BioDSL 1.0.0

data/test/BioDSL/commands/test_plot_residue_distribution.rb

@@ -0,0 +1,309 @@
+#!/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 PlotResidueDistribution.
+#
+# rubocop: disable ClassLength
+class TestPlotResidueDistribution < Test::Unit::TestCase
+  def setup
+    omit('gnuplot not found') unless BioDSL::Filesys.which('gnuplot')
+
+    @tmpdir = Dir.mktmpdir('BioDSL')
+    @file   = File.join(@tmpdir, 'test.plot')
+
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    setup_data
+    setup_expected1
+    setup_expected2
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  def setup_data
+    [{SEQ: 'AN'},
+     {SEQ: 'T'},
+     {SEQ: 'C'},
+     {SEQ: 'G'},
+     {FOO: 'BAR'}].each do |record|
+       @output.write(record)
+     end
+
+    @output.close
+  end
+
+  # rubocop: disable MethodLength
+  def setup_expected1
+    @expected1 = <<-EOF.gsub(/^\s+\|/, '').delete("\n")
+      |set terminal dumb
+      |set title \"Residue Distribution\"
+      |set xlabel \"Sequence position\"
+      |set ylabel \"%\"
+      |set output \"\"
+      |set xtics out
+      |set ytics out
+      |set yrange [0:100]
+      |set xrange [0:2]
+      |set auto fix
+      |set offsets \"1\"
+      |set key outside right top vertical Left reverse noenhanced autotitles
+      | columnhead nobox
+      |set key invert samplen 4 spacing 1 width 0 height 0
+      |set style fill solid 0.5 border
+      |set style histogram rowstacked
+      |set style data histograms
+      |set boxwidth 0.75 absolute
+      |set linetype 1 lc rgb \"#FF0010\"
+      |set linetype 2 lc rgb \"#191919\"
+      |set linetype 3 lc rgb \"#0075DC\"
+      |set linetype 4 lc rgb \"#2BCE48\"
+      |set linetype 5 lc rgb \"#FFFF00\"
+      |set linetype 6 lc rgb \"#4C005C\"
+      |set linetype 7 lc rgb \"#993F00\"
+      |set linetype 8 lc rgb \"#FFCC99\"
+      |set linetype 9 lc rgb \"#808080\"
+      |set linetype 10 lc rgb \"#94FFB5\"
+      |set linetype 11 lc rgb \"#8F7C00\"
+      |set linetype 12 lc rgb \"#9DCC00\"
+      |set linetype 13 lc rgb \"#C20088\"
+      |set linetype 14 lc rgb \"#003380\"
+      |set linetype 15 lc rgb \"#FFA405\"
+      |set linetype 16 lc rgb \"#FFA8BB\"
+      |set linetype 17 lc rgb \"#426600\"
+      |set linetype 18 lc rgb \"#F0A3FF\"
+      |set linetype 19 lc rgb \"#5EF1F2\"
+      |set linetype 20 lc rgb \"#00998F\"
+      |set linetype 21 lc rgb \"#E0FF66\"
+      |set linetype 22 lc rgb \"#740AFF\"
+      |set linetype 23 lc rgb \"#990000\"
+      |set linetype 24 lc rgb \"#FFFF80\"
+      |set linetype 25 lc rgb \"#005C31\"
+      |set linetype 26 lc rgb \"#FF5005\"
+      |set linetype cycle 26
+      |plot \"-\" using 1 with histogram lt 1 title \"T\", \"-\" using 1 with
+      | histogram lt 2 title \"N\", \"-\" using 1 with histogram lt 3
+      | title \"G\", \"-\" using 1 with histogram lt 4
+      | title \"C\", \"-\" using 1 with histogram lt 5
+      | title \"A\"
+      |0.0
+      |25.0
+      |0.0
+      |e
+      |0.0
+      |0.0
+      |100.0
+      |e
+      |0.0
+      |25.0
+      |0.0
+      |e
+      |0.0
+      |25.0
+      |0.0
+      |e
+      |0.0
+      |25.0
+      |0.0
+      |e
+    EOF
+  end
+
+  def setup_expected2
+    @expected2 = <<-EOF.gsub(/^\s+\|/, '').delete("\n")
+      |set terminal dumb
+      |set title \"Residue Distribution\"
+      |set xlabel \"Sequence position\"
+      |set ylabel \"%\"
+      |set output \"\"
+      |set xtics out
+      |set ytics out
+      |set yrange [0:100]
+      |set xrange [0:2]
+      |set auto fix
+      |set offsets \"1\"
+      |set key outside right top vertical Left reverse noenhanced autotitles
+      | columnhead nobox
+      |set key invert samplen 4 spacing 1 width 0 height 0
+      |set style fill solid 0.5 border
+      |set style histogram rowstacked
+      |set style data histograms
+      |set boxwidth 0.75 absolute
+      |set linetype 1 lc rgb \"#FF0010\"
+      |set linetype 2 lc rgb \"#191919\"
+      |set linetype 3 lc rgb \"#0075DC\"
+      |set linetype 4 lc rgb \"#2BCE48\"
+      |set linetype 5 lc rgb \"#FFFF00\"
+      |set linetype 6 lc rgb \"#4C005C\"
+      |set linetype 7 lc rgb \"#993F00\"
+      |set linetype 8 lc rgb \"#FFCC99\"
+      |set linetype 9 lc rgb \"#808080\"
+      |set linetype 10 lc rgb \"#94FFB5\"
+      |set linetype 11 lc rgb \"#8F7C00\"
+      |set linetype 12 lc rgb \"#9DCC00\"
+      |set linetype 13 lc rgb \"#C20088\"
+      |set linetype 14 lc rgb \"#003380\"
+      |set linetype 15 lc rgb \"#FFA405\"
+      |set linetype 16 lc rgb \"#FFA8BB\"
+      |set linetype 17 lc rgb \"#426600\"
+      |set linetype 18 lc rgb \"#F0A3FF\"
+      |set linetype 19 lc rgb \"#5EF1F2\"
+      |set linetype 20 lc rgb \"#00998F\"
+      |set linetype 21 lc rgb \"#E0FF66\"
+      |set linetype 22 lc rgb \"#740AFF\"
+      |set linetype 23 lc rgb \"#990000\"
+      |set linetype 24 lc rgb \"#FFFF80\"
+      |set linetype 25 lc rgb \"#005C31\"
+      |set linetype 26 lc rgb \"#FF5005\"
+      |set linetype cycle 26
+      |plot \"-\" using 1 with histogram lt 1 title \"T\", \"-\" using 1 with
+      | histogram lt 2 title \"N\", \"-\" using 1 with histogram lt 3
+      | title \"G\", \"-\" using 1 with histogram lt 4
+      | title \"C\", \"-\" using 1 with histogram lt 5
+      | title \"A\", \"-\" using 1:2 with lines lw 2 lt
+      | rgb \"black\" title \"count\"
+      |0.0
+      |25.0
+      |0.0
+      |e
+      |0.0
+      |0.0
+      |100.0
+      |e
+      |0.0
+      |25.0
+      |0.0
+      |e
+      |0.0
+      |25.0
+      |0.0
+      |e
+      |0.0
+      |25.0
+      |0.0
+      |e
+      |0 0.0
+      |0 100.0
+      |1 25.0
+      |e
+    EOF
+  end
+
+  # rubocop: enable MethodLength
+  def teardown
+    FileUtils.rm_r @tmpdir
+  end
+
+  test 'BioDSL::Pipeline::PlotResidueDistribution with invalid options ' \
+    'raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.plot_residue_distribution(foo: 'bar')
+    end
+  end
+
+  test 'BioDSL::Pipeline::PlotResidueDistribution with invalid terminal ' \
+    'raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.plot_residue_distribution(terminal: 'foo')
+    end
+  end
+
+  test 'BioDSL::Pipeline::PlotResidueDistribution with valid terminal ' \
+    'don\'t raise' do
+    %w(dumb post svg x11 aqua png pdf).each do |terminal|
+      assert_nothing_raised do
+        @p.plot_residue_distribution(terminal: terminal.to_sym)
+      end
+    end
+  end
+
+  test 'BioDSL::Pipeline::PlotResidueDistribution to file outputs OK' do
+    result = capture_stderr do
+      @p.plot_residue_distribution(output: @file, test: true).
+      run(input: @input, output: @output2)
+    end
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected1, result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::PlotResidueDistribution to file with :count ' \
+    'outputs correctly' do
+    result = capture_stderr do
+      @p.plot_residue_distribution(output: @file, count: true, test: true).
+      run(input: @input, output: @output2)
+    end
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected2, result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::PlotResidueDistribution to existing file raises' do
+    `touch #{@file}`
+    assert_raise(BioDSL::OptionError) do
+      @p.plot_residue_distribution(output: @file)
+    end
+  end
+
+  test 'BioDSL::Pipeline::PlotResidueDistribution to existing file with ' \
+    ':force outputs correctly' do
+    `touch #{@file}`
+    result = capture_stderr do
+      @p.plot_residue_distribution(output: @file, force: true, test: true).
+      run(input: @input)
+    end
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected1, result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::PlotResidueDistribution with flux outputs OK' do
+    result = capture_stderr do
+      @p.plot_residue_distribution(output: @file, force: true, test: true).
+      run(input: @input, output: @output2)
+    end
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected1, result.delete("\n"))
+
+    expected = '{:SEQ=>"AN"}{:SEQ=>"T"}{:SEQ=>"C"}{:SEQ=>"G"}{:FOO=>"BAR"}'
+    assert_equal(expected, collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::PlotResidueDistribution status outputs OK' do
+    @p.plot_residue_distribution(output: @file, force: true).
+      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[:sequences_in])
+    assert_equal(4, @p.status.first[:sequences_out])
+    assert_equal(5, @p.status.first[:residues_in])
+    assert_equal(5, @p.status.first[:residues_out])
+  end
+end

data/test/BioDSL/commands/test_plot_scores.rb

@@ -0,0 +1,308 @@
+#!/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 PlotScores.
+#
+# rubocop: disable ClassLength
+class TestPlotScores < Test::Unit::TestCase
+  def setup
+    omit('gnuplot not found') unless BioDSL::Filesys.which('gnuplot')
+
+    @tmpdir = Dir.mktmpdir('BioDSL')
+    @file   = File.join(@tmpdir, 'test.plot')
+
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    setup_data
+    setup_expected1
+    setup_expected2
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  def setup_data
+    @output.write(SCORES: %q(!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI))
+    @output.write(SCORES: %q("#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI))
+    @output.write(SCORES: %(#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI))
+    @output.write(SCORES: %($%&'()*+,-./0123456789:;<=>?@ABCDEFGHI))
+    @output.write(SCORES: %(%&'()*+,-./0123456789:;<=>?@ABCDEFGHI))
+    @output.write(SCORES: %(&'()*+,-./0123456789:;<=>?@ABCDEFGHI))
+    @output.close
+  end
+
+  # rubocop: disable MethodLength
+  def setup_expected1
+    @expected = <<-EOF.gsub(/^\s+\|/, '')
+      |set terminal dumb
+      |set title "Mean Quality Scores"
+      |set xlabel "Sequence Position"
+      |set ylabel "Mean Score"
+      |set output ""
+      |set xrange [0:42]
+      |set yrange [0:40]
+      |set style fill solid 0.5 border
+      |set xtics out
+      |set ytics out
+      |plot "-" with boxes lc rgb "red" title "mean score"
+      |1 2.5
+      |2 3.5
+      |3 4.5
+      |4 5.5
+      |5 6.5
+      |6 7.5
+      |7 8.5
+      |8 9.5
+      |9 10.5
+      |10 11.5
+      |11 12.5
+      |12 13.5
+      |13 14.5
+      |14 15.5
+      |15 16.5
+      |16 17.5
+      |17 18.5
+      |18 19.5
+      |19 20.5
+      |20 21.5
+      |21 22.5
+      |22 23.5
+      |23 24.5
+      |24 25.5
+      |25 26.5
+      |26 27.5
+      |27 28.5
+      |28 29.5
+      |29 30.5
+      |30 31.5
+      |31 32.5
+      |32 33.5
+      |33 34.5
+      |34 35.5
+      |35 36.5
+      |36 37.5
+      |37 38.0
+      |38 38.5
+      |39 39.0
+      |40 39.5
+      |41 40.0
+      |e
+    EOF
+  end
+
+  # rubocop: disable LineLength
+  def setup_expected2
+    @expected2 = <<-EOF.gsub(/^\s+\|/, '')
+      |set terminal dumb
+      |set title \"Mean Quality Scores\"
+      |set xlabel \"Sequence Position\"
+      |set ylabel \"Mean Score\"
+      |set output \"\"
+      |set xrange [0:42]
+      |set yrange [0:40]
+      |set style fill solid 0.5 border
+      |set xtics out
+      |set ytics out
+      |plot \"-\" with boxes lc rgb \"red\" title \"mean score\", \"-\" with lines lt rgb \"black\" title \"relative count\"
+      |1 2.5
+      |2 3.5
+      |3 4.5
+      |4 5.5
+      |5 6.5
+      |6 7.5
+      |7 8.5
+      |8 9.5
+      |9 10.5
+      |10 11.5
+      |11 12.5
+      |12 13.5
+      |13 14.5
+      |14 15.5
+      |15 16.5
+      |16 17.5
+      |17 18.5
+      |18 19.5
+      |19 20.5
+      |20 21.5
+      |21 22.5
+      |22 23.5
+      |23 24.5
+      |24 25.5
+      |25 26.5
+      |26 27.5
+      |27 28.5
+      |28 29.5
+      |29 30.5
+      |30 31.5
+      |31 32.5
+      |32 33.5
+      |33 34.5
+      |34 35.5
+      |35 36.5
+      |36 37.5
+      |37 38.0
+      |38 38.5
+      |39 39.0
+      |40 39.5
+      |41 40.0
+      |e
+      |1 40.0
+      |2 40.0
+      |3 40.0
+      |4 40.0
+      |5 40.0
+      |6 40.0
+      |7 40.0
+      |8 40.0
+      |9 40.0
+      |10 40.0
+      |11 40.0
+      |12 40.0
+      |13 40.0
+      |14 40.0
+      |15 40.0
+      |16 40.0
+      |17 40.0
+      |18 40.0
+      |19 40.0
+      |20 40.0
+      |21 40.0
+      |22 40.0
+      |23 40.0
+      |24 40.0
+      |25 40.0
+      |26 40.0
+      |27 40.0
+      |28 40.0
+      |29 40.0
+      |30 40.0
+      |31 40.0
+      |32 40.0
+      |33 40.0
+      |34 40.0
+      |35 40.0
+      |36 40.0
+      |37 33.33333206176758
+      |38 26.66666603088379
+      |39 20.0
+      |40 13.333333015441895
+      |41 6.666666507720947
+      |e
+    EOF
+  end
+
+  # rubocop: enable MethodLength
+  # rubocop: enable LineLength
+  def teardown
+    FileUtils.rm_r @tmpdir
+  end
+
+  test 'BioDSL::Pipeline::PlotScores with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.plot_scores(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::PlotScores with invalid terminal raises' do
+    assert_raise(BioDSL::OptionError) { @p.plot_scores(terminal: 'foo') }
+  end
+
+  test 'BioDSL::Pipeline::PlotScores with valid terminal don\'t raise' do
+    %w(dumb post svg x11 aqua png pdf).each do |terminal|
+      assert_nothing_raised { @p.plot_scores(terminal: terminal.to_sym) }
+    end
+  end
+
+  test 'BioDSL::Pipeline::PlotScores to file outputs correctly' do
+    result = capture_stderr do
+      @p.plot_scores(output: @file, test: true).
+      run(input: @input, output: @output2)
+    end
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected, result)
+  end
+
+  test 'BioDSL::Pipeline::PlotScores status outputs correctly' do
+    @p.plot_scores(output: @file).
+      run(input: @input, output: @output2)
+
+    assert_equal(6, @p.status.first[:records_in])
+    assert_equal(6, @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])
+  end
+
+  test 'BioDSL::Pipeline::PlotScores to file with count: true outputs OK' do
+    result = capture_stderr do
+      @p.plot_scores(count: true, output: @file, test: true).
+      run(input: @input, output: @output2)
+    end
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected2, result)
+  end
+
+  test 'BioDSL::Pipeline::PlotScores to existing file raises' do
+    `touch #{@file}`
+    assert_raise(BioDSL::OptionError) { @p.plot_scores(output: @file) }
+  end
+
+  test 'BioDSL::Pipeline::PlotScores to existing file with :force outputs ' \
+    'correctly' do
+    `touch #{@file}`
+    result = capture_stderr do
+      @p.plot_scores(output: @file, force: true, test: true).run(input: @input)
+    end
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected, result)
+  end
+
+  test 'BioDSL::Pipeline::PlotScores with flux outputs correctly' do
+    result = capture_stderr do
+      @p.plot_scores(output: @file, force: true, test: true).
+      run(input: @input, output: @output2)
+    end
+
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected, result)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SCORES=>"!\\"\\#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI"}
+      |{:SCORES=>"\\"\\#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI"}
+      |{:SCORES=>"\\#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI"}
+      |{:SCORES=>"$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI"}
+      |{:SCORES=>"%&'()*+,-./0123456789:;<=>?@ABCDEFGHI"}
+      |{:SCORES=>"&'()*+,-./0123456789:;<=>?@ABCDEFGHI"}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+end

data/test/BioDSL/commands/test_random.rb

@@ -0,0 +1,88 @@
+#!/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 Random.
+class TestRandom < Test::Unit::TestCase
+  def setup
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    [{TEST: 1},
+     {TEST: 2},
+     {TEST: 3},
+     {TEST: 4},
+     {TEST: 5},
+     {TEST: 6}].each do |record|
+      @output.write record
+    end
+
+    @output.close
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline#random with disallowed option raises' do
+    assert_raise(BioDSL::OptionError) { @p.random(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline#random with allowed options don\'t raise' do
+    assert_nothing_raised { @p.random(number: 2) }
+  end
+
+  test 'BioDSL::Pipeline#random returns correctly' do
+    @p.random(number: 3).run(input: @input, output: @output2)
+    size = 0
+    @input2.map { size += 1 }
+
+    assert_equal(3, size)
+  end
+
+  test 'BioDSL::Pipeline#random status returns correctly' do
+    @p.random(number: 3).run(input: @input, output: @output2)
+
+    assert_equal(6, @p.status.first[:records_in])
+    assert_equal(3, @p.status.first[:records_out])
+  end
+
+  test 'BioDSL::Pipeline#random with pairs: true returns correctly' do
+    @p.random(number: 4, pairs: true).run(input: @input, output: @output2)
+
+    size = 0
+
+    @input2.each_slice(2) do |record1, record2|
+      assert_equal(record1[:TEST].to_i, record2[:TEST].to_i - 1)
+      size += 2
+    end
+
+    assert_equal(4, size)
+  end
+end