bio 1.2.1 → 1.3.0

data/test/unit/bio/appl/blast/test_rpsblast.rb

@@ -0,0 +1,398 @@
+#
+# test/unit/bio/appl/blast/test_rpsblast.rb - Unit test for Bio::Blast::RPSBlast::Report
+#
+# Copyright::  Copyright (C) 2008
+#              Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
+#
+#  $Id:$
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'digest/sha1'
+require 'bio/io/flatfile'
+require 'bio/appl/blast/rpsblast'
+
+module Bio
+module TestRPSBlast
+  bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
+  TestFileName = Pathname.new(File.join(bioruby_root, 'test', 'data', 'rpsblast', 'misc.rpsblast')).cleanpath.to_s
+
+  class TestRPSBlastSplitter < Test::Unit::TestCase
+    def setup
+      @io = File.open(TestFileName)
+      @bstream = Bio::FlatFile::BufferedInputStream.new(@io, TestFileName)
+      @klass = Bio::Blast::RPSBlast::Report
+      @splitter = Bio::Blast::RPSBlast::RPSBlastSplitter.new(@klass, @bstream)
+    end
+
+    def teardown
+      @io.close
+    end
+
+    def test_skip_leader
+      assert_equal(nil, @splitter.skip_leader)
+      assert_equal(0, @bstream.pos)
+      # force to push back white spaces
+      @bstream.ungets("          \n\n  \t\t  \n")
+      assert_equal(nil, @splitter.skip_leader)
+      assert_equal("RPS-BLAST 2.2.18 [Mar-02-2008]\n", @bstream.gets)
+    end
+
+    def test_rewind
+      assert_nothing_raised { @splitter.rewind }
+    end
+
+    def test_get_entry
+      assert(raw = @splitter.get_entry)
+      assert_equal(4388, raw.size)
+      assert_equal('12201ff286b16f8578e2a3b0778c721438ac8278',
+                   Digest::SHA1.hexdigest(raw))
+
+      assert(raw = @splitter.get_entry)
+      assert_equal(245, raw.size)
+      assert_equal('f5fb1ac1aa62ba65a68c5c7c8240c0a9fc047a46',
+                   Digest::SHA1.hexdigest(raw))
+
+      assert(raw = @splitter.get_entry)
+      assert_equal(3144, raw.size)
+      assert_equal('db0ff4bf9901186758b2a0d6e94734a53733631f',
+                   Digest::SHA1.hexdigest(raw))
+
+      assert_nil(@splitter.get_entry)
+    end
+
+    def test_entry_pos
+      @splitter.entry_pos_flag = true
+      @splitter.get_entry
+      assert_equal(0,    @splitter.entry_start_pos)
+      assert_equal(4388, @splitter.entry_ended_pos)
+
+      @splitter.get_entry
+      assert_equal(4388, @splitter.entry_start_pos)
+      assert_equal(4461, @splitter.entry_ended_pos)
+
+      @splitter.get_entry
+      assert_equal(4461, @splitter.entry_start_pos)
+      assert_equal(7433, @splitter.entry_ended_pos)
+    end
+  end #class TestRPSBlastSplitter
+
+  class TestRPSBlastReport < Test::Unit::TestCase
+    def setup
+      @flatfile = Bio::FlatFile.open(Bio::Blast::RPSBlast::Report,
+                                     TestFileName)
+      @obj = @flatfile.next_entry
+    end
+
+    def teardown
+      @flatfile.close
+    end
+
+    def test_program
+      assert_equal('RPS-BLAST', @obj.program)
+    end
+
+    def test_version
+      exp = 'RPS-BLAST 2.2.18 [Mar-02-2008]'
+      assert_equal(exp, @obj.version)
+    end
+
+    def test_version_number
+      assert_equal('2.2.18', @obj.version_number)
+    end
+
+    def test_version_date
+      assert_equal('Mar-02-2008', @obj.version_date)
+    end
+      
+    def test_db
+      assert_equal('Pfam.v.22.0', @obj.db)
+    end
+
+    def test_query_def
+      ary =
+        [
+         'TestSequence mixture of globin and rhodopsin (computationally randomly concatenated)',
+         'randomseq3',
+         'gi|6013469|gb|AAD49229.2|AF159462_1 EHEC factor for adherence [Escherichia coli]'
+        ]
+      @flatfile.rewind
+      @flatfile.each do |rep|
+        assert_equal(ary.shift, rep.query_def)
+      end
+      assert(ary.empty?)
+    end
+
+    def test_query_len
+      ary = [ 495, 1087, 3223 ]
+      @flatfile.rewind
+      @flatfile.each do |rep|
+        assert_equal(ary.shift, rep.query_len)
+      end
+      assert(ary.empty?)
+    end
+
+    def test_hits_size
+      ary = [ 3, 0, 2 ]
+      @flatfile.rewind
+      @flatfile.each do |rep|
+        assert_equal(ary.shift, rep.hits.size)
+      end
+      assert(ary.empty?)
+    end
+
+    def test_iterations_size
+      ary = [ 1, 1, 1 ]
+      @flatfile.rewind
+      @flatfile.each do |rep|
+        assert_equal(ary.shift, rep.iterations.size)
+      end
+      assert(ary.empty?)
+    end
+  end #class TestRPSBlastReport
+
+  class TestRPSBlastReportHit < Test::Unit::TestCase
+    def setup
+      flatfile = Bio::FlatFile.open(Bio::Blast::RPSBlast::Report,
+                                     TestFileName)
+      @hits = flatfile.next_entry.hits
+      flatfile.close
+    end
+
+    def test_hsps_size
+      ary = [ 1, 2, 1 ]
+      @hits.each do |h|
+        assert_equal(ary.shift, h.hsps.size)
+      end
+      assert(ary.empty?)
+    end
+
+    def test_len
+      assert_equal(110, @hits[0].len)
+      assert_equal(258, @hits[1].len)
+      assert_equal(336, @hits[2].len)
+    end
+
+    def test_target_len
+      assert_equal(110, @hits[0].target_len)
+      assert_equal(258, @hits[1].target_len)
+      assert_equal(336, @hits[2].target_len)
+    end
+
+    def test_target_def
+      assert_equal('gnl|CDD|84466 pfam00042, Globin, Globin..',
+                   @hits[0].target_def)
+      assert_equal("gnl|CDD|84429 pfam00001, 7tm_1, 7 transmembrane receptor (rhodopsin family). This" \
+                   " family contains, amongst other G-protein-coupled" \
+                   " receptors (GCPRs), members of the opsin family, which" \
+                   " have been considered to be typical members of the" \
+                   " rhodopsin superfamily. They share several motifs, mainly" \
+                   " the seven transmembrane helices, GCPRs of the rhodopsin" \
+                   " superfamily. All opsins bind a chromophore, such as" \
+                   " 11-cis-retinal. The function of most opsins other than" \
+                   " the photoisomerases is split into two steps: light" \
+                   " absorption and G-protein activation. Photoisomerases, on" \
+                   " the other hand, are not coupled to G-proteins - they are" \
+                   " thought to generate and supply the chromophore that is" \
+                   " used by visual opsins..",
+                   @hits[1].target_def)
+      assert_equal("gnl|CDD|87195 pfam06976, DUF1300, Protein of unknown function (DUF1300). This" \
+                   " family represents a conserved region approximately 80" \
+                   " residues long within a number of proteins of unknown" \
+                   " function that seem to be specific to C. elegans. Some" \
+                   " family members contain more than one copy of this" \
+                   " region..",
+                   @hits[2].target_def)
+    end
+
+    def test_definition
+      assert_equal('gnl|CDD|84466 pfam00042, Globin, Globin..',
+                   @hits[0].definition)
+      assert_equal("gnl|CDD|84429 pfam00001, 7tm_1, 7 transmembrane receptor (rhodopsin family). This" \
+                   " family contains, amongst other G-protein-coupled" \
+                   " receptors (GCPRs), members of the opsin family, which" \
+                   " have been considered to be typical members of the" \
+                   " rhodopsin superfamily. They share several motifs, mainly" \
+                   " the seven transmembrane helices, GCPRs of the rhodopsin" \
+                   " superfamily. All opsins bind a chromophore, such as" \
+                   " 11-cis-retinal. The function of most opsins other than" \
+                   " the photoisomerases is split into two steps: light" \
+                   " absorption and G-protein activation. Photoisomerases, on" \
+                   " the other hand, are not coupled to G-proteins - they are" \
+                   " thought to generate and supply the chromophore that is" \
+                   " used by visual opsins..",
+                   @hits[1].definition)
+      assert_equal("gnl|CDD|87195 pfam06976, DUF1300, Protein of unknown function (DUF1300). This" \
+                   " family represents a conserved region approximately 80" \
+                   " residues long within a number of proteins of unknown" \
+                   " function that seem to be specific to C. elegans. Some" \
+                   " family members contain more than one copy of this" \
+                   " region..",
+                   @hits[2].definition)
+    end
+
+    def test_evalue
+      assert_equal(2.0e-25, @hits[0].evalue)
+      assert_equal(2.0e-19, @hits[1].evalue)
+      assert_equal(0.003,   @hits[2].evalue)
+    end
+
+    def test_bit_score
+      assert_equal(110.0, @hits[0].bit_score)
+      assert_equal(90.8,  @hits[1].bit_score)
+      assert_equal(37.1,  @hits[2].bit_score)
+    end
+
+    def test_identity
+      assert_equal(50, @hits[0].identity)
+      assert_equal(37, @hits[1].identity)
+      assert_equal(32, @hits[2].identity)
+    end
+
+    def test_overlap
+      assert_equal(110, @hits[0].overlap)
+      assert_equal(162, @hits[1].overlap)
+      assert_equal(145, @hits[2].overlap)
+    end
+
+    def test_query_seq
+      assert_equal("EKQLITGLWGKV--NVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHGKKVLTSFGDAVKNLDN---IKNTFSQLSELHCDKLHVDPENFRLLGDILI", @hits[0].query_seq)
+      assert_equal("HAIMGVAFTWVMALACAAPPLAGWSRY-IPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTV----KEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFY--IFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIY", @hits[1].query_seq)
+      assert_equal("IDYYTLKPEVNNESFVIYMFV--VHFT-IPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIM----MNKQFRNCMLTTICCGKN", @hits[2].query_seq)
+    end
+
+    def test_target_seq
+      assert_equal("QKALVKASWGKVKGNAPEIGAEILARLFTAYPDTKAYFPKFGDLSTAEALKSSPKFKAHGKKVLAALGEAVKHLDDDGNLKAALKKLGARHAKRGHVDPANFKLFGEALL", @hits[0].target_seq)
+      assert_equal("RAKVLILLVWVLALLLSLPPLLFSWLRTVEEGNVTTCLIDFPEESLLR---SYTLLSTLLGFVLPLLVILVCYTRILRTLRRRARSGASIARSLKRRSSSERKAAKMLLVVVVVFVLCWLPYHIVLLLDSLCLLSIIRVLPTALLITLWLAYVNSCLNPIIY", @hits[1].target_seq)
+      assert_equal("IEYIIETTELFGSSYEILLLIEGILFKLIPSIILPIATILLIFQLKKNKKVSSRSSTSSSSNDRSTKLVTFVTISFLIATVPLGILYLIKFFVFEYEGLVMIIDKLAIIFTFLSTINGTIHFLICYFMSSQYRNTVREMFGRKKK", @hits[2].target_seq)
+    end
+
+    def test_midline
+      assert_equal("+K L+   WGKV  N  E GAE LARL   YP T+ +F  FG+LS+  A+  +P  +AHGKKVL + G+AVK+LD+   +K    +L   H  + HVDP NF+L G+ L+", @hits[0].midline)
+      assert_equal(" A + +   WV+AL  + PPL       + EG   +C ID+          S+ +   ++ F +P+++I  CY +++ T+    +  A+  +       +E++  +M++++V+ F++CW+PY  V     +         P  + I  + A   +  NP+IY", @hits[1].midline)
+      assert_equal("I+Y     E+   S+ I + +  + F  IP II+      L+F +K+       S+T+  +    T++V  + I+FLI  VP   +    F         + +   A      +  N  I+ +    M+ Q+RN +       K ", @hits[2].midline)
+    end
+
+    def test_query_start
+      assert_equal(148, @hits[0].query_start)
+      assert_equal(299, @hits[1].query_start)
+      assert_equal(336, @hits[2].query_start)
+    end
+
+    def test_query_end
+      assert_equal(252, @hits[0].query_end)
+      assert_equal(453, @hits[1].query_end)
+      assert_equal(473, @hits[2].query_end)
+    end
+
+    def test_target_start
+      assert_equal(1,   @hits[0].target_start)
+      assert_equal(100, @hits[1].target_start)
+      assert_equal(192, @hits[2].target_start)
+    end
+
+    def test_target_end
+      assert_equal(110, @hits[0].target_end)
+      assert_equal(258, @hits[1].target_end)
+      assert_equal(336, @hits[2].target_end)
+    end
+
+    def test_lap_at
+      assert_equal([148, 252,   1, 110], @hits[0].lap_at)
+      assert_equal([299, 453, 100, 258], @hits[1].lap_at)
+      assert_equal([336, 473, 192, 336], @hits[2].lap_at)
+    end
+  end #class TestRPSBlastHit
+
+  class TestRPSBlastHSP < Test::Unit::TestCase
+    def setup
+      flatfile = Bio::FlatFile.open(Bio::Blast::RPSBlast::Report,
+                                     TestFileName)
+      @hsps = flatfile.next_entry.hits[1].hsps
+      flatfile.close
+    end
+
+    def test_bit_score
+      assert_equal(90.8, @hsps[0].bit_score)
+      assert_equal(73.4, @hsps[1].bit_score)
+    end
+
+    def test_score
+      assert_equal(225, @hsps[0].score)
+      assert_equal(180, @hsps[1].score)
+    end
+
+    def test_evalue
+      assert_equal(2.0e-19, @hsps[0].evalue)
+      assert_equal(3.0e-14, @hsps[1].evalue)
+    end
+
+    def test_identity
+      assert_equal(37, @hsps[0].identity)
+      assert_equal(32, @hsps[1].identity)
+    end
+
+    def test_gaps
+      assert_equal(10,  @hsps[0].gaps)
+      assert_equal(nil, @hsps[1].gaps)
+    end
+
+    def test_positive
+      assert_equal(76, @hsps[0].positive)
+      assert_equal(47, @hsps[1].positive)
+    end
+
+    def test_align_len
+      assert_equal(162, @hsps[0].align_len)
+      assert_equal(86,  @hsps[1].align_len)
+    end
+
+    def test_query_from
+      assert_equal(299, @hsps[0].query_from)
+      assert_equal(55,  @hsps[1].query_from)
+    end
+
+    def test_query_to
+      assert_equal(453, @hsps[0].query_to)
+      assert_equal(140, @hsps[1].query_to)
+    end
+
+    def test_hit_from
+      assert_equal(100, @hsps[0].hit_from)
+      assert_equal(2,   @hsps[1].hit_from)
+    end
+
+    def test_hit_to
+      assert_equal(258, @hsps[0].hit_to)
+      assert_equal(87,  @hsps[1].hit_to)
+    end
+
+    def test_qseq
+      assert_equal("HAIMGVAFTWVMALACAAPPLAGWSRY-IPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTV----KEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFY--IFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIY", @hsps[0].qseq)
+      assert_equal("NFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVC", @hsps[1].qseq)
+    end
+
+    def test_hseq
+      assert_equal("RAKVLILLVWVLALLLSLPPLLFSWLRTVEEGNVTTCLIDFPEESLLR---SYTLLSTLLGFVLPLLVILVCYTRILRTLRRRARSGASIARSLKRRSSSERKAAKMLLVVVVVFVLCWLPYHIVLLLDSLCLLSIIRVLPTALLITLWLAYVNSCLNPIIY", @hsps[0].hseq)
+      assert_equal("NLLVILVILRTKRLRTPTNIFLLNLAVADLLFLLTLPPWALYYLVGGDWPFGDALCKLVGALFVVNGYASILLLTAISIDRYLAIV", @hsps[1].hseq)
+    end
+
+    def test_midline
+      assert_equal(" A + +   WV+AL  + PPL       + EG   +C ID+          S+ +   ++ F +P+++I  CY +++ T+    +  A+  +       +E++  +M++++V+ F++CW+PY  V     +         P  + I  + A   +  NP+IY", @hsps[0].midline)
+      assert_equal("N L + V ++ K+LRTP N  LLNLAVADL  +L      LY  + G + FG   C L G    + G  ++  L  ++I+RY+ + ", @hsps[1].midline)
+    end
+
+    def test_percent_identity
+      assert_equal(22, @hsps[0].percent_identity)
+      assert_equal(37, @hsps[1].percent_identity)
+    end
+  end #class TestRPSBlastHSP
+
+end #module TestRPSBlast
+end #module Bio
+

data/test/unit/bio/appl/paml/codeml/test_rates.rb

@@ -0,0 +1,45 @@
+#
+# test/unit/bio/appl/paml/codeml/test_rates.rb - Unit test for Bio::PAML::Codeml::Rates
+#
+# Copyright::  Copyright (C) 2008 Michael D. Barton <mail@michaelbarton.me.uk>
+# License::    The Ruby License
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib'))).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/appl/paml/codeml/rates'
+
+module Bio; module TestPAMLCodeml
+class TestCodemlRates < Test::Unit::TestCase
+
+  bioruby_root  = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6)).cleanpath.to_s
+  TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data', 'paml', 'codeml')).cleanpath.to_s
+
+  def setup
+    str = File.read(File.join(TEST_DATA, 'rates'))
+    @example_rates = Bio::PAML::Codeml::Rates.new(str)
+  end
+
+  def test_rates_first_position
+    assert_equal('***M', @example_rates.first[:data])
+    assert_equal(1, @example_rates.first[:rate])
+    assert_equal(1, @example_rates.first[:freq])
+  end
+
+  def test_rates_hundred_and_fiftieth_position
+    assert('GGGG', @example_rates[149][:data])
+    assert(0.828, @example_rates[149][:rate])
+    assert(9, @example_rates[149][:freq])
+  end
+  
+  def test_rates_last_position
+    assert('PHPP', @example_rates.last[:data])
+    assert(1.752, @example_rates.last[:rate])
+    assert(1, @example_rates.last[:freq])
+  end
+end
+
+end; end #module TestPAMLCodeml; module Bio

data/test/unit/bio/appl/paml/codeml/test_report.rb

@@ -0,0 +1,45 @@
+#
+# test/unit/bio/appl/paml/codeml/test_report.rb - Unit test for Bio::PAML::Codeml::Report
+#
+# Copyright::  Copyright (C) 2008 Michael D. Barton <mail@michaelbarton.me.uk>
+# License::    The Ruby License
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib'))).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/appl/paml/codeml/report'
+
+module Bio; module TestPAMLCodeml
+class TestCodemlReport < Test::Unit::TestCase
+
+  bioruby_root  = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6)).cleanpath.to_s
+  TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data', 'paml', 'codeml')).cleanpath.to_s
+
+  def setup
+    str = File.read(File.join(TEST_DATA, 'output.txt'))
+    @example_report = Bio::PAML::Codeml::Report.new(str)
+  end
+
+  def test_tree_log_likelihood
+    assert_equal(-1817.465211, @example_report.tree_log_likelihood)
+  end
+
+  def test_tree_length
+    assert_equal(0.77902, @example_report.tree_length)
+  end
+
+  def test_alpha
+    assert_equal(0.58871, @example_report.alpha)
+  end
+
+  def test_tree
+    tree = "(((rabbit: 0.082889, rat: 0.187866): 0.038008, human: 0.055050): 0.033639, goat-cow: 0.096992, marsupial: 0.284574);"
+    assert_equal(tree, @example_report.tree)
+  end
+
+end
+
+end; end #module TestPAMLCodeml; module Bio