bio 0.7.0

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

@@ -0,0 +1,159 @@
+#
+# test/unit/bio/appl/test_blast.rb - Unit test for Bio::Blast
+#
+#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#  $Id: test_blast.rb,v 1.2 2005/11/23 02:47:19 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, 'eco:b0002.faa')).read
+    end
+
+    def self.output(format = '7')
+      case format
+      when '0'
+        File.open(File.join(TestDataBlast, 'eco:b0002.faa.m0')).read 
+      when '7'
+        File.open(File.join(TestDataBlast, 'eco:b0002.faa.m7')).read 
+      when '8'
+        File.open(File.join(TestDataBlast, 'eco: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_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_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 +1,142 @@
+#
+# test/unit/bio/appl/test_fasta.rb - Unit test for Bio::Fasta
+#
+#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#  $Id: test_fasta.rb,v 1.1 2005/12/18 16:50:20 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/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'].to_s
+      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/tmhmm/test_report.rb

@@ -0,0 +1,139 @@
+#
+# test/unit/bio/appl/tmhmm/test_report.rb - Unit test for Bio::TMHMM::Report
+#
+#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#  $Id: test_report.rb,v 1.2 2005/11/23 05:10:34 nakao 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/tmhmm/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', 'TMHMM')).cleanpath.to_s
+  TMHMMReport = File.open(File.join(test_data, 'sample.report')).read
+
+
+  class TestTMHMMReport_reports < Test::Unit::TestCase
+    def test_reports
+      assert(Bio::TMHMM.reports(""))
+    end
+  end
+
+  class TestTMHMMReport < Test::Unit::TestCase
+
+    def setup
+      @obj = Bio::TMHMM::Report.new(TMHMMReport)
+    end
+
+    def test_entry_id
+      assert_equal('O42385', @obj.entry_id)
+    end
+
+    def test_query_len
+      assert_equal(423, @obj.query_len)
+    end
+
+    def test_predicted_tmhs
+      assert_equal(7, @obj.predicted_tmhs)
+    end
+
+    def test_tmhs
+      assert_equal(Array, @obj.tmhs.class)
+      assert_equal(15, @obj.tmhs.size)
+    end
+
+    def test_exp_aas_in_tmhs
+      assert_equal(157.40784, @obj.exp_aas_in_tmhs)
+    end
+
+    def test_exp_first_60aa
+      assert_equal(13.85627, @obj.exp_first_60aa)
+    end
+
+    def test_total_prob_of_N_in
+      assert_equal(0.00993, @obj.total_prob_of_N_in)
+    end
+
+    def test_helix
+      assert_equal(7, @obj.helix.size)
+      assert_equal(Bio::TMHMM::TMH, @obj.helix[0].class)
+    end
+    
+    def test_to_s
+      str = ["# O42385\tLength:\t423",
+             "# O42385\tNumber of predicted TMHs:\t7",
+             "# O42385\tExp number of AAs in THMs:\t157.40784",
+             "# O42385\tExp number, first 60 AAs:\t13.85627",
+             "# O42385\tTotal prob of N-in:\t0.00993",
+             "O42385\tTMHMM2.0\toutside\t1\t46",
+             "O42385\tTMHMM2.0\tTMhelix\t47\t69",
+             "O42385\tTMHMM2.0\tinside\t70\t81",
+             "O42385\tTMHMM2.0\tTMhelix\t82\t104",
+             "O42385\tTMHMM2.0\toutside\t105\t118",
+             "O42385\tTMHMM2.0\tTMhelix\t119\t141",
+             "O42385\tTMHMM2.0\tinside\t142\t161",
+             "O42385\tTMHMM2.0\tTMhelix\t162\t184",
+             "O42385\tTMHMM2.0\toutside\t185\t205",
+             "O42385\tTMHMM2.0\tTMhelix\t206\t228",
+             "O42385\tTMHMM2.0\tinside\t229\t348",
+             "O42385\tTMHMM2.0\tTMhelix\t349\t371",
+             "O42385\tTMHMM2.0\toutside\t372\t380",
+             "O42385\tTMHMM2.0\tTMhelix\t381\t403",
+             "O42385\tTMHMM2.0\tinside\t404\t423"].join("\n")
+      assert_equal(str, @obj.to_s)
+    end
+
+  end # TestTMHMMReport
+
+  class TestTMHMMTMH < Test::Unit::TestCase
+
+    def setup
+      @obj = Bio::TMHMM::Report.new(TMHMMReport).tmhs.first
+    end
+
+    def test_entry_id
+      assert_equal('O42385', @obj.entry_id)
+    end
+
+    def test_version
+      assert_equal('TMHMM2.0', @obj.version)
+    end
+
+    def test_status
+      assert_equal('outside', @obj.status)
+    end
+
+    def test_range
+      assert_equal(1..46, @obj.range)
+    end
+
+    def test_pos
+      assert_equal(1..46, @obj.pos)
+    end
+
+  end # class TestTMHMMTMH
+
+
+end

data/test/unit/bio/data/test_aa.rb

@@ -0,0 +1,103 @@
+#
+# test/unit/bio/data/test_aa.rb - Unit test for Bio::AminoAcid
+#
+#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#  $Id: test_aa.rb,v 1.4 2005/11/23 05:25:10 nakao Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/data/aa'
+
+module Bio
+  class TestAAConstants < Test::Unit::TestCase
+    def test_bio_aminoacid
+      assert_equal('Ala', Bio::AminoAcid['A'])
+    end
+  end
+
+
+  class TestAA < Test::Unit::TestCase
+    def setup
+      @obj = Bio::AminoAcid.new
+    end
+
+    def test_13
+      assert_equal("Ala", @obj['A'])
+    end
+
+    def test_1n
+      assert_equal('alanine', @obj.name('A'))
+    end
+
+    def test_to_1_name
+      assert_equal('A', @obj.to_1('alanine'))
+    end
+
+    def test_to_1_3
+      assert_equal('A', @obj.to_1('Ala'))
+    end
+
+    def test_to_1_1
+      assert_equal('A', @obj.to_1('A'))
+    end
+
+    def test_to_3_name
+      assert_equal('Ala', @obj.to_3('alanine'))
+    end
+
+    def test_to_3_3
+      assert_equal('Ala', @obj.to_3('Ala'))
+    end
+
+    def test_to_3_1
+      assert_equal('Ala', @obj.to_3('A'))
+    end
+
+    def test_one2three
+      assert_equal('Ala', @obj.one2three('A'))
+    end
+
+    def test_three2one
+      assert_equal('A', @obj.three2one('Ala'))
+    end
+
+    def test_one2name
+      assert_equal('alanine', @obj.one2name('A'))
+    end
+
+    def test_name2one
+      assert_equal('A', @obj.name2one('alanine'))
+    end
+    
+    def test_three2name
+      assert_equal('alanine', @obj.three2name('Ala'))
+    end
+
+    def test_name2three
+      assert_equal('Ala', @obj.name2three('alanine'))
+    end
+    
+    def test_to_re
+      assert_equal(/[DN][EQ]ACDEFGHIKLMNPQRSTVWYU/, @obj.to_re('BZACDEFGHIKLMNPQRSTVWYU'))
+    end
+  end
+end