jandot-bio 1.2.1

data/test/unit/bio/appl/mafft/test_report.rb

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+#
+# test/unit/bio/appl/mafft/test_report.rb - Unit test for Bio::Alignment::MultiFastaFormat
+#
+# Copyright::  Copyright (C) 2007
+#              2005 Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
+#
+#  $Id: test_report.rb,v 1.1 2007/07/16 12:21:39 ngoto Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+
+require 'bio'
+
+module Bio
+  class TestAlignmentMultiFastaFormat < Test::Unit::TestCase
+    def setup
+      @na = Bio::Alignment::MultiFastaFormat.new <<__END_OF_NASEQS__
+>naseq1
+TAGATTTCGAATTTCTAGnGAACCGAACCGkACAGCCTTACATyATTCAGACCAATGTGT
+TACCAATTCGAGTATACAAGAACAGTGATAAGGTACCAAACAACGACTTCTTCCCGAACC
+>naseq2
+TAGATTTCGAATCTAGGGAATCCGATACGGACAGCCTTACATTATTCAGACCAATGTGTA
+TACCAATTCGAGAATACAAGAACGTGATAAGGTACCCAAACAACGACTTCTTCCCGAACC
+>naseq3
+TAGATTTCGAATCTAGGGAATCCGATACCGGACAGCCTTACATTATTCAGACCAATGTGT
+TACCAATTCGAGAATACAAGAACGTGATAAGGTACCCAAACAACGACTTCTTCCCGAACC
+__END_OF_NASEQS__
+
+      @aa = Bio::Alignment::MultiFastaFormat.new <<__END_OF_AASEQS__
+>aaseq1
+MVHWTAEEKQLITGLWGKVNVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHGKKVLT
+>aaseq2
+MLTAEEKAAVTGFWGKVKVDEVGAEALGRLLVVYPWTQRFFEHFGDLSSADAVMNNAKVKAHGKKVLDSF
+>aaseq3
+MVHLTDAEKSAVSCLWAKVNPDEVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNPKVKAHGKKVIT
+>aaseq4
+MVHLTDAEKAAVNGLWGKVNPDDVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNPKVKAHGKKVIN
+__END_OF_AASEQS__
+    end #def setup
+
+    def test_alignment
+      assert_equal(120, @na.alignment.alignment_length)
+      assert_equal(70, @aa.alignment.alignment_length)
+    end
+
+    def test_entries
+      assert_equal(3, @na.entries.size)
+      assert_equal(4, @aa.entries.size)
+    end
+
+    def test_determine_seq_method
+      @na.alignment
+      assert_equal(:naseq, @na.instance_eval { @seq_method })
+      @aa.alignment
+      assert_equal(:aaseq, @aa.instance_eval { @seq_method })
+    end
+  end #class TestAlignmentMultiFastaFormat
+end #module Bio

data/test/unit/bio/appl/sosui/test_report.rb

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+#
+# test/unit/bio/appl/sosui/test_report.rb - Unit test for Bio::SOSUI::Report
+#
+# Copyright::   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::     The Ruby License
+#
+#  $Id: test_report.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/appl/sosui/report'
+
+
+module Bio
+
+  bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
+  test_data = Pathname.new(File.join(bioruby_root, 'test', 'data', 'SOSUI')).cleanpath.to_s
+  SOSUIReport = File.open(File.join(test_data, 'sample.report')).read
+
+
+  class TestSOSUIReportConst  < Test::Unit::TestCase
+
+    def test_delimiter
+      assert_equal("\n>", Bio::SOSUI::Report::DELIMITER)
+    end
+
+    def test_rs
+      assert_equal("\n>", Bio::SOSUI::Report::RS)
+    end
+
+  end
+
+
+  class TestSOSUIReport < Test::Unit::TestCase
+
+    def setup
+      @obj = Bio::SOSUI::Report.new(SOSUIReport)
+    end
+
+    def test_entry_id
+      assert_equal('Q9HC19', @obj.entry_id)
+    end
+
+    def test_prediction
+      assert_equal('MEMBRANE PROTEIN', @obj.prediction)
+    end
+
+    def test_tmhs
+      assert_equal(Array, @obj.tmhs.class)
+      assert_equal(Bio::SOSUI::Report::TMH, @obj.tmhs[0].class)
+    end
+
+    def test_tmh
+      assert_equal(7, @obj.tmhs.size)
+    end
+
+  end # class TestSOSUIReport
+
+  class TestSOSUITMH < Test::Unit::TestCase
+    def setup
+      @obj = Bio::SOSUI::Report.new(SOSUIReport).tmhs.first
+    end
+
+    def test_range
+      assert_equal(31..53, @obj.range)
+    end
+
+    def test_grade
+      assert_equal('SECONDARY', @obj.grade)
+    end
+    
+    def test_sequence
+      assert_equal('HIRMTFLRKVYSILSLQVLLTTV', @obj.sequence)
+    end
+
+  end # class TestSOSUITMH
+end

data/test/unit/bio/appl/targetp/test_report.rb

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+#
+# test/unit/bio/appl/targetp/test_report.rb - Unit test for Bio::TargetP::Report
+#
+# Copyright:  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::   The Ruby License
+#
+#  $Id: test_report.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/appl/targetp/report'
+
+
+module Bio
+
+  TargetPReport_plant =<<HOGE
+ 
+### ### ###  T A R G E T P  1.0  prediction results  ### ### ### 
+ 
+# Number of input sequences:  1
+# Cleavage site predictions not included.
+# Using PLANT networks.
+ 
+#                        Name   Length	  cTP   mTP    SP other  Loc.  RC
+#----------------------------------------------------------------------------------
+                   MGI_2141503	  640	0.031 0.161 0.271 0.844   _     3
+#----------------------------------------------------------------------------------
+# cutoff                                 0.00  0.00  0.00  0.00
+
+
+HOGE
+
+TargetPReport_plant_c =<<HOGE
+ 
+### ### ###  T A R G E T P  1.0  prediction results  ### ### ### 
+ 
+# Number of input sequences:  1
+# Cleavage site predictions included.
+# Using PLANT networks.
+ 
+#                        Name   Length	  cTP   mTP    SP other  Loc.  RC     TPlen
+#----------------------------------------------------------------------------------
+                   MGI_2141503	  640	0.031 0.161 0.271 0.844   _     3	  -
+#----------------------------------------------------------------------------------
+# cutoff                                 0.00  0.00  0.00  0.00
+
+
+
+HOGE
+
+TargetPReport_non_plant_c =<<HOGE
+ 
+### ### ###  T A R G E T P  1.0  prediction results  ### ### ### 
+ 
+# Number of input sequences:  1
+# Cleavage site predictions included.
+# Using NON-PLANT networks.
+ 
+#                        Name   Length    mTP   SP  other  Loc.  RC   TPlen
+#--------------------------------------------------------------------------
+                     MGI_96083	 2187	0.292 0.053 0.746   _     3	  -
+#--------------------------------------------------------------------------
+# cutoff                                 0.00  0.00  0.00
+
+
+
+HOGE
+
+
+  class TestTargetPReportConst  < Test::Unit::TestCase
+
+    def test_delimiter
+      assert_equal("\n \n", Bio::TargetP::Report::DELIMITER)
+    end
+
+    def test_rs
+      assert_equal("\n \n", Bio::TargetP::Report::RS)
+    end
+
+  end # class TestTargetPReportConst
+
+
+  class TestTargetPReport < Test::Unit::TestCase
+
+    def setup
+      @obj = Bio::TargetP::Report.new(TargetPReport_plant)
+    end
+
+    def test_version
+      assert_equal('1.0', @obj.version)
+    end
+
+    def test_query_sequences
+      assert_equal(0, @obj.query_sequences)
+    end
+
+    def test_cleavage_site_prediction
+      assert_equal('not included', @obj.cleavage_site_prediction)
+    end
+
+    def test_networks
+      assert_equal('PLANT', @obj.networks)
+    end
+
+    def test_prediction
+      hash = {"Name"=>"MGI_2141503", "Loc."=>"_", "RC"=>3, "SP"=>0.271,
+              "other"=>0.844, "mTP"=>0.161, "cTP"=>0.031, "Length"=>640}
+      assert_equal(hash, @obj.pred)
+      assert_equal(hash, @obj.prediction)
+    end
+
+    def test_cutoff
+      hash = {"SP"=>0.0, "other"=>0.0, "mTP"=>0.0, "cTP"=>0.0}
+      assert_equal(hash, @obj.cutoff)
+    end
+
+
+    def test_entry_id
+      assert_equal('MGI_2141503', @obj.entry_id)
+    end
+
+    def test_name
+      assert_equal('MGI_2141503', @obj.name)
+    end
+
+    def test_query_len
+      assert_equal(640, @obj.query_len)
+    end
+
+    def test_length
+      assert_equal(640, @obj.length)
+    end
+
+    def test_loc
+      assert_equal('_', @obj.loc)
+    end
+
+    def test_rc
+      assert_equal(3, @obj.rc)
+    end
+  end # class TestTargetPReport
+end

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

@@ -0,0 +1,163 @@
+#
+# 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: test_blast.rb,v 1.6 2008/01/30 17:43:33 nakao Exp $
+#
+
+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
+       Bio::Blast.reports(TestBlastData.output) do |report|
+         assert(report)
+       end
+     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