bio 0.7.0

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

@@ -0,0 +1,195 @@
+#
+# test/unit/bio/appl/genscan/test_report.rb - Unit test for Bio::Genscan::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 2005/11/22 08:31:47 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/genscan/report'
+
+
+module Bio
+
+  class TestGenscanReport < Test::Unit::TestCase
+
+    def setup
+      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
+      test_data = Pathname.new(File.join(bioruby_root, 'test', 'data', 'genscan')).cleanpath.to_s
+      report = File.open(File.join(test_data, 'sample.report')).read
+
+      @obj = Bio::Genscan::Report.new(report)
+    end
+
+    def test_genscan_version
+      assert_equal('1.0', @obj.genscan_version)
+    end
+
+    def test_date_run
+      assert_equal('30-May-103', @obj.date_run)
+    end
+
+    def test_time
+      assert_equal("14:06:28", @obj.time)
+    end
+
+    def test_query_name
+      assert_equal('HUMRASH', @obj.query_name)
+    end
+
+    def test_length
+      assert_equal(12942, @obj.length)
+    end
+
+    def test_gccontent
+      assert_equal(68.17, @obj.gccontent)
+    end
+
+    def test_isochore
+      assert_equal('4 (57 - 100 C+G%)', @obj.isochore)
+    end
+
+    def test_matrix
+      assert_equal('HumanIso.smat', @obj.matrix)
+    end
+
+    def test_predictions_size
+      assert_equal(2, @obj.predictions.size)
+    end
+
+  end # TestGenscanReport
+
+
+  class TestGenscanReportGene < Test::Unit::TestCase
+
+    def setup
+      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
+      test_data = Pathname.new(File.join(bioruby_root, 'test', 'data', 'genscan')).cleanpath.to_s
+      report = File.open(File.join(test_data, 'sample.report')).read
+      @obj = Bio::Genscan::Report.new(report).predictions
+    end
+
+    def test_number
+      assert_equal(1, @obj.first.number)
+    end
+
+    def test_aaseq
+      assert_equal(Bio::FastaFormat, @obj.first.aaseq.class)
+      seq =  "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS"
+      assert_equal(seq, @obj.first.aaseq.seq)
+      definition = "HUMRASH|GENSCAN_predicted_peptide_1|189_aa"
+      assert_equal(definition, @obj.first.aaseq.definition)
+    end
+
+    def test_naseq
+      assert_equal(Bio::FastaFormat, @obj.first.naseq.class)
+      seq = "atgacggaatataagctggtggtggtgggcgccggcggtgtgggcaagagtgcgctgaccatccagctgatccagaaccattttgtggacgaatacgaccccactatagaggattcctaccggaagcaggtggtcattgatggggagacgtgcctgttggacatcctggataccgccggccaggaggagtacagcgccatgcgggaccagtacatgcgcaccggggagggcttcctgtgtgtgtttgccatcaacaacaccaagtcttttgaggacatccaccagtacagggagcagatcaaacgggtgaaggactcggatgacgtgcccatggtgctggtggggaacaagtgtgacctggctgcacgcactgtggaatctcggcaggctcaggacctcgcccgaagctacggcatcccctacatcgagacctcggccaagacccggcagggagtggaggatgccttctacacgttggtgcgtgagatccggcagcacaagctgcggaagctgaaccctcctgatgagagtggccccggctgcatgagctgcaagtgtgtgctctcctga"
+      assert_equal(seq, @obj.first.naseq.seq)
+      definition = "HUMRASH|GENSCAN_predicted_CDS_1|570_bp"
+      assert_equal(definition, @obj.first.naseq.definition)
+    end
+
+    def test_promoter
+      assert_equal(Bio::Genscan::Report::Exon, @obj.last.promoter.class)
+      assert_equal("Prom", @obj.last.promoter.exon_type)
+    end
+
+    def test_polyA
+      assert_equal(Bio::Genscan::Report::Exon, @obj.first.polyA.class)
+      assert_equal('PlyA', @obj.first.polyA.exon_type)
+    end
+
+  end # TestGenscanReportGene
+
+
+  class TestGenscanReportExon < Test::Unit::TestCase
+
+    def setup
+      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
+      test_data = Pathname.new(File.join(bioruby_root, 'test', 'data', 'genscan')).cleanpath.to_s
+      report = File.open(File.join(test_data, 'sample.report')).read
+      @obj = Bio::Genscan::Report.new(report).predictions.first.exons.first
+    end
+
+    def test_number
+      assert_equal(1, @obj.number)
+    end
+
+    def test_exon_type
+      assert_equal('Init', @obj.exon_type)
+    end
+
+    def test_exon_type_long
+      assert_equal('Initial exon',  @obj.exon_type_long)
+    end
+
+    def test_strand
+      assert_equal('+', @obj.strand)
+    end
+
+    def test_first
+      assert_equal(1664, @obj.first)
+    end
+
+    def test_last
+      assert_equal(1774, @obj.last)
+    end
+
+    def test_range
+      assert_equal(1664..1774, @obj.range)
+    end
+
+    def test_phase
+      assert_equal('0', @obj.phase)
+    end
+
+    def test_acceptor_score
+      assert_equal(94, @obj.acceptor_score)
+    end
+
+    def test_donor_score
+      assert_equal(83, @obj.donor_score)
+    end
+
+    def test_initiation_score
+      assert_equal(94, @obj.initiation_score)
+    end
+
+    def test_termination_score
+      assert_equal(83, @obj.termination_score)
+    end
+
+    def test_score
+      assert_equal(212, @obj.score)
+    end
+
+    def test_p_value
+      assert_equal(0.997, @obj.p_value)
+    end
+
+    def test_t_score
+      assert_equal(21.33, @obj.t_score)
+    end
+
+  end # TestGenscanReportExon
+
+end

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

@@ -0,0 +1,94 @@
+#
+# test/unit/bio/appl/sosui/test_report.rb - Unit test for Bio::SOSUI::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 1.3 2005/11/22 08:31:48 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/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

@@ -0,0 +1,159 @@
+#
+# test/unit/bio/appl/targetp/test_report.rb - Unit test for Bio::TargetP::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 1.3 2005/11/23 01:42:38 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/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