wwood-bioruby 1.2.11

data/test/unit/bio/appl/test_blast.rb

@@ -0,0 +1,277 @@
+#
+# test/unit/bio/appl/test_blast.rb - Unit test for Bio::Blast
+#
+# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
+#
+#  $Id:$
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib'))).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/appl/blast'
+
+
+module Bio
+  class TestBlastData
+    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4)).cleanpath.to_s
+    TestDataBlast = Pathname.new(File.join(bioruby_root, 'test', 'data', 'blast')).cleanpath.to_s
+
+    def self.input
+      File.open(File.join(TestDataBlast, 'b0002.faa')).read
+    end
+
+    def self.output(format = '7')
+      case format
+      when '0'
+        File.open(File.join(TestDataBlast, 'b0002.faa.m0')).read 
+      when '7'
+        File.open(File.join(TestDataBlast, 'b0002.faa.m7')).read 
+      when '8'
+        File.open(File.join(TestDataBlast, 'b0002.faa.m8')).read 
+      end
+    end
+  end
+
+    
+  class TestBlast < Test::Unit::TestCase
+    def setup
+      @program = 'blastp'
+      @db = 'test'
+      @option = []
+      @server = 'localhost'
+      @blast = Bio::Blast.new(@program, @db, @option, @server)
+    end
+    
+    def test_new
+      blast = Bio::Blast.new(@program, @db)
+      assert_equal(@program, blast.program)
+      assert_equal(@db, blast.db)
+      assert(blast.options)
+      assert_equal('local', blast.server)
+      assert_equal('blastall', blast.blastall)
+    end
+
+    def test_new_opt_string
+      blast = Bio::Blast.new(@program, @db, '-m 7 -F F')
+      assert_equal(['-m', '7', '-F', 'F'], blast.options)
+    end
+
+    def test_program
+      assert_equal(@program, @blast.program) 
+    end
+
+    def test_db
+      assert_equal(@db, @blast.db) 
+    end
+
+    def test_options
+      assert_equal([], @blast.options) 
+    end
+
+    def test_option
+      assert_equal('', @blast.option) 
+    end
+
+    def test_option_set
+      @blast.option = '-m 7 -p T'
+      assert_equal('-m 7 -p T', @blast.option) 
+    end
+
+    def test_option_set_m0
+      @blast.option = '-m 0'
+      assert_equal('-m 0', @blast.option) 
+    end
+
+
+    def test_server
+      assert_equal(@server, @blast.server) 
+    end
+
+    def test_blastll
+      assert_equal('blastall', @blast.blastall) 
+    end
+
+    def test_matrix
+      assert_equal(nil, @blast.matrix) 
+    end
+
+    def test_filter
+      assert_equal(nil, @blast.filter) 
+    end
+
+    def test_parser
+      assert_equal(nil, @blast.instance_eval { @parser })
+    end
+
+    def test_output
+      assert_equal('', @blast.output)  
+    end
+
+     def test_format
+       assert(@blast.format)  
+     end
+
+     def test_self_local
+       assert(Bio::Blast.local(@program, @db, @option))
+     end
+
+     def test_self_local
+       assert(Bio::Blast.remote(@program, @db, @option))
+     end
+
+     def test_query
+       # to be tested in test/functional/bio/test_blast.rb
+     end
+
+     def test_blast_reports_xml
+       ret = Bio::Blast.reports_xml(TestBlastData.output)
+       assert_instance_of(Array, ret)
+       count = 0
+       ret.each do |report|
+         count += 1
+         assert_instance_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_xml_with_block
+       count = 0
+       Bio::Blast.reports_xml(TestBlastData.output) do |report|
+         count += 1
+         assert_instance_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format0
+       ret = Bio::Blast.reports(TestBlastData.output('0'))
+       assert_instance_of(Array, ret)
+       count = 0
+       ret.each do |report|
+         count += 1
+         assert_instance_of(Bio::Blast::Default::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format7
+       ret = Bio::Blast.reports(TestBlastData.output('7'))
+       assert_instance_of(Array, ret)
+       count = 0
+       ret.each do |report|
+         count += 1
+         assert_instance_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format8
+       ret = Bio::Blast.reports(TestBlastData.output('8'))
+       assert_instance_of(Array, ret)
+       count = 0
+       ret.each do |report|
+         count += 1
+         assert_kind_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format0_with_block
+       count = 0
+       Bio::Blast.reports(TestBlastData.output('0')) do |report|
+         count += 1
+         assert_instance_of(Bio::Blast::Default::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format7_with_block
+       count = 0
+       Bio::Blast.reports(TestBlastData.output('7')) do |report|
+         count += 1
+         assert_instance_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format8_with_block
+       count = 0
+       Bio::Blast.reports(TestBlastData.output('8')) do |report|
+         count += 1
+         assert_kind_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+     
+     def test_blast_reports_format7_with_parser
+       ret = Bio::Blast.reports(TestBlastData.output('7'), :rexml)
+       assert_instance_of(Array, ret)
+       count = 0
+       ret.each do |report|
+         count += 1
+         assert_instance_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format8_with_parser
+       ret = Bio::Blast.reports(TestBlastData.output('8'), :tab)
+       assert_instance_of(Array, ret)
+       count = 0
+       ret.each do |report|
+         count += 1
+         assert_kind_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format7_with_parser_with_block
+       count = 0
+       Bio::Blast.reports(TestBlastData.output('7'), :rexml) do |report|
+         count += 1
+         assert_instance_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_blast_reports_format8_with_parser_with_block
+       count = 0
+       Bio::Blast.reports(TestBlastData.output('8'), :tab) do |report|
+         count += 1
+         assert_kind_of(Bio::Blast::Report, report)
+       end
+       assert_equal(1, count)
+     end
+
+     def test_make_command_line
+       @blast = Bio::Blast.new(@program, @db, '-m 7 -F F')
+       assert_equal(["blastall", "-p", "blastp", "-d", "test", "-m", "7", "-F", "F"], 
+                    @blast.instance_eval { make_command_line })
+     end
+     def test_make_command_line_2
+       @blast = Bio::Blast.new(@program, @db, '-m 0 -F F')
+       assert_equal(["blastall", "-p", "blastp", "-d", "test", "-m", "0", "-F",  "F"], 
+                    @blast.instance_eval { make_command_line })
+     end
+
+     def test_parse_result
+       assert(@blast.instance_eval { parse_result(TestBlastData.output) })
+     end
+
+     def test_exec_local
+       # to be tested in test/functional/bio/test_blast.rb       
+     end
+     
+     def test_exec_genomenet
+       # to be tested in test/functional/bio/test_blast.rb
+     end
+
+     def test_exec_ncbi
+       # to be tested in test/functional/bio/test_blast.rb
+     end
+   end
+ end

data/test/unit/bio/appl/test_fasta.rb

@@ -0,0 +1,130 @@
+#
+# test/unit/bio/appl/test_fasta.rb - Unit test for Bio::Fasta
+#
+# Copyright::   Copyright (C) 2006
+#               Mitsuteru C. Nakao <n@bioruby.org>
+# License::     The Ruby License
+#
+#  $Id:$
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib'))).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/appl/fasta'
+
+
+module Bio
+
+  class TestFastaInitialize < Test::Unit::TestCase
+    def test_new_1
+      program = 'string'
+      db = 'string'
+      option = ['-e', '0.001']
+      server = 'local'
+      assert_raise(ArgumentError) { Bio::Fasta.new() }
+      assert_raise(ArgumentError) { Bio::Fasta.new(program) }
+      assert(Bio::Fasta.new(program, db))
+      assert(Bio::Fasta.new(program, db, option))
+      assert(Bio::Fasta.new(program, db, option, server))
+      assert_raise(ArgumentError) {  Bio::Fasta.new(program, db, option, server, nil) }
+    end
+
+    def test_option_backward_compatibility
+      fasta = Bio::Fasta.new('program', 'db', "-e 10")
+      assert_equal([ '-Q', '-H', '-m','10', '-e',  '10'], fasta.options)
+    end
+
+    def test_option
+      fasta = Bio::Fasta.new('program', 'db', ["-e", "10"])
+      assert_equal([ '-Q', '-H', '-m','10', '-e', '10'], fasta.options)
+    end
+  end
+
+
+  class TestFasta < Test::Unit::TestCase
+
+    def setup
+      program = 'ssearch'
+      db = 'nr'
+      option = ['-e', '10']
+      @obj = Bio::Fasta.new(program, db, option)
+    end
+
+    def test_program
+      assert_equal('ssearch', @obj.program)
+      @obj.program = 'lalign'
+      assert_equal('lalign', @obj.program)
+    end
+
+    def test_db
+      assert_equal('nr', @obj.db)
+      @obj.db = 'refseq'
+      assert_equal('refseq', @obj.db)
+    end
+
+    def test_options
+      assert_equal(["-Q", "-H", "-m", "10", "-e", "10"], @obj.options)
+      @obj.options = ['-Q', '-H', '-m', '8']
+      assert_equal(['-Q', '-H', '-m', '8'], @obj.options)
+    end
+
+    def test_server
+      assert_equal('local', @obj.server)
+      @obj.server = 'genomenet'
+      assert_equal('genomenet', @obj.server)
+    end
+
+    def test_ktup
+      assert_equal(nil, @obj.ktup)
+      @obj.ktup = 6
+      assert_equal(6, @obj.ktup)
+    end
+    def test_matrix
+      assert_equal(nil, @obj.matrix)
+      @obj.matrix = 'PAM120'
+      assert_equal('PAM120', @obj.matrix)
+    end
+
+    def test_output
+      assert_equal('', @obj.output)
+#      assert_raise(NoMethodError) { @obj.output = "" }
+    end
+    
+    def test_option
+      option = ['-M'].join(' ')
+      assert(@obj.option = option)
+      assert_equal(option, @obj.option)
+    end
+    
+    def test_format
+      assert_equal(10, @obj.format)
+    end
+
+    def test_format_arg_str
+      assert(@obj.format = '1')
+      assert_equal(1, @obj.format)
+    end
+
+    def test_format_arg_integer
+      assert(@obj.format = 2)
+      assert_equal(2, @obj.format)
+    end
+  end
+
+  class TestFastaQuery < Test::Unit::TestCase
+    def test_self_parser
+    end
+    def test_self_local
+      # test/functional/bio/test_fasta.rb
+    end
+    def test_self_remote
+      # test/functional/bio/test_fasta.rb
+    end
+    def test_query
+    end
+  end
+
+end

data/test/unit/bio/appl/test_psort.rb

@@ -0,0 +1,57 @@
+#
+# test/unit/bio/appl/test_psort.rb - Unit test for Bio::WoLF_PSORT
+#
+# Copyright::   Copyright (C) 2008
+#               Ben J Woodcroft <donttrustben somewhere near gmail.com>
+# License::     The Ruby License
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib'))).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/appl/psort'
+
+class WoLFPsortTest < Test::Unit::TestCase
+  def test_parse_summary_line_nil
+    assert_nil Bio::PSORT::WoLF_PSORT::Report.parse_from_summary('plant', "# k used for kNN is: 14\n")
+  end
+  
+  def test_parse_summary_one_line
+    assert_equal Bio::PSORT::WoLF_PSORT::Report.new('gcn5a', 'plant', {'nucl' => 12, 'cyto' => 1, 'plas' => 1, 'cyto_plas' => 1}),
+      Bio::PSORT::WoLF_PSORT::Report.parse_from_summary('plant', "gcn5a nucl 12, cyto 1, plas 1, cyto_plas 1")
+  end
+  
+  def test_parse_summary_one_line_fungi
+    assert_equal Bio::PSORT::WoLF_PSORT::Report.new('gcn5a', 'plant', {'cyto' => 17, 'nucl' => 9, 'cyto_pero' => 9}),
+      Bio::PSORT::WoLF_PSORT::Report.parse_from_summary('plant', "gcn5a cyto 17, nucl 9, cyto_pero 9")
+  end
+  
+  def test_amino_acid_sequence_prediction
+    # catalase pero 8, nucl 2, mito 1.5, cyto_nucl 1.5, mito_plas 1.5
+    assert_equal Bio::PSORT::WoLF_PSORT::Report.new('wolf', 'plant', {'pero' => 8.0, 'nucl' => 2.0, 'mito' => 1.5, 'mito_plas' => 1.5, 'cyto_nucl' => 1.5}),
+      Bio::PSORT::WoLF_PSORT.exec_local_from_sequence(
+      'MTQVPPVTFQQYGPVITTSAGNPVDDNQNSVTAGPYGPAILSNFHLIDKLAHFDRERIPE
+RVVHAKGGGAFGYFEVTHDITRFCKAKLFEKIGKRTPVFARFSTVAGESGSADTRRDPRG
+FALKFYTEEGNWDMVGNNTPIFFVRDAIKFPDFIHTQKRHPQTHLHDPNMVWDFFSLVPE
+SVHQVTFLYTDRGTPDGFRHMNGYGSHTFKFINKDNEAFYVKWHFKTNQGIKNLNRQRAK
+ELESEDPDYAVRDLFNAIAKREFPSWTFCIQVMPLKDAETYKWNVFDVTKVWPHGDYPLI
+PVGRLVLDRNPENYFQDVEQAAFAPAHMVPGIEPSEDRMLQGRMFSYIDTHRHRLGANYH
+QIPVNRPWNARGGDYSVRDGPMCVDGNKGSQLNYEPNSVDGFPKEDRNAAVSGTTTVSGT
+VACHPQEHPNSDFEQPGNFYRTVLSEPEREALIGNIAEHLRQARRDIQERQVKIFYKCDP
+EYGERVARAIGLPTAACYPAKM*'.gsub(/\s/,''),
+      'plant'
+    )
+  end
+  
+  def test_too_small_amino_acid_sequence_prediction
+    # known problem - too short for WoLF_PSORT?
+    assert_nil Bio::PSORT::WoLF_PSORT.exec_local_from_sequence('MRTLKTEVEKGFLSTMFVQELATPKG', 'animal')
+  end
+  
+  def test_highest_predicted_localization
+    assert_equal 'cyto', Bio::PSORT::WoLF_PSORT::Report.new('gcn5a', 'plant', {'cyto' => 17, 'nucl' => 9, 'cyto_pero' => 9}).highest_predicted_localization
+    assert_equal 'cyto_pero', Bio::PSORT::WoLF_PSORT::Report.new('gcn5a', 'plant', {'cyto' => 17, 'nucl' => 9, 'cyto_pero' => 90}).highest_predicted_localization
+  end
+end