bio 1.5.2 → 1.6.0.pre.20181210

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

@@ -1,334 +0,0 @@
-#
-# = 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) { |px| px.next_tree }
-      
-      writer.write(tree)
-
-      assert_nothing_thrown do
-        Bio::PhyloXML::Parser.open(filename) { |px| true }
-      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.readlines(filename)
-      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) { |px| px.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
-        Bio::PhyloXML::Parser.open(filename) { |px| true }
-      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
-      phyloxml.close
-      
-      filename = @writeto.file('example_tree2.xml')
-      writer = Bio::PhyloXML::Writer.new(filename)
-      writer.write(@tree)
-
-      assert_nothing_thrown do
-        Bio::PhyloXML::Parser.open(filename) { |px| true }
-      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
-      phyloxml.close
-      #@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) { |px| px.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
-      phyloxml.close
-
-      assert_nothing_thrown do
-        @phyloxml_test = Bio::PhyloXML::Parser.open(filename)
-      end
-
-      5.times do
-        @tree = @phyloxml_test.next_tree
-      end
-
-      @phyloxml_test.close
-
-      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) { |px| px.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) { |px| true }
-      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      
-      phyloxml.close
-    end
-
-  end
-
-
-end if defined?(LibXML) #end module Bio
-

data/test/unit/bio/shell/plugin/test_seq.rb

@@ -1,187 +0,0 @@
-#
-# test/unit/bio/shell/plugin/test_seq.rb - Unit test for Bio::Shell plugin for biological sequence manipulations
-#
-# 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__), ['..'] * 4,
-                            'bioruby_test_helper.rb')).cleanpath.to_s
-
-# libraries needed for the tests
-require 'test/unit'
-require 'bio/shell'
-require 'bio/shell/plugin/seq'
-
-module Bio
-
-  class TestShellPluginSeq < Test::Unit::TestCase
-    include Bio::Shell
-
-    Bio::Shell.config = {:color => false}
-
-    def test_htmlseq
-      str = 'ATGC'
-      html =<<END
-<div style="font-family:monospace;">
-<span style="background:#64F73F;">a</span>
-<span style="background:#3C88EE;">t</span>
-<span style="background:#EB413C;">g</span>
-<span style="background:#FFB340;">c</span>
-<br>
-</div>
-END
-      assert_equal(html, htmlseq(str))
-    end
-
-
-    def test_naseq
-      str = 'ACGT'
-      assert_equal(Bio::Sequence, getseq(str).class)
-      assert_equal(Bio::Sequence::NA, getseq(str).moltype)
-      assert_equal('acgt', getseq(str).seq)
-    end
-
-
-    def test_aaseq
-      str = 'WD'
-      assert_equal(Bio::Sequence, getseq(str).class)
-      assert_equal(Bio::Sequence::AA, getseq(str).moltype)
-      assert_equal('WD', getseq(str).seq)
-    end
-
-
-    def test_na_seqstat
-      naseq = 'atgcatgcatgc'
-      output =<<END
-
-* * * Sequence statistics * * *
-
-5'->3' sequence   : atgcatgcatgc
-3'->5' sequence   : gcatgcatgcat
-Translation   1   : MHAC
-Translation   2   : CMH
-Translation   3   : ACM
-Translation  -1   : ACMH
-Translation  -2   : HAC
-Translation  -3   : MHA
-Length            : 12 bp
-GC percent        : 50 %
-Composition       : a -  3 ( 25.00 %)
-                    c -  3 ( 25.00 %)
-                    g -  3 ( 25.00 %)
-                    t -  3 ( 25.00 %)
-Codon usage       :
-
- *---------------------------------------------*
- |       |              2nd              |     |
- |  1st  |-------------------------------| 3rd |
- |       |  U    |  C    |  A    |  G    |     |
- |-------+-------+-------+-------+-------+-----|
- | U   U |F  0.0%|S  0.0%|Y  0.0%|C  0.0%|  u  |
- | U   U |F  0.0%|S  0.0%|Y  0.0%|C 25.0%|  c  |
- | U   U |L  0.0%|S  0.0%|*  0.0%|*  0.0%|  a  |
- |  UUU  |L  0.0%|S  0.0%|*  0.0%|W  0.0%|  g  |
- |-------+-------+-------+-------+-------+-----|
- |  CCCC |L  0.0%|P  0.0%|H 25.0%|R  0.0%|  u  |
- | C     |L  0.0%|P  0.0%|H  0.0%|R  0.0%|  c  |
- | C     |L  0.0%|P  0.0%|Q  0.0%|R  0.0%|  a  |
- |  CCCC |L  0.0%|P  0.0%|Q  0.0%|R  0.0%|  g  |
- |-------+-------+-------+-------+-------+-----|
- |   A   |I  0.0%|T  0.0%|N  0.0%|S  0.0%|  u  |
- |  A A  |I  0.0%|T  0.0%|N  0.0%|S  0.0%|  c  |
- | AAAAA |I  0.0%|T  0.0%|K  0.0%|R  0.0%|  a  |
- | A   A |M 25.0%|T  0.0%|K  0.0%|R  0.0%|  g  |
- |-------+-------+-------+-------+-------+-----|
- |  GGGG |V  0.0%|A  0.0%|D  0.0%|G  0.0%|  u  |
- | G     |V  0.0%|A  0.0%|D  0.0%|G  0.0%|  c  |
- | G GGG |V  0.0%|A 25.0%|E  0.0%|G  0.0%|  a  |
- |  GG G |V  0.0%|A  0.0%|E  0.0%|G  0.0%|  g  |
- *---------------------------------------------*
-
-Molecular weight  : 3701.61444
-Protein weight    : 460.565
-//
-END
-      $str = ''
-      alias puts_orig puts
-      def puts(*args)
-        args.each do |obj|
-          $str << obj.to_s
-        end
-      end
-      seqstat(naseq)
-      undef puts
-      alias puts puts_orig
-      assert_equal(output, $str)
-    end
-
-
-    def test_aa_seqstat
-      aaseq = 'WD'
-      output =<<END
-
-* * * Sequence statistics * * *
-
-N->C sequence     : WD
-Length            : 2 aa
-Composition       : D Asp - 1 ( 50.00 %) aspartic acid
-                    W Trp - 1 ( 50.00 %) tryptophan
-Protein weight    : 319.315
-//
-END
-      $str = ''
-      alias puts_orig puts
-      def puts(*args)
-        args.each do |obj|
-          $str << obj.to_s
-        end
-      end
-      seqstat(aaseq)
-      undef puts
-      alias puts puts_orig
-      assert_equal(output, $str)
-    end
-
-
-    def test_doublehelix
-      seq = 'ACGTACGTACGTACGT'
-      output = <<END
-     at
-    c--g
-   g---c
-  t----a
- a----t
-c---g
-g--c
- ta
- ta
-g--c
-c---g
- a----t
-  t----a
-   g---c
-    c--g
-     at
-END
-      $str = ''
-      alias puts_orig puts
-      def puts(*args)
-        args.each do |obj|
-          $str << obj.to_s
-        end
-      end
-      doublehelix(seq)
-      undef puts
-      alias puts puts_orig
-      assert_equal(output, $str)
-    end
-
-  end
-
-end