BioDSL 1.0.0

data/test/BioDSL/commands/test_mask_seq.rb

@@ -0,0 +1,98 @@
+#!/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 MaskSeq.
+#
+# rubocop:disable Metrics/LineLength
+class TestMaskSeq < Test::Unit::TestCase
+  def setup
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    hash = {
+      SEQ_NAME: 'test',
+      SEQ: 'gatcgatcgtacgagcagcatctgacgtatcgatcatgcagtctacgacgagcatgctagctag',
+      SEQ_LEN: 82,
+      SCORES: '!"#$%&()*+,-013456;<=>?@ABCDEIIHGCBA@?>=<;:9843210/.-,+*)(&%$III'
+    }
+
+    @output.write hash
+    @output.close
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline::MaskSeq with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.mask_seq(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::MaskSeq with valid options don\'t raise' do
+    assert_nothing_raised { @p.mask_seq(mask: :hard) }
+  end
+
+  test 'BioDSL::Pipeline::MaskSeq with mask: :soft returns correctly' do
+    @p.mask_seq.run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"test",
+      | :SEQ=>"gatcgatcgtacgagcAGCATCTGACGTATCGATCATGCAGTCTAcgacgagcatgctagcTAG",
+      | :SEQ_LEN=>64,
+      | :SCORES=>"!\\\"\\\#$%&()*+,-013456;<=>?@ABCDEIIHGCBA@?>=<;:9843210/.-,+*)(&%$III"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::MaskSeq with mask: :hard returns correctly' do
+    @p.mask_seq(mask: 'hard').run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"test",
+      | :SEQ=>"NNNNNNNNNNNNNNNNAGCATCTGACGTATCGATCATGCAGTCTANNNNNNNNNNNNNNNNTAG",
+      | :SEQ_LEN=>64,
+      | :SCORES=>"!\\\"\\\#$%&()*+,-013456;<=>?@ABCDEIIHGCBA@?>=<;:9843210/.-,+*)(&%$III"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::MaskSeq status returns correctly' do
+    @p.mask_seq(mask: 'hard').run(input: @input, output: @output2)
+
+    assert_equal(1, @p.status.first[:records_in])
+    assert_equal(1, @p.status.first[:records_out])
+    assert_equal(1, @p.status.first[:sequences_in])
+    assert_equal(1, @p.status.first[:sequences_out])
+    assert_equal(64, @p.status.first[:residues_in])
+    assert_equal(64, @p.status.first[:residues_out])
+  end
+end

data/test/BioDSL/commands/test_mean_scores.rb

@@ -0,0 +1,111 @@
+#!/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 MeanScores.
+class TestMeanScores < Test::Unit::TestCase
+  def setup
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    @output.write(SCORES: 'IIIIIIIIIIIIIIIIIIII')
+    @output.write(SCORES: '!!!!!IIIIIIIIIIIIIII')
+    @output.write(SCORES: 'IIIIIIIIIIIIIII!!!!!')
+    @output.close
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline::MeanScores with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.mean_scores(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::MeanScores with valid options don\'t raise' do
+    assert_nothing_raised { @p.mean_scores(local: true) }
+  end
+
+  test 'BioDSL::Pipeline::MeanScores with window_size and local: false ' \
+    'raises' do
+    assert_raise(BioDSL::OptionError) { @p.mean_scores(window_size: 10) }
+  end
+
+  test 'BioDSL::Pipeline::MeanScores returns correctly' do
+    @p.mean_scores.run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SCORES=>"IIIIIIIIIIIIIIIIIIII", :SCORES_MEAN=>40.0}
+      |{:SCORES=>"!!!!!IIIIIIIIIIIIIII", :SCORES_MEAN=>30.0}
+      |{:SCORES=>"IIIIIIIIIIIIIII!!!!!", :SCORES_MEAN=>30.0}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::MeanScores status returns correctly' do
+    @p.mean_scores.run(input: @input, output: @output2)
+
+    assert_equal(3,     @p.status.first[:records_in])
+    assert_equal(3,     @p.status.first[:records_out])
+    assert_equal(0,     @p.status.first[:sequences_in])
+    assert_equal(0,     @p.status.first[:sequences_out])
+    assert_equal(0,     @p.status.first[:residues_in])
+    assert_equal(0,     @p.status.first[:residues_out])
+    assert_equal(0,     @p.status.first[:min_mean])
+    assert_equal(40,    @p.status.first[:max_mean])
+    assert_equal(33.33, @p.status.first[:mean_mean])
+  end
+
+  test 'BioDSL::Pipeline::MeanScores with local: true returns correctly' do
+    @p.mean_scores(local: true).run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SCORES=>"IIIIIIIIIIIIIIIIIIII", :SCORES_MEAN_LOCAL=>40.0}
+      |{:SCORES=>"!!!!!IIIIIIIIIIIIIII", :SCORES_MEAN_LOCAL=>0.0}
+      |{:SCORES=>"IIIIIIIIIIIIIII!!!!!", :SCORES_MEAN_LOCAL=>0.0}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::MeanScores with local: true and :window_size ' \
+    'returns correctly' do
+    @p.mean_scores(local: true, window_size: 10).
+      run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SCORES=>"IIIIIIIIIIIIIIIIIIII", :SCORES_MEAN_LOCAL=>40.0}
+      |{:SCORES=>"!!!!!IIIIIIIIIIIIIII", :SCORES_MEAN_LOCAL=>20.0}
+      |{:SCORES=>"IIIIIIIIIIIIIII!!!!!", :SCORES_MEAN_LOCAL=>20.0}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+end

data/test/BioDSL/commands/test_merge_pair_seq.rb

@@ -0,0 +1,115 @@
+#!/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 MergePairSeq.
+class TestMergePairSeq < Test::Unit::TestCase
+  # rubocop:disable MethodLength
+  def setup
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    [
+      {SEQ_NAME: 'M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14',
+       SEQ: 'TGGGGAATATTGGACAATGG',
+       SEQ_LEN: 20,
+       SCORES: '<??????BDDDDDDDDGGGG'},
+      {SEQ_NAME: 'M01168:16:000000000-A1R9L:1:1101:14862:1868 2:N:0:14',
+       SEQ: 'CCTGTTTGCTACCCACGCTT',
+       SEQ_LEN: 20,
+       SCORES: '?????BB<-<BDDDDDFEEF'},
+      {SEQ_NAME: 'M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14',
+       SEQ: 'TAGGGAATCTTGCACAATGG',
+       SEQ_LEN: 20,
+       SCORES: '<???9?BBBDBDDBDDFFFF'},
+      {SEQ_NAME: 'M01168:16:000000000-A1R9L:1:1101:13906:2139 2:N:0:14',
+       SEQ: 'ACTCTTCGCTACCCATGCTT',
+       SEQ_LEN: 20,
+       SCORES: ',5<??BB?DDABDBDDFFFF'},
+      {SEQ_NAME: 'M01168:16:000000000-A1R9L:1:1101:14865:2158 1:N:0:14',
+       SEQ: 'TAGGGAATCTTGCACAATGG',
+       SEQ_LEN: 20,
+       SCORES: '?????BBBBBDDBDDBFFFF'},
+      {SEQ_NAME: 'M01168:16:000000000-A1R9L:1:1101:14865:2158 2:N:0:14',
+       SEQ: 'CCTCTTCGCTACCCATGCTT',
+       SEQ_LEN: 20,
+       SCORES: '??,<??B?BB?BBBBBFF?F'}
+    ].each do |record|
+      @output.write record
+    end
+
+    @output.close
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline::MergePairSeq with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.merge_pair_seq(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::MergePairSeq returns correctly' do
+    @p.merge_pair_seq.run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14",
+      | :SEQ=>"TGGGGAATATTGGACAATGGCCTGTTTGCTACCCACGCTT",
+      | :SEQ_LEN=>40,
+      | :SCORES=>"<??????BDDDDDDDDGGGG?????BB<-<BDDDDDFEEF",
+      | :SEQ_LEN_LEFT=>20,
+      | :SEQ_LEN_RIGHT=>20}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14",
+      | :SEQ=>"TAGGGAATCTTGCACAATGGACTCTTCGCTACCCATGCTT",
+      | :SEQ_LEN=>40,
+      | :SCORES=>"<???9?BBBDBDDBDDFFFF,5<??BB?DDABDBDDFFFF",
+      | :SEQ_LEN_LEFT=>20,
+      | :SEQ_LEN_RIGHT=>20}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14865:2158 1:N:0:14",
+      | :SEQ=>"TAGGGAATCTTGCACAATGGCCTCTTCGCTACCCATGCTT",
+      | :SEQ_LEN=>40,
+      | :SCORES=>"?????BBBBBDDBDDBFFFF??,<??B?BB?BBBBBFF?F",
+      | :SEQ_LEN_LEFT=>20,
+      | :SEQ_LEN_RIGHT=>20}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::MergePairSeq status returns correctly' do
+    @p.merge_pair_seq.run(input: @input, output: @output2)
+
+    assert_equal(6, @p.status.first[:records_in])
+    assert_equal(3, @p.status.first[:records_out])
+    assert_equal(6, @p.status.first[:sequences_in])
+    assert_equal(3, @p.status.first[:sequences_out])
+    assert_equal(120, @p.status.first[:residues_in])
+    assert_equal(120, @p.status.first[:residues_out])
+  end
+end

data/test/BioDSL/commands/test_merge_table.rb

@@ -0,0 +1,131 @@
+#!/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 MergeTable.
+class TestMergeTable < Test::Unit::TestCase
+  def setup
+    @tmpdir = Dir.mktmpdir('BioDSL')
+
+    @file = File.join(@tmpdir, 'test.tab')
+
+    setup_data_file
+
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    @output.write(ID: 1, COUNT: 5423)
+    @output.write(ID: 2, COUNT: 34)
+    @output.write(ID: 3, COUNT: 2423)
+    @output.write(ID: 4, COUNT: 234)
+    @output.write(ID: 5, COUNT: 2334)
+
+    @output.close
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  def setup_data_file
+    data = <<-EOF.gsub(/^\s+\|/, '')
+      |#ID ORGANISM
+      |1   parrot
+      |2   eel
+      |3   platypus
+      |4   beetle
+    EOF
+
+    File.open(@file, 'w') do |ios|
+      ios.puts data
+    end
+  end
+
+  def teardown
+    FileUtils.rm_r @tmpdir
+  end
+
+  test 'BioDSL::Pipeline::MergeTable with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.merge_table(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::MergeTable without required options raises' do
+    assert_raise(BioDSL::OptionError) { @p.merge_table }
+  end
+
+  test 'BioDSL::Pipeline::MergeTable with non-existing input file raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.merge_table(input: '___adsf', key: :ID)
+    end
+  end
+
+  test 'BioDSL::Pipeline::MergeTable with bad skip value file raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.merge_table(input: @file, key: :ID, skip: -1)
+    end
+  end
+
+  test 'BioDSL::Pipeline::MergeTable with duplicate keys raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.merge_table(input: @file, key: :ID, keys: [:a, :a])
+    end
+  end
+
+  test 'BioDSL::Pipeline::MergeTable with duplicate columns raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.merge_table(input: @file, key: :ID, columns: [1, 1])
+    end
+  end
+
+  test 'BioDSL::Pipeline::MergeTable returns correctly' do
+    @p.merge_table(input: @file, key: :ID).run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:ID=>1, :COUNT=>5423, :ORGANISM=>"parrot"}
+      |{:ID=>2, :COUNT=>34, :ORGANISM=>"eel"}
+      |{:ID=>3, :COUNT=>2423, :ORGANISM=>"platypus"}
+      |{:ID=>4, :COUNT=>234, :ORGANISM=>"beetle"}
+      |{:ID=>5, :COUNT=>2334}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::MergeTable status returns correctly' do
+    @p.merge_table(input: @file, key: :ID).run(input: @input, output: @output2)
+
+    assert_equal(5, @p.status.first[:records_in])
+    assert_equal(5, @p.status.first[:records_out])
+    assert_equal(4, @p.status.first[:merged])
+    assert_equal(1, @p.status.first[:non_merged])
+    assert_equal(4, @p.status.first[:rows_matched])
+    assert_equal(0, @p.status.first[:rows_unmatched])
+    assert_equal(4, @p.status.first[:rows_total])
+  end
+end

data/test/BioDSL/commands/test_merge_values.rb

@@ -0,0 +1,83 @@
+#!/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 MergeValues.
+class TestMergeValues < Test::Unit::TestCase
+  def setup
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    @output.write(ID: 'FOO', COUNT: 10, SEQ: 'gataag')
+    @output.write(ID: 'FOO', SEQ: 'gataag')
+    @output.close
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline::MergeValues with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.merge_values(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::MergeValues with valid options don\'t raise' do
+    assert_nothing_raised { @p.merge_values(keys: [:ID]) }
+  end
+
+  test 'BioDSL::Pipeline::MergeValues returns correctly' do
+    @p.merge_values(keys: [:COUNT, :ID]).run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:ID=>"FOO", :COUNT=>"10_FOO", :SEQ=>"gataag"}
+      |{:ID=>"FOO", :SEQ=>"gataag"}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::MergeValues status returns correctly' do
+    @p.merge_values(keys: [:COUNT, :ID]).run(input: @input, output: @output2)
+
+    assert_equal(2, @p.status.first[:records_in])
+    assert_equal(2, @p.status.first[:records_out])
+  end
+
+  test 'BioDSL::Pipeline::MergeValues with :delimiter returns correctly' do
+    @p.merge_values(keys: [:ID, :COUNT], delimiter: ':count=').
+      run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:ID=>"FOO:count=10", :COUNT=>10, :SEQ=>"gataag"}
+      |{:ID=>"FOO", :SEQ=>"gataag"}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+end