bio 1.3.1 → 1.4.0

data/test/unit/bio/db/test_phyloxml_writer.rb

@@ -0,0 +1,328 @@
+#
+# = test/unit/bio/db/test_phyloxml_writer.rb - Unit test for Bio::PhyloXML::Writer
+#
+# Copyright::   Copyright (C) 2009
+#               Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
+# License::     The Ruby License
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'singleton'
+require 'bio/command'
+
+begin
+  require 'libxml'
+rescue LoadError
+end
+
+if defined?(LibXML) then
+  require 'bio/db/phyloxml/phyloxml_writer'
+end
+
+module Bio
+  class TestPhyloXMLWriter_Check_LibXML < Test::Unit::TestCase
+    def test_libxml
+      assert(defined?(LibXML),
+             "Error: libxml-ruby library is not present. Please install libxml-ruby library. It is needed for Bio::PhyloXML module. Unit test for PhyloXML will not be performed.")
+    end
+  end #class TestPhyloXMLWriter_Check_LibXML
+end #module Bio
+
+module Bio
+
+  module TestPhyloXMLWriterData
+
+  PHYLOXML_WRITER_TEST_DATA = Pathname.new(File.join(BioRubyTestDataPath, 'phyloxml')).cleanpath.to_s
+
+  def self.example_xml
+    File.join PHYLOXML_WRITER_TEST_DATA, 'phyloxml_examples.xml'
+  end
+
+  def self.mollusca_short_xml
+    File.join PHYLOXML_WRITER_TEST_DATA, 'ncbi_taxonomy_mollusca_short.xml'
+  end
+
+  def self.made_up_xml
+    File.join PHYLOXML_WRITER_TEST_DATA, 'made_up.xml'
+  end
+
+  end #end module TestPhyloXMLWriterData
+
+  class TestPhyloXMLWriter < Test::Unit::TestCase
+
+    # helper class to write files using temporary directory
+    class WriteTo
+      include Singleton
+
+      def initialize
+        @leave_tmpdir = ENV['BIORUBY_TEST_DEBUG'].to_s.empty? ? false : true
+        @tests = nil
+        @tests_passed = 0
+        @tmpdir = nil
+      end
+
+      attr_accessor :tests
+
+      def test_passed
+        @tests_passed += 1
+        if !@leave_tmpdir and @tmpdir and @tests and
+            @tests_passed >= @tests then
+          #$stderr.print "Removing #{@tmpdir.path}\n"
+          @tmpdir.close!
+          @tmpdir = nil
+          @tests_passed = 0
+        end
+      end
+
+      def tmpdir
+        @tmpdir ||= Bio::Command::Tmpdir.new('PhyloXML')
+        @tmpdir
+      end
+
+      def file(f)
+        File.join(self.tmpdir.path, f)
+      end
+    
+      def example_xml_test
+        self.file('phyloxml_examples_written.xml')
+      end
+    end #class WriteTo
+
+    def setup
+      @writeto = WriteTo.instance
+      @writeto.tests ||= self.methods.collect { |x|
+        x.to_s }.find_all { |y|
+        /\Atest\_/ =~ y }.size
+    end
+
+    def teardown
+      @writeto.test_passed
+    end
+
+#    def test_write
+#       # @todo this is test for Tree.write
+#      tree = Bio::PhyloXML::Tree.new
+#      filename = @writeto.file('test.xml')
+#      tree.write(filename)
+#    end
+
+    def test_init
+      filename = @writeto.file("test2.xml")
+      writer = Bio::PhyloXML::Writer.new(filename)
+      
+      tree = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.mollusca_short_xml).next_tree
+      
+      writer.write(tree)
+
+      assert_nothing_thrown do
+        Bio::PhyloXML::Parser.open(filename)
+      end
+
+      #File.delete(filename)
+    end
+
+    def test_simple_xml
+      filename = @writeto.file("sample.xml")
+      writer = Bio::PhyloXML::Writer.new(filename)
+      tree = Bio::PhyloXML::Tree.new
+      tree.rooted = true
+      tree.name = "Test tree"
+      root_node = Bio::PhyloXML::Node.new
+      tree.root = root_node
+      root_node.name = "A"
+      #root_node.taxonomies[0] = Bio::PhyloXML::Taxonomy.new
+      root_node.taxonomies << Bio::PhyloXML::Taxonomy.new
+      root_node.taxonomies[0].scientific_name = "Animal animal"
+      node2 = Bio::PhyloXML::Node.new
+      node2.name = "B"
+      tree.add_node(node2)
+      tree.add_edge(root_node, node2)
+      writer.write(tree)
+      
+      lines = File.open(filename).readlines()
+      assert_equal("<phyloxml xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd\" xmlns=\"http://www.phyloxml.org\">",
+                    lines[1].chomp)
+      assert_equal("  <phylogeny rooted=\"true\">", lines[2].chomp)
+      assert_equal("    <name>Test tree</name>", lines[3].chomp)
+      assert_equal("    <clade>", lines[4].chomp)
+      assert_equal("      <name>A</name>", lines[5].chomp)
+      assert_equal("      <taxonomy>", lines[6].chomp)
+      assert_equal("        <scientific_name>Animal animal</scientific_name>", lines[7].chomp)
+      assert_equal("      </taxonomy>", lines[8].chomp)
+      assert_equal("        <name>B</name>", lines[10].chomp)
+      assert_equal("    </clade>", lines[12].chomp)
+      assert_equal("  </phylogeny>", lines[13].chomp)
+      assert_equal("</phyloxml>", lines[14].chomp)
+
+      #File.delete(filename)
+    end
+
+    def test_phyloxml_examples_tree1
+      tree = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.example_xml).next_tree
+
+      filename = @writeto.file('example_tree1.xml')
+      writer = Bio::PhyloXML::Writer.new(filename)
+      writer.write_branch_length_as_subelement = false
+      writer.write(tree)
+
+      assert_nothing_thrown do
+        tree2  = Bio::PhyloXML::Parser.open(filename)
+      end
+
+      #File.delete(filename)
+
+      #@todo check if branch length is written correctly
+    end
+
+    def test_phyloxml_examples_tree2
+      phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.example_xml)
+      2.times do
+        @tree = phyloxml.next_tree
+      end
+      
+      filename = @writeto.file('example_tree2.xml')
+      writer = Bio::PhyloXML::Writer.new(filename)
+      writer.write(@tree)
+
+      assert_nothing_thrown do
+        tree2  = Bio::PhyloXML::Parser.open(filename)
+      end
+      
+      #File.delete(filename)
+    end
+
+    def test_phyloxml_examples_tree4
+      phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.example_xml)
+      4.times do
+        @tree = phyloxml.next_tree
+      end
+      #@todo tree = phyloxml[4]
+      filename = @writeto.file('example_tree4.xml')
+      writer = Bio::PhyloXML::Writer.new(filename)
+      writer.write(@tree)
+      assert_nothing_thrown do
+        @tree2 = Bio::PhyloXML::Parser.open(filename).next_tree
+      end
+      assert_equal(@tree.name, @tree2.name)
+      assert_equal(@tree.get_node_by_name('A').taxonomies[0].scientific_name, @tree2.get_node_by_name('A').taxonomies[0].scientific_name)
+      assert_equal(@tree.get_node_by_name('B').sequences[0].annotations[0].desc,
+        @tree2.get_node_by_name('B').sequences[0].annotations[0].desc)
+     # assert_equal(@tree.get_node_by_name('B').sequences[0].annotations[0].confidence.value,@tree2.get_node_by_name('B').sequences[0].annotations[0].confidence.value)
+     #File.delete(filename)
+    end
+
+    def test_phyloxml_examples_sequence_relation
+      phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.example_xml)
+      filename = @writeto.example_xml_test
+      writer = Bio::PhyloXML::Writer.new(filename)
+      phyloxml.each do |tree|
+        writer.write(tree)
+      end
+
+      assert_nothing_thrown do
+        @phyloxml_test = Bio::PhyloXML::Parser.open(filename)
+      end
+
+      5.times do
+        @tree = @phyloxml_test.next_tree
+      end
+
+      assert_equal("x", @tree.sequence_relations[0].id_ref_0)
+      assert_equal("z", @tree.sequence_relations[1].id_ref_1)
+      assert_equal(nil, @tree.sequence_relations[2].distance)
+      assert_equal("orthology", @tree.sequence_relations[2].type)
+
+      #File.delete(filename)
+    end
+
+    def test_generate_xml_with_sequence
+      tree = Bio::PhyloXML::Tree.new
+      r = Bio::PhyloXML::Node.new
+      tree.add_node(r)
+      tree.root = r
+      n = Bio::PhyloXML::Node.new
+      tree.add_node(n)
+      tree.add_edge(tree.root, n)
+      tree.rooted = true
+
+      n.name = "A"
+      seq = PhyloXML::Sequence.new
+      n.sequences[0] = seq
+      seq.annotations[0] = PhyloXML::Annotation.new
+      seq.annotations[0].desc = "Sample annotation"
+      seq.name = "sequence name"
+      seq.location = "somewhere"
+      seq.accession = PhyloXML::Accession.new
+      seq.accession.source = "ncbi"
+      seq.accession.value = "AAB80874"
+      seq.symbol = "adhB"
+      seq.mol_seq = "TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD"
+      seq.uri = PhyloXML::Uri.new
+      seq.uri.desc = "EMBL REPTILE DATABASE"
+      seq.uri.uri = "http://www.embl-heidelberg.de/~uetz/families/Varanidae.html"
+      seq.domain_architecture = PhyloXML::DomainArchitecture.new
+      seq.domain_architecture.length = 1249
+      domain1 = PhyloXML::ProteinDomain.new
+      seq.domain_architecture.domains << domain1
+      domain1.from = 6
+      domain1.to = 90
+      domain1.confidence = "7.0E-26"
+      domain1.value = "CARD"
+      domain2 = PhyloXML::ProteinDomain.new
+      seq.domain_architecture.domains << domain2
+      domain2.from = 109
+      domain2.to = 414
+      domain2.confidence = "7.2E-117"
+      domain2.value = "NB-ARC"
+
+      filename = @writeto.file('sequence.xml')
+      Bio::PhyloXML::Writer.new(filename).write(tree)
+
+      assert_nothing_thrown do
+        Bio::PhyloXML::Parser.open(filename).next_tree
+      end
+
+      #File.delete(filename)
+    end
+
+    def test_phyloxml_examples_file
+      outputfn = "phyloxml_examples_generated_in_test.xml"
+      phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.example_xml)
+      filename = @writeto.file(outputfn)
+      writer = Bio::PhyloXML::Writer.new(filename)
+      phyloxml.each do |tree|
+        writer.write(tree)
+      end
+      writer.write_other(phyloxml.other)
+
+      assert_nothing_thrown do
+        Bio::PhyloXML::Parser.open(filename)
+      end
+      # The output file is not deleted since it might be used in the phyloxml
+      # parser test. But since the order of tests can't be assumed, I can't
+      # hard code it in.
+    end
+
+    def test_made_up_xml_file
+      phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLWriterData.made_up_xml)
+      filename = @writeto.file("made_up_generated_in_test.xml")
+      writer = Bio::PhyloXML::Writer.new(filename)
+      # The output file is not deleted since it might be used in the phyloxml
+      # parser test. But since the order of tests can't be assumed, I can't
+      # hard code it in.
+      phyloxml.each do |tree|
+        writer.write(tree)
+      end      
+    end
+
+  end
+
+
+end if defined?(LibXML) #end module Bio
+

data/test/unit/bio/db/test_prosite.rb

@@ -4,13 +4,15 @@
 # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_prosite.rb,v 1.6 2007/04/05 23:35:43 trevor Exp $
+#  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/db/prosite'
 
@@ -32,8 +34,7 @@ module Bio
   class TestPROSITE < Test::Unit::TestCase
 
     def setup
-      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4)).cleanpath.to_s
-      data = File.open(File.join(bioruby_root, 'test', 'data', 'prosite', 'prosite.dat')).read
+      data = File.open(File.join(BioRubyTestDataPath, 'prosite', 'prosite.dat')).read
       data = data.split(Bio::PROSITE::RS)[0]
       @obj = Bio::PROSITE.new(data)
     end

data/test/unit/bio/db/test_qual.rb

@@ -0,0 +1,63 @@
+#
+# test/unit/bio/db/test_qual.rb - Unit test for Bio::FastaNumericFormat
+#
+# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# License::    The Ruby License
+#
+#  $Id:$
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/db/fasta/qual'
+
+module Bio
+  class TestFastaNumericFormat < Test::Unit::TestCase
+
+    def setup
+      text =<<END
+>CRA3575282.F 
+24 15 23 29 20 13 20 21 21 23 22 25 13 22 17 15 25 27 32 26  
+32 29 29 25
+END
+      @obj = Bio::FastaNumericFormat.new(text)
+    end
+
+    def test_entry
+      assert_equal(">CRA3575282.F\n24 15 23 29 20 13 20 21 21 23 22 25 13 22 17 15 25 27 32 26  \n32 29 29 25\n", @obj.entry)
+    end
+
+    def test_entry_id
+      assert_equal('CRA3575282.F', @obj.entry_id) 
+    end
+
+    def test_definition
+      assert_equal('CRA3575282.F', @obj.definition)
+    end
+
+    def test_data
+      data = [24, 15, 23, 29, 20, 13, 20, 21, 21, 23, 22, 25, 13, 22, 17, 15, 25, 27, 32, 26, 32, 29, 29, 25]
+      assert_equal(data, @obj.data)
+    end
+
+    def test_length
+      assert_equal(24, @obj.length)
+    end
+
+    def test_each
+      assert(@obj.each {|x| })
+    end
+
+    def test_arg
+      assert(@obj[0], '')
+      assert(@obj[-1], '')
+    end
+
+
+  end #class TestFastaNumericFormat
+end #module Bio

data/test/unit/bio/db/test_rebase.rb

@@ -5,13 +5,15 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: test_rebase.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
+#  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/db/rebase'
 

data/test/unit/bio/db/test_soft.rb

@@ -1,17 +1,19 @@
 #
-# test/unit/bio/db/test_rebase.rb - Unit test for Bio::REBASE
+# test/unit/bio/db/test_soft.rb - Unit test for Bio::SOFT
 #
 # Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: test_soft.rb,v 1.3 2007/04/05 23:35:43 trevor Exp $
+#  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/db/soft'
 
@@ -19,8 +21,7 @@ module Bio #:nodoc:
   class TestSOFT < Test::Unit::TestCase #:nodoc:
     
     def setup
-      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4)).cleanpath.to_s
-      test_data_path = Pathname.new(File.join(bioruby_root, 'test', 'data', 'soft')).cleanpath.to_s
+      test_data_path = Pathname.new(File.join(BioRubyTestDataPath, 'soft')).cleanpath.to_s
       series_filename = File.join(test_data_path, 'GSE3457_family_partial.soft')
       dataset_filename = File.join(test_data_path, 'GDS100_partial.soft')