bio 0.7.1 → 1.0.0

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

@@ -17,7 +17,7 @@
 #  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 $
+#  $Id: test_report.rb,v 1.3 2006/02/03 17:21:51 nakao Exp $
 #
 
 require 'pathname'
@@ -34,17 +34,17 @@ module Bio
     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
+      File.open(File.join(TestDataBlast, 'b0002.faa')).read
     end
 
     def self.output(format = 7)
       case format
       when 0
-        File.open(File.join(TestDataBlast, 'eco:b0002.faa.m0')).read 
+        File.open(File.join(TestDataBlast, 'b0002.faa.m0')).read 
       when 7
-        File.open(File.join(TestDataBlast, 'eco:b0002.faa.m7')).read 
+        File.open(File.join(TestDataBlast, 'b0002.faa.m7')).read 
       when 8
-        File.open(File.join(TestDataBlast, 'eco:b0002.faa.m8')).read 
+        File.open(File.join(TestDataBlast, 'b0002.faa.m8')).read 
       end
     end
   end
@@ -80,12 +80,12 @@ module Bio
     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), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs",  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(xml_quoted_str, @report.reference)
       assert_equal(text_str, @report.reference)
     end
 
     def test_db
-      assert_equal('eco:b0002.faa', @report.db)
+      assert_equal('b0002.faa', @report.db)
     end
 
     def test_query_id
@@ -133,11 +133,11 @@ module Bio
     end
 
     def test_pattern
-      assert(@report.pattern)
+      assert_equal(nil, @report.pattern)
     end
 
     def test_extrez_query
-      assert(@report.entrez_query)
+      assert_equal(nil, @report.entrez_query)
     end
 
     def test_each_iteration
@@ -185,7 +185,7 @@ module Bio
     end
 
     def test_message
-      assert(@report.message)
+      assert_equal(nil, @report.message)
     end
   end
   
@@ -201,7 +201,10 @@ module Bio
     end
 
     def test_statistics
-      assert(@itr.statistics)
+      stat = {"kappa" => 0.041, "eff-space" => 605284, "db-num" => 1, 
+              "hsp-len" => 42, "db-len" => 820, "lambda" => 0.267, 
+              "entropy" => 0.14}
+      assert_equal(stat, @itr.statistics)
     end
 
     def test_num
@@ -209,7 +212,7 @@ module Bio
     end
 
     def test_message
-      assert(@itr.message)
+      assert_equal(nil, @itr.message)
     end
   end
 

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

@@ -17,7 +17,7 @@
 #  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 $
+#  $Id: test_xmlparser.rb,v 1.4 2006/02/03 17:21:51 nakao Exp $
 #
 
 require 'pathname'
@@ -34,11 +34,11 @@ module Bio
     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
+      File.open(File.join(TestDataBlast, 'b0002.faa')).read
     end
 
     def self.output
-      File.open(File.join(TestDataBlast, 'eco:b0002.faa.m7')).read 
+      File.open(File.join(TestDataBlast, 'b0002.faa.m7')).read 
     end
   end
 
@@ -71,7 +71,7 @@ module Bio
     end
 
     def test_db
-      assert_equal("eco:b0002.faa", @report.db)
+      assert_equal("b0002.faa", @report.db)
     end
 
     def test_query_id

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

@@ -0,0 +1,355 @@
+#
+# test/unit/bio/appl/hmmer/test_report.rb - Unit test for Bio::HMMER::Report
+#
+#   Copyright (C) 2006 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 1.1 2006/02/02 17:10:08 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/hmmer/report'
+
+
+module Bio
+
+  class TestHMMERReportData
+    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
+    TestDataHMMER = Pathname.new(File.join(bioruby_root, 'test', 'data', 'HMMER')).cleanpath.to_s
+
+    def self.hmmpfam
+      File.open(File.join(TestDataHMMER, 'hmmpfam.out')).read 
+    end
+
+    def self.output
+      self.hmmpfam
+    end
+
+    def self.hmmsearch
+      File.open(File.join(TestDataHMMER, 'hmmsearch.out')).read 
+    end
+  end
+
+
+  class TestHMMERReportClassMethods < Test::Unit::TestCase
+    def test_reports_ary
+      ary = Bio::HMMER.reports(Bio::TestHMMERReportData.output)
+      assert_equal(Array, ary.class)
+    end
+
+    def test_reports_ary
+      Bio::HMMER.reports(Bio::TestHMMERReportData.output).each do |report|
+        assert_equal(Bio::HMMER::Report, report.class)
+      end
+    end
+  end
+
+  
+  class TestHMMERReportConstants < Test::Unit::TestCase
+    def test_rs
+      assert_equal("\n//\n", Bio::HMMER::Report::RS)
+      assert_equal("\n//\n", Bio::HMMER::Report::DELIMITER)
+    end
+  end
+
+    
+  class TestHMMERReportHmmpfam < Test::Unit::TestCase
+    def setup
+      @obj = Bio::HMMER::Report.new(Bio::TestHMMERReportData.hmmpfam)
+    end
+    
+    def test_program
+      assert_equal(Hash, @obj.program.class)
+      assert_equal("hmmpfam - search one or more sequences against HMM database", @obj.program['name'])
+      assert_equal("HMMER 2.3.2 (Oct 2003)", @obj.program['version'])
+      assert_equal("Copyright (C) 1992-2003 HHMI/Washington University School of Medicine", @obj.program['copyright'])
+      assert_equal("Freely distributed under the GNU General Public License (GPL)", @obj.program['license'])
+    end
+
+    def test_parameter
+      assert_equal(Hash, @obj.parameter.class)
+      assert_equal("/Users/nakao/Sites/iprscan/tmp/20050517/iprscan-20050517-16244071/chunk_1/iprscan-20050517-16244071.nocrc", @obj.parameter["Sequence file"])
+      assert_equal("/Users/nakao/Sites/iprscan/data/Pfam", @obj.parameter['HMM file'])
+    end
+
+    def test_query_info
+      assert_equal(Hash, @obj.query_info.class)
+      assert_equal("104K_THEPA", @obj.query_info["Query sequence"])
+      assert_equal("[none]", @obj.query_info["Accession"])
+      assert_equal("[none]", @obj.query_info["Description"])
+    end
+
+    def test_hits
+      assert_equal(Bio::HMMER::Report::Hit, @obj.hits.first.class)
+    end
+
+    def test_hsps
+      assert_equal(Bio::HMMER::Report::Hsp, @obj.hsps.first.class)
+    end
+
+    def test_histogram
+      assert_equal(nil, @obj.histogram)
+    end
+
+    def test_statistical_detail
+      assert_equal(nil, @obj.statistical_detail)
+    end
+
+    def test_total_seq_searched
+      assert_equal(nil, @obj.total_seq_searched)
+    end
+
+    def test_whole_seq_top_hits
+      assert_equal(nil, @obj.whole_seq_top_hits)
+    end
+
+    def test_domain_top_hits
+      assert_equal(nil, @obj.domain_top_hits)
+    end
+
+    def test_each
+      @obj.each do |hit|
+        assert_equal(Bio::HMMER::Report::Hit, hit.class)
+      end
+    end
+
+    def test_each_hit
+      @obj.each_hit do |hit|
+        assert_equal(Bio::HMMER::Report::Hit, hit.class)
+      end
+    end
+  end 
+
+
+  class TestHMMERReportHit < Test::Unit::TestCase
+    def setup
+      @obj = Bio::HMMER::Report.new(Bio::TestHMMERReportData.output).hits.first
+    end
+
+    def test_hit
+      assert_equal(Bio::HMMER::Report::Hit, @obj.class)
+    end
+
+    def test_hsps
+      assert_equal(Bio::HMMER::Report::Hsp, @obj.hsps.first.class)
+    end
+
+    def test_accession
+      assert_equal("PF04385.4", @obj.accession)
+    end
+    def test_target_id
+      assert_equal("PF04385.4", @obj.target_id)
+    end
+    def test_hit_id
+      assert_equal("PF04385.4", @obj.hit_id)
+    end
+    def test_entry_id
+      assert_equal("PF04385.4", @obj.entry_id)
+    end
+
+    def test_description
+      assert_equal("Domain of unknown function, DUF529", @obj.description)
+    end
+    def test_definition
+      assert_equal("Domain of unknown function, DUF529", @obj.definition)
+    end
+
+    def test_score
+      assert_equal(259.3, @obj.score)
+    end
+    def test_bit_score
+      assert_equal(259.3, @obj.bit_score)
+    end
+
+    def test_evalue
+      assert_equal(6.6e-75, @obj.evalue)
+    end
+
+    def test_num
+      assert_equal(4, @obj.num)
+    end
+    
+    def test_each
+      @obj.each do |hsp|
+        assert_equal(Bio::HMMER::Report::Hsp, hsp.class)
+      end
+    end
+
+    def test_each_hsp
+      @obj.each_hsp do |hsp|
+        assert_equal(Bio::HMMER::Report::Hsp, hsp.class)
+      end
+    end
+
+    def test_target_def
+      assert_equal("<4> Domain of unknown function, DUF529", @obj.target_def)
+    end
+
+    def test_append_hsp
+      hsp = @obj.hsps.first
+      assert_equal(5, @obj.append_hsp(hsp).size)
+    end
+  end
+
+  class TestHMMERReportHsp < Test::Unit::TestCase
+
+    def setup
+      @obj = Bio::HMMER::Report.new(Bio::TestHMMERReportData.output).hits.first.hsps.first
+    end
+
+    def test_hsp
+      assert_equal(Bio::HMMER::Report::Hsp, @obj.class)
+    end
+    
+    def test_accession
+      assert_equal("PF04385.4", @obj.accession)
+    end
+
+    def test_domain
+      assert_equal("1/4", @obj.domain)
+    end
+
+    def test_seq_f
+      assert_equal(36, @obj.seq_f)
+    end
+
+    def test_seq_t
+      assert_equal(111, @obj.seq_t)
+    end
+
+    def test_seq_ft
+      assert_equal("..", @obj.seq_ft)
+    end
+
+    def test_hmm_f
+      assert_equal(1, @obj.hmm_f)
+    end
+
+    def test_hmm_t
+      assert_equal(80, @obj.hmm_t)
+    end
+
+    def test_score
+      assert_equal(65.0, @obj.score)
+    end
+    def test_bit_score
+      assert_equal(65.0, @obj.bit_score)
+    end
+
+    def test_evalue
+      assert_equal(2.0e-16, @obj.evalue)
+    end
+
+    def test_midline
+      assert_equal("t+D+n++++    f  +v+++g+++ + ++ ++v+++++++Gn+v+We++   + +l++ ++++++++++++++++ +++", @obj.midline)
+    end
+
+    def test_hmmseq
+      assert_equal("tLDlndtgstlkqfdykvalngdivvtytpkpGvkftkitdGnevvWeseddpefglivtlsfyldsnkfLvlllintak", @obj.hmmseq)
+    end
+
+    def test_flatseq
+      assert_equal("TFDINSNQTG-PAFLTAVEMAGVKYLQVQHGSNVNIHRLVEGNVVIWENA---STPLYTGAIVTNNDGPYMAYVEVLGDP", @obj.flatseq)
+    end
+
+    def test_query_frame
+      assert_equal(1, @obj.query_frame)
+    end
+
+    def test_target_frame
+      assert_equal(1, @obj.target_frame)
+    end
+
+    def test_csline
+      assert_equal(nil, @obj.csline)
+    end
+
+    def test_rfline
+      assert_equal(nil, @obj.rfline)
+    end
+
+    def test_set_alignment
+    end
+
+    def test_query_seq
+      assert_equal("TFDINSNQTG-PAFLTAVEMAGVKYLQVQHGSNVNIHRLVEGNVVIWENA---STPLYTGAIVTNNDGPYMAYVEVLGDP", @obj.query_seq)
+    end
+
+    def test_target_seq
+      assert_equal("tLDlndtgstlkqfdykvalngdivvtytpkpGvkftkitdGnevvWeseddpefglivtlsfyldsnkfLvlllintak", @obj.target_seq)
+    end
+
+    def test_target_from
+      assert_equal(1, @obj.target_from)
+    end
+
+    def test_targat_to
+      assert_equal(80, @obj.target_to)
+    end
+
+    def test_query_from
+      assert_equal(36, @obj.query_from)
+    end
+
+    def test_query_to
+      assert_equal(111, @obj.query_to)
+    end
+  end
+
+  class TestHMMERReportHmmsearch < Test::Unit::TestCase
+    def setup
+      @obj = Bio::HMMER::Report.new(Bio::TestHMMERReportData.hmmsearch)
+    end
+
+    def test_histogram
+      hist = "score    obs    exp  (one = represents 1 sequences)\n-----    ---    ---\n  377      1      0|="
+      assert_equal(hist, @obj.histogram)
+    end
+    
+    def test_statistical_detail
+      hash = {"P(chi-square)" => 0.0, "chi-sq statistic" => 0.0, "lambda" => 0.7676, "mu" => -10.6639}
+      assert_equal(hash, @obj.statistical_detail)
+      hash.keys.each do |key|
+        assert_equal(hash[key], @obj.statistical_detail[key])
+      end
+    end
+    
+    def test_total_seq_searched
+      assert_equal(1, @obj.total_seq_searched)
+    end
+
+    def test_whole_seq_top_hit
+      hash = {"Total memory" => "16K", "Satisfying E cutoff" => 1, "Total hits" => 1}
+      assert_equal(hash, @obj.whole_seq_top_hits)
+      hash.keys.each do |key|
+        assert_equal(hash[key], @obj.whole_seq_top_hits[key])
+      end
+    end
+
+    def test_domain_top_hits
+      hash = {"Total memory" => "17K", "Satisfying E cutoff" => 1, "Total hits" => 1}
+      assert_equal(hash, @obj.domain_top_hits)
+      hash.keys.each do |key|
+        assert_equal(hash[key], @obj.domain_top_hits[key])
+      end
+    end
+  end
+
+end # module Bio