BioDSL 1.0.0

data/test/BioDSL/test_serializer.rb

@@ -0,0 +1,72 @@
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__), '..', '..')
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                  #
+#                                                                                #
+# This program is free software; you can redistribute it and/or                  #
+# modify it under the terms of the GNU General Public License                    #
+# as published by the Free Software Foundation; either version 2                 #
+# of the License, or (at your option) any later version.                         #
+#                                                                                #
+# This program 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 General Public License for more details.                                   #
+#                                                                                #
+# You should have received a copy of the GNU General Public License              #
+# along with this program; if not, write to the Free Software                    #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
+#                                                                                #
+# http://www.gnu.org/copyleft/gpl.html                                           #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# This software is part of BioDSL (www.BioDSL.org).                        #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+require 'test/helper'
+
+class TestSerializer < Test::Unit::TestCase 
+  def setup
+    @records = [
+      {"foo" => 1},
+      {"bar" => 2}
+    ]
+  end
+
+  test "BioDSL::Serializer with no block raises" do
+    assert_raise(BioDSL::SerializerError) { BioDSL::Serializer.new("foo") }
+  end
+
+  test "BioDSL::Serializer returns correctly" do
+    require 'tempfile'
+
+    file = Tempfile.new("serializer")
+
+    begin
+      File.open(file, 'wb') do |io|
+        BioDSL::Serializer.new(io) do |s|
+          @records.each { |r| s << r }
+        end
+      end
+
+      result = []
+
+      File.open(file, 'rb') do |io|
+        BioDSL::Serializer.new(io) do |s|
+          s.each do |record|
+            result << record
+          end
+        end
+      end
+
+      assert_equal(@records, result)
+    ensure
+      file.close
+      file.unlink
+    end
+  end
+end

data/test/BioDSL/test_stream.rb

@@ -0,0 +1,55 @@
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__), '..', '..')
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                  #
+#                                                                                #
+# This program is free software; you can redistribute it and/or                  #
+# modify it under the terms of the GNU General Public License                    #
+# as published by the Free Software Foundation; either version 2                 #
+# of the License, or (at your option) any later version.                         #
+#                                                                                #
+# This program 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 General Public License for more details.                                   #
+#                                                                                #
+# You should have received a copy of the GNU General Public License              #
+# along with this program; if not, write to the Free Software                    #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
+#                                                                                #
+# http://www.gnu.org/copyleft/gpl.html                                           #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# This software is part of BioDSL (www.BioDSL.org).                        #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+require 'test/helper'
+
+class TestStream < Test::Unit::TestCase 
+  def setup
+    @obj = {foo: "bar"}
+    @reader, @writer = BioDSL::Stream.pipe
+  end
+
+  def teardown
+    @reader.close unless @reader.closed?
+    @writer.close unless @writer.closed?
+  end
+
+  test "BioDSL::Stream.pipe writing and reading an object returns correctly" do
+    @writer.write @obj
+    @writer.close
+    assert_equal(@obj, @reader.read)
+  end
+
+  test "BioDSL::Stream.pipe writing and reading multiple object returns correctly" do
+    10.times { @writer.write @obj }
+    @writer.close
+    result = @reader.inject([]) { |memo, obj| memo << obj }
+    assert_equal(Array.new(10, @obj), result)
+  end
+end

data/test/BioDSL/test_taxonomy.rb

@@ -0,0 +1,336 @@
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__), '..', '..')
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                  #
+#                                                                                #
+# This program is free software; you can redistribute it and/or                  #
+# modify it under the terms of the GNU General Public License                    #
+# as published by the Free Software Foundation; either version 2                 #
+# of the License, or (at your option) any later version.                         #
+#                                                                                #
+# This program 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 General Public License for more details.                                   #
+#                                                                                #
+# You should have received a copy of the GNU General Public License              #
+# along with this program; if not, write to the Free Software                    #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
+#                                                                                #
+# http://www.gnu.org/copyleft/gpl.html                                           #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# This software is part of BioDSL (www.BioDSL.org).                        #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+require 'test/helper'
+
+class TestTaxonomy < Test::Unit::TestCase 
+  def setup
+    @tmpdir = Dir.mktmpdir("Taxonomy")
+
+    @index = BioDSL::Taxonomy::Index.new(kmer_size: 3, step_size: 1, output_dir: @tmpdir, prefix: "test")
+
+    @index2 = BioDSL::Taxonomy::Index.new(kmer_size: 3, step_size: 1, output_dir: @tmpdir, prefix: "test")
+    @index2.add(BioDSL::Seq.new(seq_name: "K#b;P#e;C#;O#;F#;G#;S#",  seq: "aaga"))
+    @index2.add(BioDSL::Seq.new(seq_name: "K#b;P#f;C#;O#;F#;G#;S#",  seq: "aagu"))
+    @index2.add(BioDSL::Seq.new(seq_name: "K#b;P#;C#;O#;F#;G#;S#",   seq: "aag"))
+    @index2.add(BioDSL::Seq.new(seq_name: "K#b;P#e;C#g;O#;F#;G#;S#", seq: "aagag"))
+    
+    @index3 = BioDSL::Taxonomy::Index.new(kmer_size: 3, step_size: 1, output_dir: @tmpdir, prefix: "test")
+    @index3.add(BioDSL::Seq.new(seq_name: "K#a;P#b;C#;O#;F#;G#;S#",      seq: "aagc"))
+    @index3.add(BioDSL::Seq.new(seq_name: "K#a;P#c;C#d;O#;F#;G#;S#",     seq: "aagag"))
+    @index3.add(BioDSL::Seq.new(seq_name: "K#a;P#c;C#d_1;O#;F#;G#;S#",   seq: "aagag"))
+    @index3.add(BioDSL::Seq.new(seq_name: "K#a;P#c;C#d_1_2;O#;F#;G#;S#", seq: "aagac"))
+    @index3.save
+
+    @tree_file = File.join(@tmpdir, "test_tax_index.dat")
+    @kmer_file = File.join(@tmpdir, "test_kmer_index.dat")
+  end
+
+  def teardown
+    FileUtils.rm_r @tmpdir
+  end
+
+  test "BioDSL::Taxonomy::Index#new without options[:kmer_size] raises" do
+    assert_raise(BioDSL::TaxonomyError) { BioDSL::Taxonomy::Index.new(step_size: 1, output_dir: @tmpdir, prefix: "test") }
+  end
+
+  test "BioDSL::Taxonomy::Index#new without options[:step_size] raises" do
+    assert_raise(BioDSL::TaxonomyError) { BioDSL::Taxonomy::Index.new(kmer_size: 3, output_dir: @tmpdir, prefix: "test") }
+  end
+
+  test "BioDSL::Taxonomy::Index#new without options[:output_dir] raises" do
+    assert_raise(BioDSL::TaxonomyError) { BioDSL::Taxonomy::Index.new(kmer_size: 3, step_size: 1, prefix: "test") }
+  end
+
+  test "BioDSL::Taxonomy::Index#new without options[:prefix] raises" do
+    assert_raise(BioDSL::TaxonomyError) { BioDSL::Taxonomy::Index.new(kmer_size: 3, step_size: 1, output_dir: @tmpdir) }
+  end
+
+  test "BioDSL::Taxonomy::Index#add with bad header with wrong number of tax levels raises" do
+    assert_raise(BioDSL::TaxonomyError) { @index.add(BioDSL::Seq.new(seq_name: "K#1;P#2", seq: "aaga")) }
+  end
+
+  test "BioDSL::Taxonomy::Index#add with bad header with wrong tax order raises" do
+    assert_raise(BioDSL::TaxonomyError) { @index.add(BioDSL::Seq.new(seq_name: "K#1;C#;P#3;O#;F#;G#;S#", seq: "aaga")) }
+  end
+
+  test "BioDSL::Taxonomy::Index#add with bad header with gapped info raises" do
+    assert_raise(BioDSL::TaxonomyError) { @index.add(BioDSL::Seq.new(seq_name: "K#1;P#;C#3;O#;F#;G#;S#", seq: "aaga")) }
+  end
+
+  test "BioDSL::Taxonomy::Index#add with OK header don't raise" do
+    assert_nothing_raised { @index.add(BioDSL::Seq.new(seq_name: "K#;P#;C#;O#;F#;G#;S#", seq: "aaga")) }
+    assert_nothing_raised { @index.add(BioDSL::Seq.new(seq_name: "K#1;P#2;C#3;O#4;F#5;G#6;S#7", seq: "aaga")) }
+  end
+
+  # '00' then oligo << 'a'
+  # '01' then oligo << 't'
+  # '10' then oligo << 'c'
+  # '11' then oligo << 'g'
+
+  test "BioDSL::Taxonomy::Index#add with empty tree returns correctly" do
+    assert_equal(1, @index.size)
+    @index.add(BioDSL::Seq.new(seq_name: "K#b;P#e;C#;O#;F#;G#;S#", seq: "aaga"))
+    assert_equal(3,       @index.size)
+    assert_equal("root",  @index.get_node(0).name)
+    assert_equal("b",     @index.get_node(1).name)
+    assert_equal("e",     @index.get_node(2).name)
+    assert_equal([],      @index.get_node(0).kmers.to_a)
+    assert_equal([],      @index.get_node(1).kmers.to_a)
+    assert_equal([3, 12], @index.get_node(2).kmers.to_a) # aag=000011=3, aga=001100=12 
+  end
+
+  test "BioDSL::Taxonomy::Index#add with edge split returns correctly" do
+    @index.add(BioDSL::Seq.new(seq_name: "K#b;P#e;C#;O#;F#;G#;S#", seq: "aaga"))
+    @index.add(BioDSL::Seq.new(seq_name: "K#b;P#f;C#;O#;F#;G#;S#", seq: "aagu"))
+    assert_equal(4,       @index.size)
+    assert_equal("root",  @index.get_node(0).name)
+    assert_equal("b",     @index.get_node(1).name)
+    assert_equal("e",     @index.get_node(2).name)
+    assert_equal("f",     @index.get_node(3).name)
+    assert_equal([],      @index.get_node(0).kmers.to_a)
+    assert_equal([],      @index.get_node(1).kmers.to_a)
+    assert_equal([3, 12], @index.get_node(2).kmers.to_a) # aag=000011=3, aga=001100=12 
+    assert_equal([3, 13], @index.get_node(3).kmers.to_a) # aag=000011=3, agu=001101=13 
+  end
+
+  test "BioDSL::Taxonomy::Index#add to existing non-leaf node returns correctly" do
+    @index.add(BioDSL::Seq.new(seq_name: "K#b;P#e;C#;O#;F#;G#;S#", seq: "aaga"))
+    @index.add(BioDSL::Seq.new(seq_name: "K#b;P#f;C#;O#;F#;G#;S#", seq: "aagu"))
+    @index.add(BioDSL::Seq.new(seq_name: "K#b;P#;C#;O#;F#;G#;S#",  seq: "aag"))
+    assert_equal(4,       @index.size)
+    assert_equal("root",  @index.get_node(0).name)
+    assert_equal("b",     @index.get_node(1).name)
+    assert_equal("e",     @index.get_node(2).name)
+    assert_equal("f",     @index.get_node(3).name)
+    assert_equal([],      @index.get_node(0).kmers.to_a)
+    assert_equal([3],     @index.get_node(1).kmers.to_a) # aag=000011=3
+    assert_equal([3, 12], @index.get_node(2).kmers.to_a) # aag=000011=3, aga=001100=12 
+    assert_equal([3, 13], @index.get_node(3).kmers.to_a) # aag=000011=3, agu=001101=13 
+  end
+
+  test "BioDSL::Taxonomy::Index#add exteding existing leaf node returns correctly" do
+    @index.add(BioDSL::Seq.new(seq_name: "K#b;P#e;C#;O#;F#;G#;S#",  seq: "aaga"))
+    @index.add(BioDSL::Seq.new(seq_name: "K#b;P#f;C#;O#;F#;G#;S#",  seq: "aagu"))
+    @index.add(BioDSL::Seq.new(seq_name: "K#b;P#;C#;O#;F#;G#;S#",   seq: "aag"))
+    @index.add(BioDSL::Seq.new(seq_name: "K#b;P#e;C#g;O#;F#;G#;S#", seq: "aagag"))
+    assert_equal(5,           @index.size)
+    assert_equal("root",      @index.get_node(0).name)
+    assert_equal("b",         @index.get_node(1).name)
+    assert_equal("e",         @index.get_node(2).name)
+    assert_equal("f",         @index.get_node(3).name)
+    assert_equal("g",         @index.get_node(4).name)
+    assert_equal([],          @index.get_node(0).kmers.to_a.sort)
+    assert_equal([3],         @index.get_node(1).kmers.to_a.sort) # aag=000011=3
+    assert_equal([3, 12],     @index.get_node(2).kmers.to_a.sort) # aag=000011=3, aga=001100=12 
+    assert_equal([3, 13],     @index.get_node(3).kmers.to_a.sort) # aag=000011=3, agu=001101=13 
+    assert_equal([3, 12, 51], @index.get_node(4).kmers.to_a.sort) # aag=000011=3, aga=001101=12, gag=110011=51 
+  end
+
+  test "BioDSL::Taxonomy::Index#tree_union returns correctly" do
+    @index.add(BioDSL::Seq.new(seq_name: "K#b;P#e;C#;O#;F#;G#;S#",  seq: "aaga"))
+    @index.add(BioDSL::Seq.new(seq_name: "K#b;P#f;C#;O#;F#;G#;S#",  seq: "aagu"))
+    @index.add(BioDSL::Seq.new(seq_name: "K#b;P#;C#;O#;F#;G#;S#",   seq: "aag"))
+    @index.add(BioDSL::Seq.new(seq_name: "K#b;P#e;C#g;O#;F#;G#;S#", seq: "aagag"))
+    @index.tree_union
+    assert_equal(5,               @index.size)
+    assert_equal("root",          @index.get_node(0).name)
+    assert_equal("b",             @index.get_node(1).name)
+    assert_equal("e",             @index.get_node(2).name)
+    assert_equal("f",             @index.get_node(3).name)
+    assert_equal("g",             @index.get_node(4).name)
+    assert_equal([3, 12, 13, 51], @index.get_node(0).kmers.to_a.sort)
+    assert_equal([3, 12, 13, 51], @index.get_node(1).kmers.to_a.sort)
+    assert_equal([3, 12, 51],     @index.get_node(2).kmers.to_a.sort)
+    assert_equal([3, 13],         @index.get_node(3).kmers.to_a.sort)
+    assert_equal([3, 12, 51],     @index.get_node(4).kmers.to_a.sort)
+  end
+
+  test "BioDSL::Taxonomy::Index#save outputs correct tax tree inxex" do
+    @index2.save
+
+    expected = <<EOD
+#SEQ_ID\tNODE_ID\tLEVEL\tNAME\tPARENT_ID
+\t0\tr\troot\t
+0\t1\tk\tb\t0
+1\t3\tp\tf\t1
+0\t2\tp\te\t1
+3\t4\tc\tg\t2
+EOD
+
+    assert_equal(expected, File.read(@tree_file))
+  end
+
+  # r             0
+  #             /
+  # k          1
+  #          /   \
+  # p       2     3
+  #       /
+  # c    4
+  #
+  # aag=000011=3
+  # aga=001101=12
+  # agu=001101=13
+  # gag=110011=51
+  #
+  # node 0 - [3, 12, 13, 51]
+  # node 1 - [3, 12, 13, 51]
+  # node 2 - [3, 12, 51]
+  # node 3 - [3, 13]
+  # node 4 - [3, 12, 51]
+  test "BioDSL::Taxonomy::Index#save outputs correct kmer index" do
+    @index2.save
+
+    expected = <<EOD
+#LEVEL\tKMER\tNODES
+r\t3\t0
+r\t12\t0
+r\t13\t0
+r\t51\t0
+k\t3\t1
+k\t12\t1
+k\t13\t1
+k\t51\t1
+p\t3\t2;3
+p\t12\t2
+p\t13\t3
+p\t51\t2
+c\t3\t4
+c\t12\t4
+c\t51\t4
+EOD
+
+    assert_equal(expected, File.read(@kmer_file))
+  end
+
+  test "BioDSL::Taxonomy::Search#new without options[:kmer_size] raises" do
+    assert_raise(BioDSL::TaxonomyError) { BioDSL::Taxonomy::Search.new(step_size: 1, dir: @tmpdir, prefix: "test", coverage: 0.99, hits_max: 5, consensus: 0.5) }
+  end
+
+  test "BioDSL::Taxonomy::Search#new without options[:step_size] raises" do
+    assert_raise(BioDSL::TaxonomyError) { BioDSL::Taxonomy::Search.new(kmer_size: 3, dir: @tmpdir, prefix: "test", coverage: 0.99, hits_max: 5, consensus: 0.5) }
+  end
+
+  test "BioDSL::Taxonomy::Search#new without options[:dir] raises" do
+    assert_raise(BioDSL::TaxonomyError) { BioDSL::Taxonomy::Search.new(kmer_size: 3, step_size: 1, prefix: "test", coverage: 0.99, hits_max: 5, consensus: 0.5) }
+  end
+
+  test "BioDSL::Taxonomy::Search#new without options[:prefix] raises" do
+    assert_raise(BioDSL::TaxonomyError) { BioDSL::Taxonomy::Search.new(kmer_size: 3, step_size: 1, dir: @tmpdir, coverage: 0.99, hits_max: 5, consensus: 0.5) }
+  end
+
+  test "BioDSL::Taxonomy::Search#new without options[:coverage] raises" do
+    assert_raise(BioDSL::TaxonomyError) { BioDSL::Taxonomy::Search.new(kmer_size: 3, step_size: 1, dir: @tmpdir, prefix: "test", hits_max: 5, consensus: 0.5) }
+  end
+
+  test "BioDSL::Taxonomy::Search#new without options[:hits_max] raises" do
+    assert_raise(BioDSL::TaxonomyError) { BioDSL::Taxonomy::Search.new(kmer_size: 3, step_size: 1, dir: @tmpdir, prefix: "test", coverage: 0.99, consensus: 0.5) }
+  end
+
+  test "BioDSL::Taxonomy::Search#new without options[:consensus] raises" do
+    assert_raise(BioDSL::TaxonomyError) { BioDSL::Taxonomy::Search.new(kmer_size: 3, step_size: 1, dir: @tmpdir, prefix: "test", coverage: 0.99, hits_max: 5) }
+  end
+
+  # R          r
+  #            |
+  # K          a
+  #          /   \
+  # P       c     b
+  #       / | \
+  # C    d  |  d_1_2
+  #         d_1
+  #
+  # R: aag: r
+  # R: aga: r
+  # R: gag: r
+  # R: gac: r
+  # R: agc: r
+  # K: aag: a
+  # K: aga: a
+  # K: gag: a
+  # K: gac: a
+  # K: agc: a
+  # P: aag: c
+  # P: aga: c
+  # P: gag: c
+  # P: gac: c
+  # P: agc: b
+  # C: aag: d, d_1, d_1_2
+  # C: aga: d, d_1, d_1_2
+  # C: gag: d, d_1
+  # C: gac: f
+  test "BioDSL::Taxonomy::Search#execute return correctly" do
+    @search = BioDSL::Taxonomy::Search.new(kmer_size: 3, step_size: 1, dir: @tmpdir, prefix: "test", coverage: 1.0, hits_max: 5, consensus: 0.0)
+    result  = @search.execute(BioDSL::Seq.new(seq_name: "test", seq: "aaga"))
+
+    assert_equal(3, result.hits)
+    assert_equal("K#a(100);P#c(100);C#d 1 2(100/66/33)", result.taxonomy)
+  end
+
+  test "BioDSL::Taxonomy::Search#execute with coverage limit returns correctly" do
+    @search = BioDSL::Taxonomy::Search.new(kmer_size: 3, step_size: 1, dir: @tmpdir, prefix: "test", coverage: 1.0, hits_max: 5, consensus: 0.0)
+    result  = @search.execute(BioDSL::Seq.new(seq_name: "test", seq: "aagat"))
+
+    assert_equal(0, result.hits)
+    assert_equal("Unclassified", result.taxonomy)
+  end
+
+  test "BioDSL::Taxonomy::Search#execute with hits_max limit returns correctly" do
+    @search = BioDSL::Taxonomy::Search.new(kmer_size: 3, step_size: 1, dir: @tmpdir, prefix: "test", coverage: 0.0, hits_max: 2, consensus: 0.0)
+    result  = @search.execute(BioDSL::Seq.new(seq_name: "test", seq: "aaga"))
+
+    assert_equal(2, result.hits)
+    assert_equal("K#a(100);P#c(100);C#d 1(100/50)", result.taxonomy)
+  end
+
+  test "BioDSL::Taxonomy::Search#execute with consensus returns correctly" do
+    @search = BioDSL::Taxonomy::Search.new(kmer_size: 3, step_size: 1, dir: @tmpdir, prefix: "test", coverage: 0.0, hits_max: 5, consensus: 0.34)
+    result  = @search.execute(BioDSL::Seq.new(seq_name: "test", seq: "aaga"))
+
+    assert_equal(3, result.hits)
+    assert_equal("K#a(100);P#c(100);C#d 1(100/66)", result.taxonomy)
+  end
+
+  test "BioDSL::Taxonomy::Search#execute with best_only returns correctly" do
+    @search = BioDSL::Taxonomy::Search.new(kmer_size: 3, step_size: 1, dir: @tmpdir, prefix: "test", coverage: 0.0, hits_max: 5, consensus: 0.0, best_only: true)
+    result  = @search.execute(BioDSL::Seq.new(seq_name: "test", seq: "aagag"))
+
+    assert_equal(2, result.hits)
+    assert_equal("K#a(100);P#c(100);C#d 1(100/50)", result.taxonomy)
+  end
+
+  test "BioDSL::Taxonomy::Search#execute with no hits a C level moves to P level and returns correctly" do
+    @search = BioDSL::Taxonomy::Search.new(kmer_size: 3, step_size: 1, dir: @tmpdir, prefix: "test", coverage: 0.0, hits_max: 5, consensus: 0.0)
+    result  = @search.execute(BioDSL::Seq.new(seq_name: "test", seq: "agc"))
+
+    assert_equal(1, result.hits)
+    assert_equal("K#a(100);P#b(100)", result.taxonomy)
+  end
+end

data/test/BioDSL/test_test.rb

@@ -0,0 +1,42 @@
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__), '..', '..')
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                  #
+#                                                                                #
+# This program is free software; you can redistribute it and/or                  #
+# modify it under the terms of the GNU General Public License                    #
+# as published by the Free Software Foundation; either version 2                 #
+# of the License, or (at your option) any later version.                         #
+#                                                                                #
+# This program 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 General Public License for more details.                                   #
+#                                                                                #
+# You should have received a copy of the GNU General Public License              #
+# along with this program; if not, write to the Free Software                    #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
+#                                                                                #
+# http://www.gnu.org/copyleft/gpl.html                                           #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# This software is part of BioDSL (www.BioDSL.org).                        #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+require 'test/helper'
+
+class TestTest < Test::Unit::TestCase
+  def teardown
+    BioDSL::test = false
+  end
+
+  test "BioDSL::test returns correctly" do
+    BioDSL::test = true
+    assert_equal(true, BioDSL::test)
+  end
+end
+

data/test/BioDSL/test_tmp_dir.rb

@@ -0,0 +1,58 @@
+#!/usr/bin/env ruby
+$LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..')
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                #
+#                                                                              #
+# This program is free software; you can redistribute it and/or                #
+# modify it under the terms of the GNU General Public License                  #
+# as published by the Free Software Foundation; either version 2               #
+# of the License, or (at your option) any later version.                       #
+#                                                                              #
+# This program 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 General Public License for more details.                                 #
+#                                                                              #
+# You should have received a copy of the GNU General Public License            #
+# along with this program; if not, write to the Free Software                  #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,    #
+# USA.                                                                         #
+#                                                                              #
+# http://www.gnu.org/copyleft/gpl.html                                         #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# This software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+require 'test/helper'
+
+# Test class for TmpDir
+class TmpDirTest < Test::Unit::TestCase
+  test 'BioDSL::TmpDir#create with no files returns correctly' do
+    dir = ''
+
+    BioDSL::TmpDir.create do |tmp_dir|
+      dir = tmp_dir
+      assert_true(File.directory? dir)
+    end
+
+    assert_false(File.directory? dir)
+  end
+
+  test 'BioDSL::TmpDir#create with files returns correctly' do
+    dir = ''
+
+    BioDSL::TmpDir.create('foo', 'bar') do |foo, bar, tmp_dir|
+      dir = tmp_dir
+      assert_true(File.directory? dir)
+      assert_equal(File.join(dir, 'foo'), foo)
+      assert_equal(File.join(dir, 'bar'), bar)
+    end
+
+    assert_false(File.directory? dir)
+  end
+end

data/test/BioDSL/test_usearch.rb

@@ -0,0 +1,33 @@
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__), '..', '..')
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                  #
+#                                                                                #
+# This program is free software; you can redistribute it and/or                  #
+# modify it under the terms of the GNU General Public License                    #
+# as published by the Free Software Foundation; either version 2                 #
+# of the License, or (at your option) any later version.                         #
+#                                                                                #
+# This program 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 General Public License for more details.                                   #
+#                                                                                #
+# You should have received a copy of the GNU General Public License              #
+# along with this program; if not, write to the Free Software                    #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
+#                                                                                #
+# http://www.gnu.org/copyleft/gpl.html                                           #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# This software is part of BioDSL (www.BioDSL.org).                        #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+require 'test/helper'
+
+class TestUsearch < Test::Unit::TestCase 
+end

data/test/BioDSL/test_verbose.rb

@@ -0,0 +1,42 @@
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__), '..', '..')
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                  #
+#                                                                                #
+# This program is free software; you can redistribute it and/or                  #
+# modify it under the terms of the GNU General Public License                    #
+# as published by the Free Software Foundation; either version 2                 #
+# of the License, or (at your option) any later version.                         #
+#                                                                                #
+# This program 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 General Public License for more details.                                   #
+#                                                                                #
+# You should have received a copy of the GNU General Public License              #
+# along with this program; if not, write to the Free Software                    #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
+#                                                                                #
+# http://www.gnu.org/copyleft/gpl.html                                           #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# This software is part of BioDSL (www.BioDSL.org).                        #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+require 'test/helper'
+
+class VerboseTest < Test::Unit::TestCase
+  def teardown
+    BioDSL::verbose = false
+  end
+
+  test "BioDSL::verbose returns correctly" do
+    BioDSL::verbose = true
+    assert_equal(true, BioDSL::verbose)
+  end
+end
+