bio 0.7.0

data/test/runner.rb

@@ -0,0 +1,10 @@
+#!/usr/bin/env ruby
+
+require 'test/unit'
+require 'pathname'
+
+bioruby_libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'], 'lib')).cleanpath.to_s
+$:.unshift(bioruby_libpath) unless $:.include?(bioruby_libpath)
+
+exit Test::Unit::AutoRunner.run(false, File.dirname($0))
+

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

@@ -0,0 +1,427 @@
+#
+# test/unit/bio/appl/blast/test_report.rb - Unit test for Bio::Blast::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.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/appl/blast/report'
+
+
+module Bio
+  class TestBlastReportData
+    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).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 TestBlastReport < Test::Unit::TestCase
+    require 'bio/appl/blast/report'
+
+    def setup
+      @report = Bio::Blast::Report.new(Bio::TestBlastReportData.output)
+    end
+    
+    def test_iterations
+      assert(@report.iterations)
+    end
+
+    def test_parameters
+      assert_equal('BLOSUM62', @report.parameters['matrix'])
+      assert_equal(10, @report.parameters['expect'])
+      assert_equal(11, @report.parameters['gap-open'])
+      assert_equal(1, @report.parameters['gap-extend'])
+      assert_equal('S', @report.parameters['filter'])
+    end
+
+    def test_program
+      assert_equal('blastp', @report.program)
+    end
+
+    def test_version
+      assert_equal('blastp 2.2.10 [Oct-19-2004]', @report.version)
+    end
+
+    def test_reference
+      xml_quoted_str = "~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~&quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs&quot;,  Nucleic Acids Res. 25:3389-3402."
+      text_str = '~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs",  Nucleic Acids Res. 25:3389-3402.'
+      assert_equal(xml_quoted_str, @report.reference)
+      assert_equal(text_str, @report.reference)
+    end
+
+    def test_db
+      assert_equal('eco:b0002.faa', @report.db)
+    end
+
+    def test_query_id
+      assert_equal('lcl|QUERY', @report.query_id)
+    end
+
+    def test_query_def
+      assert_equal('eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)', @report.query_def)
+    end
+
+    def test_query_len
+      assert_equal(820, @report.query_len)
+    end
+
+    def test_matrix
+      assert_equal('BLOSUM62', @report.matrix)
+    end
+
+    def test_expect
+      assert_equal(10, @report.expect)
+    end
+
+    def test_inclusion
+      assert(@report.inclusion)
+    end
+
+    def test_sc_match
+      assert(@report.sc_match)
+    end
+
+    def test_sc_mismatch
+      assert(@report.sc_mismatch)
+    end
+
+    def test_gap_open
+      assert_equal(11, @report.gap_open)
+    end
+
+    def test_gap_extend
+      assert_equal(1, @report.gap_extend)
+    end
+
+    def test_filter
+      assert_equal('S', @report.filter)
+    end
+
+    def test_pattern
+      assert(@report.pattern)
+    end
+
+    def test_extrez_query
+      assert(@report.entrez_query)
+    end
+
+    def test_each_iteration
+      @report.each_iteration { |itr| }
+    end
+
+    def test_each_hit
+      @report.each_hit { |hit| }
+    end
+
+    def test_hits
+      assert(@report.hits)
+    end
+
+    def test_statistics
+      assert_equal({"kappa"=>0.041, "db-num"=>1, "eff-space"=>605284.0, "hsp-len"=>42, "db-len"=>820, "lambda"=>0.267, "entropy"=>0.14}, @report.statistics)
+    end
+
+    def test_db_num
+      assert_equal(1, @report.db_num)
+    end
+
+    def test_db_len
+      assert_equal(820, @report.db_len)
+    end
+
+    def test_hsp_len
+      assert_equal(42, @report.hsp_len)
+    end
+
+    def test_eff_space
+      assert_equal(605284, @report.eff_space)
+    end
+
+    def test_kappa
+      assert_equal(0.041, @report.kappa)
+    end
+
+    def test_lambda
+      assert_equal(0.267, @report.lambda)
+    end
+
+    def test_entropy
+      assert_equal(0.14, @report.entropy)
+    end
+
+    def test_message
+      assert(@report.message)
+    end
+  end
+  
+  class TestBlastReportIteration < Test::Unit::TestCase
+    def setup
+      data = Bio::TestBlastReportData.output
+      report = Bio::Blast::Report.new(data)
+      @itr = report.iterations.first
+    end
+
+    def test_hits
+      assert(@itr.hits)
+    end
+
+    def test_statistics
+      assert(@itr.statistics)
+    end
+
+    def test_num
+      assert_equal(1, @itr.num)
+    end
+
+    def test_message
+      assert(@itr.message)
+    end
+  end
+
+  class TestBlastReportHit < Test::Unit::TestCase
+    def setup
+      data = Bio::TestBlastReportData.output
+      report = Bio::Blast::Report.new(data)
+      @hit = report.hits.first
+    end
+
+    def test_Hit_hsps
+      assert(@hit.hsps)
+    end
+
+    def test_Hit_query_id
+      assert_equal('lcl|QUERY', @hit.query_id)
+    end
+
+    def test_Hit_query_def
+      assert_equal('eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)', @hit.query_def)
+    end
+
+    def test_Hit_query_len
+      assert_equal(820, @hit.query_len)
+    end
+
+    def test_Hit_num
+      assert(@hit.num)
+    end
+
+    def test_Hit_hit_id
+      assert_equal('gnl|BL_ORD_ID|0', @hit.hit_id) 
+    end
+
+    def test_Hit_len
+      assert_equal(820, @hit.len)
+    end
+
+    def test_Hit_target_len
+      assert_equal(820, @hit.target_len)
+    end
+
+    def test_Hit_definition
+      assert(@hit.definition)
+    end
+
+    def test_Hit_taeget_def
+      assert(@hit.target_def)
+    end
+
+    def test_Hit_accession
+      assert(@hit.accession)
+    end
+
+    def test_Hit_target_id
+      assert(@hit.target_id)
+    end
+    
+    def test_Hit_evalue
+      assert_equal(0, @hit.evalue)
+    end
+
+    def test_Hit_bit_score
+      assert_equal(1567.75, @hit.bit_score)
+    end
+
+    def test_Hit_identity
+      assert_equal(820, @hit.identity)
+    end
+
+    def test_Hit_overlap
+      assert_equal(820, @hit.overlap)
+    end
+
+    def test_Hit_query_seq
+      seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
+      assert_equal(seq, @hit.query_seq)
+    end
+
+    def test_Hit_target_seq
+      seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
+      assert_equal(seq, @hit.target_seq)
+    end
+
+    def test_Hit_midline
+      seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
+      assert_equal(seq, @hit.midline)
+    end
+
+    def test_Hit_query_start
+      assert_equal(1, @hit.query_start)
+#      assert_equal(1, @hit.query_from)
+    end
+
+    def test_Hit_query_end
+      assert_equal(820, @hit.query_end)
+#      assert_equal(820, @hit.query_to)
+    end
+
+    def test_Hit_target_start
+      assert_equal(1, @hit.target_start)
+#      assert_equal(1, @hit.hit_from)
+    end
+
+    def test_Hit_target_end
+      assert_equal(820, @hit.target_end)
+#      assert_equal(820, @hit.hit_to)
+    end
+
+    def test_Hit_lap_at
+      assert_equal([1, 820, 1, 820], @hit.lap_at)
+    end
+  end
+
+  class TestBlastReportHsp < Test::Unit::TestCase
+    def setup
+      data = Bio::TestBlastReportData.output
+      report = Bio::Blast::Report.new(data)
+      @hsp = report.hits.first.hsps.first
+    end
+    
+    def test_Hsp_num
+      assert_equal(1, @hsp.num)
+    end
+
+    def test_Hsp_hit_score
+      assert_equal(1567.75, @hsp.bit_score)
+    end
+
+    def test_Hsp_score
+      assert_equal(4058, @hsp.score)
+    end
+
+    def test_Hsp_evalue
+      assert_equal(0, @hsp.evalue)
+    end
+
+    def test_Hsp_identity
+      assert_equal(820, @hsp.identity)
+    end
+
+    def test_Hsp_gaps
+      assert(@hsp.gaps)
+    end
+
+    def test_Hsp_positive
+      assert_equal(820, @hsp.positive)
+    end
+
+    def test_Hsp_align_len
+      assert_equal(820, @hsp.align_len)
+    end
+
+    def test_Hsp_density
+      assert(@hsp.density)
+    end
+
+    def test_Hsp_query_frame
+      assert_equal(1, @hsp.query_frame)
+    end
+
+    def test_Hsp_query_from
+      assert_equal(1, @hsp.query_from)
+    end
+
+    def test_Hsp_query_to
+      assert_equal(820, @hsp.query_to)
+    end
+
+    def test_Hsp_hit_frame
+      assert_equal(1, @hsp.hit_frame)
+    end
+
+    def test_Hsp_hit_from
+      assert_equal(1, @hsp.hit_from)
+    end
+
+    def test_Hsp_hit_to
+      assert_equal(820, @hsp.hit_to)
+    end
+
+    def test_Hsp_pattern_from
+      @hsp.pattern_from
+    end
+
+    def test_Hsp_pattern_to
+      @hsp.pattern_to 
+    end
+
+    def test_Hsp_qseq
+      seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
+      assert_equal(seq, @hsp.qseq)
+    end
+
+    def test_Hsp_midline
+      seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
+      assert_equal(seq, @hsp.midline)
+    end
+
+    def test_Hsp_hseq
+      seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
+      assert_equal(seq, @hsp.hseq)
+    end
+
+    def test_Hsp_percent_identity
+      @hsp.percent_identity
+    end
+
+    def test_Hsp_mismatch_count
+      @hsp.mismatch_count
+    end
+
+  end 
+
+end # module Bio

data/test/unit/bio/appl/blast/test_xmlparser.rb

@@ -0,0 +1,400 @@
+#
+# test/unit/bio/appl/blast/test_xmlparser.rb - Unit test for Bio::Blast::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_xmlparser.rb,v 1.3 2005/12/18 17:06:56 nakao Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/appl/blast'
+
+
+module Bio
+  class TestBlastFormat7XMLParserData
+    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).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
+      File.open(File.join(TestDataBlast, 'eco:b0002.faa.m7')).read 
+    end
+  end
+
+    
+  class TestBlastReport < Test::Unit::TestCase
+    require 'bio/appl/blast/report'
+
+    def setup
+      @report = Bio::Blast::Report.new(Bio::TestBlastFormat7XMLParserData.output)
+    end
+    
+    def test_iterations
+      @report.iterations
+    end
+
+    def test_parameters
+      @report.parameters
+    end
+
+    def test_program
+      @report.program
+    end
+
+    def test_version
+      @report.version
+    end
+
+    def test_reference
+      @report.reference
+    end
+
+    def test_db
+      assert_equal("eco:b0002.faa", @report.db)
+    end
+
+    def test_query_id
+      @report.query_id
+    end
+
+    def test_query_def
+      @report.query_def
+    end
+
+    def test_query_len
+      @report.query_len
+    end
+
+    def test_matrix
+      @report.matrix
+    end
+
+    def test_expect
+      @report.expect
+    end
+
+    def test_inclusion
+      @report.inclusion
+    end
+
+    def test_sc_match
+      @report.sc_match
+    end
+
+    def test_sc_mismatch
+      @report.sc_mismatch
+    end
+
+    def test_gap_open
+      @report.gap_open
+    end
+
+    def test_gap_extend
+      @report.gap_extend
+    end
+
+    def test_filter
+      @report.filter
+    end
+
+    def test_pattern
+      @report.pattern
+    end
+
+    def test_extrez_query
+      @report.entrez_query
+    end
+
+    def test_each_iteration
+    end
+
+    def test_each_hit
+    end
+
+    def test_hits
+    end
+
+    def test_statistics
+    end
+
+    def test_db_num
+      @report.db_num
+    end
+
+    def test_db_len
+      @report.db_len
+    end
+
+    def test_hsp_len
+      @report.hsp_len
+    end
+
+    def test_eff_space
+      @report.eff_space
+    end
+
+    def test_kappa
+      @report.kappa
+    end
+
+    def test_lambda
+      @report.lambda
+    end
+
+    def test_entropy
+      @report.entropy
+    end
+    
+    def test_message
+      @report.message
+    end
+  end
+  
+
+  class TestBlastReportIteration < Test::Unit::TestCase
+    def setup
+      data = TestBlastFormat7XMLParserData.output
+      report = Bio::Blast::Report.new(data)
+      @itr = report.iterations.first
+    end
+
+    def test_hits
+      @itr.hits
+    end
+
+    def test_statistics
+      @itr.statistics
+    end
+
+    def test_num
+      @itr.num
+    end
+
+    def test_message
+      @itr.message
+    end
+  end
+
+
+  class TestBlastReportHit < Test::Unit::TestCase
+    def setup
+      data = Bio::TestBlastFormat7XMLParserData.output
+      report = Bio::Blast::Report.new(data)
+      @hit = report.hits.first
+    end
+
+    def test_hsps
+      @hit.hsps
+    end
+
+    def test_query_id
+      @hit.query_id
+    end
+
+    def test_query_def
+      @hit.query_def
+    end
+
+    def test_query_len
+      @hit.query_len
+    end
+
+    def test_num
+      @hit.num
+    end
+
+    def test_hit_id
+      @hit.hit_id
+    end
+
+    def test_len
+      @hit.len
+    end
+
+    def test_target_len
+      @hit.target_len
+    end
+
+    def test_definition
+      @hit.definition
+    end
+
+    def test_taeget_def
+      @hit.target_def
+    end
+
+    def test_accession
+      @hit.accession
+    end
+
+    def test_target_id
+      @hit.target_id
+    end
+    
+    def test_evalue
+      @hit.evalue
+    end
+
+    def test_bit_score
+      @hit.bit_score
+    end
+
+    def test_identity
+      @hit.identity
+    end
+
+    def test_overlap
+      @hit.overlap
+    end
+
+    def test_query_seq
+      @hit.query_seq
+    end
+
+    def test_target_seq
+      @hit.target_seq
+    end
+
+    def test_midline
+      @hit.midline
+    end
+
+    def test_query_start
+      @hit.query_start
+    end
+
+    def test_query_end
+      @hit.query_end
+    end
+
+    def test_target_start
+      @hit.target_start
+    end
+
+    def test_target_end
+      @hit.target_end
+    end
+
+    def test_lap_at
+      @hit.lap_at
+    end
+  end
+
+
+  class TestBlastReportHsp < Test::Unit::TestCase
+    def setup
+      data = Bio::TestBlastFormat7XMLParserData.output
+      report = Bio::Blast::Report.new(data)
+      @hsp = report.hits.first.hsps.first
+    end
+    
+    def test_num
+      assert_equal(1, @hsp.num)
+    end
+
+    def test_hit_score
+      @hsp.bit_score
+    end
+
+    def test_score
+      @hsp.score
+    end
+
+    def test_evalue
+      @hsp.evalue
+    end
+
+    def test_identity
+      @hsp.identity
+    end
+
+    def test_gaps
+      @hsp.gaps
+    end
+
+    def test_positive
+      @hsp.positive
+    end
+
+    def test_align_len
+      @hsp.align_len
+    end
+
+    def test_density
+      @hsp.density
+    end
+
+    def test_query_frame
+      @hsp.query_frame
+    end
+
+    def test_query_from
+      @hsp.query_from
+    end
+
+    def test_query_to
+      @hsp.query_to
+    end
+
+    def test_hit_frame
+      @hsp.hit_frame
+    end
+
+    def test_hit_from
+      @hsp.hit_from
+    end
+
+    def test_hit_to
+      @hsp.hit_to
+    end
+
+    def test_pattern_from
+      @hsp.pattern_from
+    end
+
+    def test_pattern_to
+      @hsp.pattern_to 
+    end
+
+    def test_qseq
+      @hsp.qseq
+    end
+
+    def test_midline
+      @hsp.midline
+    end
+
+    def test_hseq
+      @hsp.hseq
+    end
+
+    def test_percent_identity
+      @hsp.percent_identity
+    end
+
+    def test_mismatch_count
+      @hsp.mismatch_count
+    end
+  end
+end