bio 1.0.0 → 1.1.0

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

@@ -0,0 +1,63 @@
+#
+# 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

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/appl/sosui/test_report.rb - Unit test for Bio::SOSUI::Report
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::     The Ruby License
 #
-#  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 1.3 2005/11/22 08:31:48 nakao Exp $
+#  $Id: test_report.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'

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

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/appl/targetp/test_report.rb - Unit test for Bio::TargetP::Report
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright:  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::   The Ruby License
 #
-#  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 1.3 2005/11/23 01:42:38 nakao Exp $
+#  $Id: test_report.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'

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

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/appl/test_blast.rb - Unit test for Bio::Blast
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
 #
-#  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 1.3 2006/02/03 17:39:13 nakao Exp $
+#  $Id: test_blast.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'

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

@@ -1,23 +1,11 @@
 #
 # test/unit/bio/appl/test_fasta.rb - Unit test for Bio::Fasta
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::   Copyright (C) 2006
+#               Mitsuteru C. Nakao <n@bioruby.org>
+# License::     The Ruby License
 #
-#  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 $
+#  $Id: test_fasta.rb,v 1.3 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'

data/test/unit/bio/appl/test_pts1.rb

@@ -0,0 +1,140 @@
+#
+# = test/unit/bio/appl/test_pts1.rb - Unit test for Bio::PTS1
+#
+# Copyright::   Copyright (C) 2006 
+#               Mitsuteru Nakao <n@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: test_pts1.rb,v 1.3 2007/04/05 23:35:43 trevor 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/appl/pts1'
+
+
+module Bio
+
+  class TestPTS1Constant < Test::Unit::TestCase
+    def test_FUNCTION
+      keys = ['METAZOA-specific','FUNGI-specific','GENERAL'].sort
+      assert_equal(keys, Bio::PTS1::FUNCTION.keys.sort)
+    end
+
+  end
+
+  class TestPTS1New < Test::Unit::TestCase
+    def test_metazoa
+      pts1 = Bio::PTS1.new_with_metazoa_function
+      assert_equal('METAZOA-specific', pts1.function)
+    end
+
+    def test_fungi
+      pts1 = Bio::PTS1.new_with_fungi_function
+      assert_equal('FUNGI-specific', pts1.function)
+    end
+
+    def test_general
+      pts1 = Bio::PTS1.new_with_general_function
+      assert_equal('GENERAL', pts1.function)
+    end
+  end
+
+  class TestPTS1 < Test::Unit::TestCase
+
+    def setup
+      @seq =<<END
+>AB000464
+MRTGGDNAGPSHSHIKRLPTSGLSTWLQGTQTCVLHLPTGTRPPAHHPLLGYSSRRSYRL
+LENPAAGCWARFSFCQGAAWDWDLEGVQWLRALAGGVSTAPSAPPGNLVFLSVSIFLCGS
+LLLETCPAYFSSLDPD*
+END
+      @serv = Bio::PTS1.new
+    end
+
+
+    def test_function_set
+      @serv.function("GENERAL")
+      assert_equal("GENERAL", @serv.function)
+    end
+
+    def test_function_show
+      assert_equal("METAZOA-specific", @serv.function)
+    end
+
+    def test_function_set_number_1
+      @serv.function(1)
+      assert_equal("METAZOA-specific", @serv.function)
+    end
+
+    def test_function_set_number_2
+      @serv.function(2)
+      assert_equal("FUNGI-specific", @serv.function)
+    end
+
+    def test_function_set_number_3
+      @serv.function(3)
+      assert_equal("GENERAL", @serv.function)
+    end
+
+
+    def test_exec
+      report = @serv.exec(@seq)
+      assert_equal(Bio::PTS1::Report, report.class)
+    end
+
+    def test_exec_with_faa
+      report = @serv.exec(Bio::FastaFormat.new(@seq))
+      assert_equal(Bio::PTS1::Report, report.class)
+    end
+
+  end
+
+  class TestPTS1Report < Test::Unit::TestCase
+    def setup
+      serv = Bio::PTS1.new
+      seq = ">hoge\nAVSFLSMRRARL\n"
+      @report = serv.exec(seq)
+    end
+    
+
+    def test_output_size
+      assert_equal(1634, @report.output.size)
+    end
+
+    def test_entry_id
+      assert_equal("hoge", @report.entry_id)
+    end
+
+    def test_prediction
+      assert_equal("Targeted", @report.prediction)
+    end
+    
+    def test_cterm
+      assert_equal("AVSFLSMRRARL", @report.cterm)
+    end
+    
+    def test_score
+      assert_equal("7.559", @report.score)
+    end
+
+    def test_fp
+      assert_equal("2.5e-04", @report.fp)
+    end
+    
+    def test_sppta
+      assert_equal("-5.833", @report.sppta)
+    end
+    
+    def test_spptna
+      assert_equal("-1.698", @report.spptna)
+    end
+
+    def test_profile
+      assert_equal("15.091", @report.profile)
+    end
+  end
+end

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

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/appl/tmhmm/test_report.rb - Unit test for Bio::TMHMM::Report
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
 #
-#  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 $
+#  $Id: test_report.rb,v 1.4 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'

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

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/data/test_aa.rb - Unit test for Bio::AminoAcid
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
 #
-#  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 $
+#  $Id: test_aa.rb,v 1.7 2007/04/06 04:46:36 k Exp $
 #
 
 require 'pathname'
@@ -97,7 +84,7 @@ module Bio
     end
     
     def test_to_re
-      assert_equal(/[DN][EQ]ACDEFGHIKLMNPQRSTVWYU/, @obj.to_re('BZACDEFGHIKLMNPQRSTVWYU'))
+      assert_equal(/[DNB][EQZ]ACDEFGHIKLMNPQRSTVWYU/, @obj.to_re('BZACDEFGHIKLMNPQRSTVWYU'))
     end
   end
 end

data/test/unit/bio/data/test_codontable.rb

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/data/test_codontable.rb - Unit test for Bio::CodonTable
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
 #
-#  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_codontable.rb,v 1.4 2005/11/23 05:25:10 nakao Exp $
+#  $Id: test_codontable.rb,v 1.6 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'

data/test/unit/bio/data/test_na.rb

@@ -2,9 +2,9 @@
 # test/unit/bio/data/test_na.rb - Unit test for Bio::NucleicAcid
 #
 # Copyright::  Copyright (C) 2005,2006 Mitsuteru Nakao <n@bioruby.org>
-# Lisence::    Ruby's
+# License::    The Ruby License
 #
-#  $Id: test_na.rb,v 1.6 2006/02/08 13:57:01 nakao Exp $
+#  $Id: test_na.rb,v 1.9 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'
@@ -40,7 +40,7 @@ module Bio
     end
 
     def test_to_re
-      re = /[tc][ag][at][gc][tg][ac][tgc][atg][agc][atgc]atgc/
+      re = /[tcy][agr][atw][gcw][tgk][acm][tgcyskb][atgrwkd][agcmrsv][atgcyrwskmbdhvn]atgc/
       str = 'yrwskmbdvnatgc'
       str0 = str.clone
       assert_equal(re, @obj.to_re(str))

data/test/unit/bio/db/embl/test_common.rb

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/db/embl/common.rb - Unit test for Bio::EMBL::COMMON module
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
 #
-#  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_common.rb,v 1.2 2005/11/23 10:00:54 nakao Exp $
+#  $Id: test_common.rb,v 1.4 2007/04/05 23:35:43 trevor Exp $
 #
 
 require 'pathname'