BioDSL 1.0.0

data/test/BioDSL/commands/test_plot_heatmap.rb

@@ -0,0 +1,185 @@
+#!/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 PlotHeatmap.
+# rubocop:disable ClassLength
+# rubocop:disable MethodLength
+class TestPlotHeatmap < 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(V0: 1, V1: 2, V2: 3, V3: 4)
+    @output.write(V0: 5, V1: 6, V2: 7, V3: 8)
+    @output.write(V0: 9, V1: 10, V2: 11, V3: 12)
+    @output.close
+  end
+
+  def setup_expected1
+    @expected = <<-EOF.gsub(/^\s+\|/, '')
+      |set terminal dumb
+      |set title \"Heatmap\"
+      |set xlabel \"x\"
+      |set ylabel \"y\"
+      |set output \"\"
+      |set view map
+      |set autoscale xfix
+      |set autoscale yfix
+      |set nokey
+      |set tic scale 0
+      |set palette rgbformulae 22,13,10
+      |unset xtics
+      |unset ytics
+      |plot \"-\" matrix with image
+      |1 2 3 4
+      |5 6 7 8
+      |9 10 11 12
+      |e
+    EOF
+  end
+
+  def setup_expected2
+    @expected2 = <<-EOF.gsub(/^\s+\|/, '')
+      |set terminal dumb
+      |set title \"Heatmap\"
+      |set xlabel \"x\"
+      |set ylabel \"y\"
+      |set output \"\"
+      |set view map
+      |set autoscale xfix
+      |set autoscale yfix
+      |set nokey
+      |set tic scale 0
+      |set palette rgbformulae 22,13,10
+      |set logscale cb
+      |unset xtics
+      |unset ytics
+      |plot \"-\" matrix with image
+      |1 2 3 4
+      |5 6 7 8
+      |9 10 11 12
+      |e
+    EOF
+  end
+
+  def teardown
+    FileUtils.rm_r @tmpdir
+  end
+
+  test 'BioDSL::Pipeline::PlotHeatmap with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.plot_heatmap(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::PlotHeatmap with invalid terminal raises' do
+    assert_raise(BioDSL::OptionError) { @p.plot_heatmap(terminal: 'foo') }
+  end
+
+  test 'BioDSL::Pipeline::PlotHeatmap with valid terminal don\'t raise' do
+    %w(dumb post svg x11 aqua png pdf).each do |terminal|
+      assert_nothing_raised { @p.plot_heatmap(terminal: terminal.to_sym) }
+    end
+  end
+
+  test 'BioDSL::Pipeline::PlotHeatmap to file outputs correctly' do
+    result = capture_stderr do
+      @p.plot_heatmap(output: @file, test: true).
+      run(input: @input, output: @output2)
+    end
+
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected, result)
+  end
+
+  test 'BioDSL::Pipeline::PlotHeatmap to file with logscale outputs OK' do
+    result = capture_stderr do
+      @p.plot_heatmap(output: @file, logscale: true, test: true).
+      run(input: @input, output: @output2)
+    end
+
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected2, result)
+  end
+
+  test 'BioDSL::Pipeline::PlotHeatmap to existing file raises' do
+    `touch #{@file}`
+    assert_raise(BioDSL::OptionError) { @p.plot_heatmap(output: @file) }
+  end
+
+  test 'BioDSL::Pipeline::PlotHeatmap to existing file with :force' \
+    'outputs correctly' do
+    `touch #{@file}`
+    result = capture_stderr do
+      @p.plot_heatmap(output: @file, force: true, test: true).
+      run(input: @input)
+    end
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected, result)
+  end
+
+  test 'BioDSL::Pipeline::PlotHeatmap with flux outputs correctly' do
+    result = capture_stderr do
+      @p.plot_heatmap(output: @file, force: true, test: true).
+      run(input: @input, output: @output2)
+    end
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected, result)
+
+    stream_expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:V0=>1, :V1=>2, :V2=>3, :V3=>4}
+      |{:V0=>5, :V1=>6, :V2=>7, :V3=>8}
+      |{:V0=>9, :V1=>10, :V2=>11, :V3=>12}
+    EXP
+
+    assert_equal(stream_expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::PlotHeatmap status outputs correctly' do
+    @p.plot_heatmap(output: @file, force: true).
+      run(input: @input, output: @output2)
+
+    assert_equal(3, @p.status.first[:records_in])
+    assert_equal(3, @p.status.first[:records_out])
+  end
+end

data/test/BioDSL/commands/test_plot_histogram.rb

@@ -0,0 +1,194 @@
+#!/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 PlotHistogram.
+# rubocop:disable ClassLength
+class TestPlotHistogram < 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_stream
+    setup_expected1
+    setup_expected2
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  def setup_stream
+    @output.write(ID: 'x', LEN: 1)
+    @output.write(ID: 'x', LEN: 2)
+    @output.write(ID: 'x', LEN: 2)
+    @output.write(ID: 'x', LEN: 3)
+    @output.write(ID: 'y', LEN: 3)
+    @output.write(ID: 'y', LEN: 3)
+    @output.close
+  end
+
+  # rubocop:disable MethodLength
+  def setup_expected1
+    @expected1 = <<-EOF.gsub(/^\s+\|/, '')
+      |set terminal dumb
+      |set title \"Histogram\"
+      |set xlabel \"LEN\"
+      |set ylabel \"n\"
+      |set autoscale xfix
+      |set style fill solid 0.5 border
+      |set xtics out
+      |set ytics out
+      |set yrange [0:*]
+      |set output \"\"
+      |plot \"-\" using 1:2 with boxes notitle
+      |0 0
+      |1 1
+      |2 2
+      |3 3
+      |e
+    EOF
+  end
+
+  def setup_expected2
+    @expected2 = <<-EOF.gsub(/^\s+\|/, '')
+      |set terminal dumb
+      |set title \"Histogram\"
+      |set xlabel \"ID\"
+      |set ylabel \"n\"
+      |set autoscale xfix
+      |set style fill solid 0.5 border
+      |set xtics out
+      |set ytics out
+      |set yrange [0:*]
+      |set output \"\"
+      |plot \"-\" using 2:xticlabels(1) with boxes notitle lc rgb \"red\"
+      |x 4
+      |y 2
+      |e
+    EOF
+  end
+
+  # rubocop:enable MethodLength
+  def teardown
+    FileUtils.rm_r @tmpdir
+  end
+
+  test 'BioDSL::Pipeline::PlotHistogram with invalid options raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.plot_histogram(key: :LEN, foo: 'bar')
+    end
+  end
+
+  test 'BioDSL::Pipeline::PlotHistogram with invalid terminal raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.plot_histogram(key: :LEN, terminal: 'foo')
+    end
+  end
+
+  test 'BioDSL::Pipeline::PlotHistogram with valid terminal don\'t raise' do
+    %w(dumb post svg x11 aqua png pdf).each do |terminal|
+      assert_nothing_raised do
+        @p.plot_histogram(key: :LEN, terminal: terminal.to_sym)
+      end
+    end
+  end
+
+  test 'BioDSL::Pipeline::PlotHistogram to file with numeric outputs OK' do
+    result = capture_stderr do
+      @p.plot_histogram(key: :LEN, output: @file, test: true).
+      run(input: @input, output: @output2)
+    end
+
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected1, result)
+  end
+
+  test 'BioDSL::Pipeline::PlotHistogram to file with non-numeric outputs ' \
+    'correctly' do
+    result = capture_stderr do
+      @p.plot_histogram(key: :ID, output: @file, test: true).
+      run(input: @input, output: @output2)
+    end
+
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected2, result)
+  end
+
+  test 'BioDSL::Pipeline::PlotHistogram to existing file raises' do
+    `touch #{@file}`
+    assert_raise(BioDSL::OptionError) { @p.plot_histogram(output: @file) }
+  end
+
+  test 'BioDSL::Pipeline::PlotHistogram to existing file with :force ' \
+    'outputs correctly' do
+    `touch #{@file}`
+    result = capture_stderr do
+      @p.plot_histogram(key: :LEN, output: @file, force: true, test: true).
+      run(input: @input)
+    end
+
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected1, result)
+  end
+
+  test 'BioDSL::Pipeline::PlotHistogram with flux outputs correctly' do
+    result = capture_stderr do
+      @p.plot_histogram(key: :LEN, output: @file, force: true, test: true).
+      run(input: @input, output: @output2)
+    end
+
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected1, result)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:ID=>"x", :LEN=>1}
+      |{:ID=>"x", :LEN=>2}
+      |{:ID=>"x", :LEN=>2}
+      |{:ID=>"x", :LEN=>3}
+      |{:ID=>"y", :LEN=>3}
+      |{:ID=>"y", :LEN=>3}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::PlotHistogram status outputs correctly' do
+    @p.plot_histogram(key: :LEN, output: @file, force: true).
+      run(input: @input, output: @output2)
+
+    assert_equal(6, @p.status.first[:records_in])
+    assert_equal(6, @p.status.first[:records_out])
+  end
+end

data/test/BioDSL/commands/test_plot_matches.rb

@@ -0,0 +1,157 @@
+#!/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 PlotMatches
+class TestPlotMatches < 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_expected
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  def setup_data
+    @output.write(Q_BEG: 0, S_BEG: 0, Q_END: 10, S_END: 10, STRAND: '+')
+    @output.write(Q_BEG: 0, S_BEG: 0, Q_END: 10, S_END: 10, STRAND: '-')
+    @output.write(Q_BEG: 3, S_BEG: 3, Q_END: 6, S_END: 6, DIRECTION: 'forward')
+    @output.write(Q_BEG: 3, S_BEG: 3, Q_END: 6, S_END: 6, DIRECTION: 'reverse')
+    @output.close
+  end
+
+  # rubocop:disable MethodLength
+  def setup_expected
+    @expected = <<-EOF.gsub(/^\s+\|/, '').delete("\n")
+      |set terminal dumb
+      |set title "Matches"
+      |set xlabel "x"
+      |set ylabel "y"
+      |set autoscale xfix
+      |set autoscale yfix
+      |set style fill solid 0.5 border
+      |set style line 1 linetype 1 linecolor rgb "green" linewidth 2 pointtype
+      | 6 pointsize default
+      |set style line 2 linetype 1 linecolor rgb "red"   linewidth 2 pointtype
+      | 6 pointsize default
+      |set xtics border out
+      |set ytics border out
+      |set grid
+      |set nokey
+      |set output ""
+      |plot "-" using 1:2:3:4 with vectors nohead ls 1, "-" using 1:2:3:4 with
+      | vectors nohead ls 2
+      |0 0 10 10
+      |3 3 3 3
+      |e
+      |10 0 -10 10
+      |6 3 -3 3
+      |e
+    EOF
+  end
+
+  def teardown
+    FileUtils.rm_r @tmpdir
+  end
+
+  test 'BioDSL::Pipeline::PlotMatches with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.plot_matches(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::PlotMatches with invalid terminal raises' do
+    assert_raise(BioDSL::OptionError) { @p.plot_matches(terminal: 'foo') }
+  end
+
+  test 'BioDSL::Pipeline::PlotMatches with valid terminal don\'t raise' do
+    %w(dumb post svg x11 aqua png pdf).each do |terminal|
+      assert_nothing_raised { @p.plot_matches(terminal: terminal.to_sym) }
+    end
+  end
+
+  test 'BioDSL::Pipeline::PlotMatches to file outputs correctly' do
+    result = capture_stderr do
+      @p.plot_matches(output: @file, test: true).
+      run(input: @input, output: @output2)
+    end
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected, result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::PlotMatches to existing file raises' do
+    `touch #{@file}`
+    assert_raise(BioDSL::OptionError) { @p.plot_matches(output: @file) }
+  end
+
+  test 'BioDSL::Pipeline::PlotMatches to existing file with :force ' \
+    'outputs correctly' do
+    `touch #{@file}`
+    result = capture_stderr do
+      @p.plot_matches(output: @file, force: true, test: true).run(input: @input)
+    end
+
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+    assert_equal(@expected, result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::PlotMatches with flux outputs correctly' do
+    result = capture_stderr do
+      @p.plot_matches(output: @file, force: true, test: true).
+      run(input: @input, output: @output2)
+    end
+    result.sub!(/set output "[^"]+"/, 'set output ""')
+
+    assert_equal(@expected, result.delete("\n"))
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:Q_BEG=>0, :S_BEG=>0, :Q_END=>10, :S_END=>10, :STRAND=>"+"}
+      |{:Q_BEG=>0, :S_BEG=>0, :Q_END=>10, :S_END=>10, :STRAND=>"-"}
+      |{:Q_BEG=>3, :S_BEG=>3, :Q_END=>6, :S_END=>6, :DIRECTION=>"forward"}
+      |{:Q_BEG=>3, :S_BEG=>3, :Q_END=>6, :S_END=>6, :DIRECTION=>"reverse"}
+    EXP
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::PlotMatches status outputs correctly' do
+    @p.plot_matches(output: @file, force: true).
+      run(input: @input, output: @output2)
+
+    assert_equal(4, @p.status.first[:records_in])
+    assert_equal(4, @p.status.first[:records_out])
+    assert_equal(4, @p.status.first[:matches_in])
+  end
+end