queries = @report.parse
+    expect(@report).to be_a(MgNu::Parser::Blast)
+  end
+
+  it 'should correctly parse' do
+    expect(@queries.length).to eq(2)
+  end
+
+  it 'should report the correct information for queries' do
+    expect(@queries[0].sbjcts.length).to eq(3)
+    expect(@queries[1].sbjcts.length).to eq(3)
+
+    expect(@queries[0].sbjcts[0].hsps.length).to eq(3)
+    expect(@queries[0].sbjcts[1].hsps.length).to eq(3)
+    expect(@queries[0].sbjcts[2].hsps.length).to eq(3)
+
+    expect(@queries[1].sbjcts[0].hsps.length).to eq(8)
+    expect(@queries[1].sbjcts[1].hsps.length).to eq(1)
+    expect(@queries[1].sbjcts[2].hsps.length).to eq(1)
+  end
+end

data/spec/mgnu/parser/blast_multihsp_spec.rb

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+require 'spec_helper'
+
+describe 'MgNu::Parser::Blast parsing a multihsp report' do
+  before do
+    @report = MgNu::Parser::Blast.new('data/multihsp.blast', 0)
+    @queries = @report.parse
+    @query = @queries[0]
+    @sbjct = @query.sbjcts[0]
+  end
+  
+  it 'should have one query' do
+    expect(@queries.length).to eq(1)
+  end
+
+  it 'should have 1 sbjcts for query 1' do
+    expect(@queries[0].sbjcts.length).to eq(1)
+  end
+
+  it 'should have the correct sbjct_id for query 1' do
+    expect(@sbjct.sbjct_id).to eq('Contig17100_1_5')
+  end
+
+  it 'should have the correct sbjct length' do
+    expect(@sbjct.length).to eq(2190)
+  end
+
+  it 'should have a non-empty array of Hsps' do
+    expect(@sbjct.hsps.length).to be > 0
+  end
+
+  describe 'Query 1, Sbjct 1, Hsp 1' do
+    before do
+      @hsp = @sbjct.hsps[0]
+    end
+
+    it 'should have a known query sequence' do
+      str = 'gatcgacggcaagct'
+      expect(@hsp.query_sequence).to eq(str)
+    end
+
+    it 'should have a known midline' do
+      str = '|||||||||||||||'
+      expect(@hsp.midline).to eq(str)
+    end
+
+    it 'should have a known sbjct sequence' do
+      str = 'gatcgacggcaagct'
+      expect(@hsp.sbjct_sequence).to eq(str)
+    end
+
+    it 'should have the correct bit score and raw score' do
+      expect(@hsp.bit_score).to eq(30.2)
+      expect(@hsp.score).to eq(15)
+    end
+
+    it 'should have a correct evalue' do
+      expect(@hsp.evalue).to eq(0.12)
+    end
+  end # end - hsp 1 context
+
+  describe 'Query 1, Sbjct 1, Hsp 4' do
+    before do
+      @hsp = @sbjct.hsps[3]
+    end
+
+    it 'should have a known query sequence' do
+      str = 'gatcgataaagtg'
+      expect(@hsp.query_sequence).to eq(str)
+    end
+
+    it 'should have a known midline' do
+      str = '|||||||||||||'
+      expect(@hsp.midline).to eq(str)
+    end
+
+    it 'should have a known sbjct sequence' do
+      str = 'gatcgataaagtg'
+      expect(@hsp.sbjct_sequence).to eq(str)
+    end
+
+    it 'should have the correct bit score and raw score' do
+      expect(@hsp.bit_score).to eq(26.3)
+      expect(@hsp.score).to eq(13)
+    end
+
+    it 'should have a correct evalue' do
+      expect(@hsp.evalue).to eq(1.8)
+    end
+
+    it 'should have the correct query start/stop positions' do
+      expect(@hsp.query_from).to eq(64175)
+      expect(@hsp.query_to).to eq(64187)
+    end
+
+    it 'should have the correct sbjct start/stop positions' do
+      expect(@hsp.sbjct_from).to eq(1566)
+      expect(@hsp.sbjct_to).to eq(1578)
+    end
+  end
+end

data/spec/mgnu/parser/blast_oof_spec.rb

@@ -0,0 +1,53 @@
+require 'spec_helper'
+
+describe 'MgNu::Parser::Blast parsing a oof report' do
+  before do
+    @report = MgNu::Parser::Blast.new('data/test_blastx_oof.blast', 0)
+    @queries = @report.parse
+    @query = @queries[0]
+  end
+
+  it 'should have 1 query' do
+    expect(@queries.length).to eq(1)
+  end
+
+  it 'should have 1 sbjcts for query 1' do
+    expect(@query.sbjcts.length).to eq(1)
+  end
+
+  describe 'Query 1, Sbjct 1' do
+    before do
+      @sbjct = @query.sbjcts[0]
+    end
+
+    it 'should have the correct sbjct_id' do
+      expect(@sbjct.sbjct_id).to eq('spe:Spro_0261')
+    end
+
+    it 'should have the correct length' do
+      expect(@sbjct.length).to eq(729)
+    end
+
+    it 'should have a non-empty array of Hsps' do
+      expect(@sbjct.hsps.length).to be > 0
+    end
+
+    describe 'Query 1, Sbjct 1, Hsp 1' do
+      before do
+        @hsp = @sbjct.hsps[0]
+      end
+
+      it 'should contain one frame-shift characters in the query sequence' do
+        expect(@hsp.query_sequence.split(%r{\/}).length).to be(2)
+      end
+
+      it 'should respond to query_frameshifts and return a hash with the correct key/value pair' do
+        expect(@hsp).to respond_to(:query_frameshifts)
+        expect(@hsp.query_frameshifts).to be_a(Hash)
+        expect(@hsp.query_frameshifts.keys.length).to eq(1)
+        expect(@hsp.query_frameshifts.keys[0]).to eq(576)
+        expect(@hsp.query_frameshifts.values[0]).to eq(1)
+      end
+    end
+  end
+end

data/spec/mgnu/parser/clustalw_spec.rb

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+require 'spec_helper'
+
+describe MgNu::Parser::ClustalW do
+  before do
+    @clw = MgNu::Parser::ClustalW.new('data/clustalw_test.aln')
+  end
+
+  it 'should be a correct object' do
+    expect(@clw).to be_a(MgNu::Parser::ClustalW)
+    expect(@clw).to respond_to(:file)
+    expect(@clw).to respond_to(:buffer)
+    expect(@clw).to respond_to(:alignment)
+  end
+
+  it 'should be parsed after creation' do
+    expect(@clw.buffer.length).to be > 0
+  end
+
+  it 'return a MgNu::Alignment' do
+    expect(@clw.alignment).to be_a(MgNu::Alignment)
+  end
+
+  describe 'MgNu::Alignment' do
+    before do
+      @a = @clw.alignment
+    end
+
+    it 'should act like an array' do
+      count = 0
+      @a.each do |s|
+        count += 1
+        expect(s).to be_a(String)
+      end
+      expect(count).to eq(7)
+    end
+
+    it 'can iterate by column' do
+      count = 0
+      @a.each_position do
+        count += 1
+      end
+      expect(count).to eq(@a.length)
+      expect(@a.each_position).to be_a(Array)
+    end
+
+    it 'can iterate of a range of columns' do
+      count = 0
+      @a.each_position(10..20) do
+        count += 1
+      end
+      r = []
+      (10..20).each { |x| r << x }
+      expect(count).to eq(r.length)
+    end
+
+    it 'can fetch a single position in in the alignment' do
+      m = nil
+      @a.each_position(3) do |pos|
+        m = pos
+      end
+      expect(m).to be_a(Array)
+      expect(m[0]).to eq('K')
+      expect(m[1]).to eq('N')
+    end
+
+    it 'should behave like an enumerable' do
+      expect(@a[10..20]).to be_a(Array)
+      m = @a[3]
+      expect(m).to be_a(Array)
+      expect(m[0][0]).to eq('K')
+      expect(m[0][1]).to eq('N')
+    end
+
+    it 'reports the correct match length' do
+      expect(@a.match.length).to eq(@a.length)
+    end
+
+    it 'reports correct match data using a range operator' do
+      expect(@a.match(107..112)).to eq('. : .*')
+    end
+
+    it 'reports single position match values correctly' do
+      expect(@a.match(3)).to eq(' ')
+      expect(@a.match(107)).to eq('.')
+      expect(@a.match(108)).to eq(' ')
+      expect(@a.match(109)).to eq(':')
+      expect(@a.match(112)).to eq('*')
+    end
+  end
+end

data/spec/mgnu/parser/fasta_header_index_tc_parser_spec.rb

@@ -0,0 +1,25 @@
+require 'spec_helper'
+
+describe MgNu::Parser::FastaHeaderIndex do
+  before do
+    @ff = MgNu::Parser::FastaHeaderIndex.new('data/test.fasta')
+  end
+
+  it 'should know about attributes' do
+    expect(@ff).to be_a(MgNu::Parser::FastaHeaderIndex)
+    expect(File.exist?('data/test.fasta.hdr.tch')).to be(true)
+    expect(@ff).to respond_to(:filename)
+  end
+
+  it 'should allow hash-like access using Fasta header names' do
+    expect(@ff['name1']).to eq('description1')
+  end
+
+  after(:each) do
+    @ff.close
+  end
+
+  after do
+    File.delete('data/test.fasta.hdr.tch') if File.exist?('data/test.fasta.hdr.tch')
+  end
+end

data/spec/mgnu/parser/fasta_index_tc_parser_spec.rb

@@ -0,0 +1,25 @@
+require 'spec_helper'
+
+describe MgNu::Parser::FastaIndex do
+  before do
+    @ff = MgNu::Parser::FastaIndex.new('data/test.fasta')
+  end
+
+  it 'should know about attributes' do
+    expect(@ff).to be_a(MgNu::Parser::FastaIndex)
+    expect(File.exist?('data/test.fasta.tch')).to be(true)
+    expect(@ff).to respond_to(:filename)
+  end
+
+  it 'should allow hash-like access using Fasta header names' do
+    expect(@ff['name1'].sequence).to eq('ACCG')
+  end
+
+  after(:each) do
+    @ff.close
+  end
+
+  after do
+    File.delete('data/test.fasta.tch') if File.exist?('data/test.fasta.tch')
+  end
+end