BioDSL 1.0.0

data/test/BioDSL/commands/test_assemble_pairs.rb

@@ -0,0 +1,459 @@
+#!/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 AssemblePairs.
+# rubocop:disable ClassLength
+class TestAssemblePairs < Test::Unit::TestCase
+  # rubocop:disable MethodLength
+  def setup
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    @output.write(SEQ_NAME: 'test1/1', SEQ: 'aaaaaaaagagtcat',
+                  SCORES: 'IIIIIIIIIIIIIII', SEQ_LEN: 15)
+    @output.write(SEQ_NAME: 'test1/2', SEQ: 'gagtcataaaaaaaa',
+                  SCORES: '!!!!!!!!!!!!!!!', SEQ_LEN: 15)
+    @output.write(SEQ_NAME: 'test2/1', SEQ: 'aaaaaaaagagGcaG',
+                  SCORES: 'IIIIIIIIIIIIIII', SEQ_LEN: 15)
+    @output.write(SEQ_NAME: 'test2/2', SEQ: 'gagtcataaaaaaaa',
+                  SCORES: '!!!!!!!!!!!!!!!', SEQ_LEN: 15)
+    @output.write(SEQ_NAME: 'test3/1', SEQ: 'aaaaaaaagagtcat',
+                  SCORES: 'IIIIIIIIIIIIIII', SEQ_LEN: 15)
+    @output.write(SEQ_NAME: 'test3/2', SEQ: 'ttttttttatgactc',
+                  SCORES: '!!!!!!!!!!!!!!!', SEQ_LEN: 15)
+    @output.write(SEQ_NAME: 'test4/1', SEQ: 'aaaaaaaaaaaaaaa',
+                  SCORES: 'IIIIIIIIIIIIIII', SEQ_LEN: 15)
+    @output.write(SEQ_NAME: 'test4/2', SEQ: 'ggggggggggggggg',
+                  SCORES: '!!!!!!!!!!!!!!!', SEQ_LEN: 15)
+    @output.write(FOO: 'SEQ')
+
+    @output.close
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline::AssemblePairs with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.assemble_pairs(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::AssemblePairs with allow_unassembled and ' \
+    'merge_unassembled raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.assemble_pairs(allow_unassembled: true, merge_unassembled: true)
+    end
+  end
+
+  test 'BioDSL::Pipeline::AssemblePairs with valid options don\'t raise' do
+    assert_nothing_raised { @p.assemble_pairs(reverse_complement: true) }
+  end
+
+  test 'BioDSL::Pipeline::AssemblePairs returns correctly' do
+    @p.assemble_pairs.run(input: @input, output: @output2)
+    expected = <<-EXP.gsub(/\s+\|/, '')
+      |{:SEQ_NAME=>"test1/1:overlap=7:hamming=0",
+      | :SEQ=>"aaaaaaaaGAGTCATaaaaaaaa",
+      | :SEQ_LEN=>23,
+      | :SCORES=>"IIIIIIII5555555!!!!!!!!",
+      | :OVERLAP_LEN=>7,
+      | :HAMMING_DIST=>0}
+      |{:SEQ_NAME=>"test2/1:overlap=3:hamming=1",
+      | :SEQ=>"aaaaaaaagaggCAGtcataaaaaaaa",
+      | :SEQ_LEN=>27,
+      | :SCORES=>"IIIIIIIIIIII555!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>3,
+      | :HAMMING_DIST=>1}
+      |{:SEQ_NAME=>"test3/1:overlap=1:hamming=0",
+      | :SEQ=>"aaaaaaaagagtcaTtttttttatgactc",
+      | :SEQ_LEN=>29,
+      | :SCORES=>"IIIIIIIIIIIIII5!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>1,
+      | :HAMMING_DIST=>0}
+      |{:FOO=>"SEQ"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::AssemblePairs status returns correctly' do
+    @p.assemble_pairs.run(input: @input, output: @output2)
+
+    assert_equal(10,  @p.status.first[:records_in])
+    assert_equal(4,   @p.status.first[:records_out])
+    assert_equal(8,   @p.status.first[:sequences_in])
+    assert_equal(8,   @p.status.first[:sequences_in])
+    assert_equal(120, @p.status.first[:residues_in])
+    assert_equal(120, @p.status.first[:residues_in])
+  end
+
+  test 'BioDSL::Pipeline::AssemblePairs with merge_unassembled: true ' \
+    'returns correctly' do
+    @p.assemble_pairs(merge_unassembled: true).
+      run(input: @input, output: @output2)
+    expected = <<-EXP.gsub(/\s+\|/, '')
+      |{:SEQ_NAME=>"test1/1:overlap=7:hamming=0",
+      | :SEQ=>"aaaaaaaaGAGTCATaaaaaaaa",
+      | :SEQ_LEN=>23,
+      | :SCORES=>"IIIIIIII5555555!!!!!!!!",
+      | :OVERLAP_LEN=>7,
+      | :HAMMING_DIST=>0}
+      |{:SEQ_NAME=>"test2/1:overlap=3:hamming=1",
+      | :SEQ=>"aaaaaaaagaggCAGtcataaaaaaaa",
+      | :SEQ_LEN=>27,
+      | :SCORES=>"IIIIIIIIIIII555!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>3, :HAMMING_DIST=>1}
+      |{:SEQ_NAME=>"test3/1:overlap=1:hamming=0",
+      | :SEQ=>"aaaaaaaagagtcaTtttttttatgactc",
+      | :SEQ_LEN=>29,
+      | :SCORES=>"IIIIIIIIIIIIII5!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>1,
+      | :HAMMING_DIST=>0}
+      |{:SEQ_NAME=>"test4/1",
+      | :SEQ=>"aaaaaaaaaaaaaaaggggggggggggggg",
+      | :SEQ_LEN=>30,
+      | :SCORES=>"IIIIIIIIIIIIIII!!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>30}
+      |{:FOO=>"SEQ"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::AssemblePairs with :mismatch_percent returns OK' do
+    @p.assemble_pairs(mismatch_percent: 0).run(input: @input, output: @output2)
+    expected = <<-EXP.gsub(/\s+\|/, '')
+      |{:SEQ_NAME=>"test1/1:overlap=7:hamming=0",
+      | :SEQ=>"aaaaaaaaGAGTCATaaaaaaaa",
+      | :SEQ_LEN=>23,
+      | :SCORES=>"IIIIIIII5555555!!!!!!!!",
+      | :OVERLAP_LEN=>7,
+      | :HAMMING_DIST=>0}
+      |{:SEQ_NAME=>"test2/1:overlap=1:hamming=0",
+      | :SEQ=>"aaaaaaaagaggcaGagtcataaaaaaaa",
+      | :SEQ_LEN=>29,
+      | :SCORES=>"IIIIIIIIIIIIII5!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>1,
+      | :HAMMING_DIST=>0}
+      |{:SEQ_NAME=>"test3/1:overlap=1:hamming=0",
+      | :SEQ=>"aaaaaaaagagtcaTtttttttatgactc",
+      | :SEQ_LEN=>29,
+      | :SCORES=>"IIIIIIIIIIIIII5!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>1,
+      | :HAMMING_DIST=>0}
+      |{:FOO=>"SEQ"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::AssemblePairs with :overlap_min returns OK' do
+    @p.assemble_pairs(overlap_min: 5).run(input: @input, output: @output2)
+    expected = <<-EXP.gsub(/\s+\|/, '')
+      |{:SEQ_NAME=>"test1/1:overlap=7:hamming=0",
+      | :SEQ=>"aaaaaaaaGAGTCATaaaaaaaa",
+      | :SEQ_LEN=>23,
+      | :SCORES=>"IIIIIIII5555555!!!!!!!!",
+      | :OVERLAP_LEN=>7,
+      | :HAMMING_DIST=>0}
+      |{:FOO=>"SEQ"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::AssemblePairs with :overlap_min and ' \
+    'merge_unassembled: true returns correctly' do
+    @p.assemble_pairs(overlap_min: 5, merge_unassembled: true).
+      run(input: @input, output: @output2)
+    expected = <<-EXP.gsub(/\s+\|/, '')
+      |{:SEQ_NAME=>"test1/1:overlap=7:hamming=0",
+      | :SEQ=>"aaaaaaaaGAGTCATaaaaaaaa",
+      | :SEQ_LEN=>23, :SCORES=>"IIIIIIII5555555!!!!!!!!",
+      | :OVERLAP_LEN=>7,
+      | :HAMMING_DIST=>0}
+      |{:SEQ_NAME=>"test2/1",
+      | :SEQ=>"aaaaaaaagagGcaGgagtcataaaaaaaa",
+      | :SEQ_LEN=>30,
+      | :SCORES=>"IIIIIIIIIIIIIII!!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>30}
+      |{:SEQ_NAME=>"test3/1",
+      | :SEQ=>"aaaaaaaagagtcatttttttttatgactc",
+      | :SEQ_LEN=>30,
+      | :SCORES=>"IIIIIIIIIIIIIII!!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>30}
+      |{:SEQ_NAME=>"test4/1",
+      | :SEQ=>"aaaaaaaaaaaaaaaggggggggggggggg",
+      | :SEQ_LEN=>30,
+      | :SCORES=>"IIIIIIIIIIIIIII!!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>30}
+      |{:FOO=>"SEQ"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::AssemblePairs with :overlap_max returns OK' do
+    @p.assemble_pairs(overlap_max: 5).run(input: @input, output: @output2)
+    expected = <<-EXP.gsub(/\s+\|/, '')
+      |{:SEQ_NAME=>"test2/1:overlap=3:hamming=1",
+      | :SEQ=>"aaaaaaaagaggCAGtcataaaaaaaa",
+      | :SEQ_LEN=>27,
+      | :SCORES=>"IIIIIIIIIIII555!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>3,
+      | :HAMMING_DIST=>1}
+      |{:SEQ_NAME=>"test3/1:overlap=1:hamming=0",
+      | :SEQ=>"aaaaaaaagagtcaTtttttttatgactc",
+      | :SEQ_LEN=>29,
+      | :SCORES=>"IIIIIIIIIIIIII5!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>1,
+      | :HAMMING_DIST=>0}
+      |{:FOO=>"SEQ"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::AssemblePairs with :reverse_complement ' \
+    'returns correctly' do
+    @p.assemble_pairs(reverse_complement: true).
+      run(input: @input, output: @output2)
+    expected = <<-EXP.gsub(/\s+\|/, '')
+      |{:SEQ_NAME=>"test1/1:overlap=1:hamming=0",
+      | :SEQ=>"aaaaaaaagagtcaTtttttttatgactc",
+      | :SEQ_LEN=>29,
+      | :SCORES=>"IIIIIIIIIIIIII5!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>1,
+      | :HAMMING_DIST=>0}
+      |{:SEQ_NAME=>"test3/1:overlap=7:hamming=0",
+      | :SEQ=>"aaaaaaaaGAGTCATaaaaaaaa",
+      | :SEQ_LEN=>23,
+      | :SCORES=>"IIIIIIII5555555!!!!!!!!",
+      | :OVERLAP_LEN=>7,
+      | :HAMMING_DIST=>0}
+      |{:FOO=>"SEQ"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::AssemblePairs with :reverse_complement and ' \
+    ':overlap_min returns correctly' do
+    @p.assemble_pairs(reverse_complement: true, overlap_min: 5).
+      run(input: @input, output: @output2)
+    expected = <<-EXP.gsub(/\s+\|/, '')
+      |{:SEQ_NAME=>"test3/1:overlap=7:hamming=0",
+      | :SEQ=>"aaaaaaaaGAGTCATaaaaaaaa",
+      | :SEQ_LEN=>23,
+      | :SCORES=>"IIIIIIII5555555!!!!!!!!",
+      | :OVERLAP_LEN=>7,
+      | :HAMMING_DIST=>0}
+      |{:FOO=>"SEQ"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::AssemblePairs with :reverse_complement and ' \
+    'overlap_max returns correctly' do
+    @p.assemble_pairs(reverse_complement: true, overlap_max: 5).
+      run(input: @input, output: @output2)
+    expected = <<-EXP.gsub(/\s+\|/, '')
+      |{:SEQ_NAME=>"test1/1:overlap=1:hamming=0",
+      | :SEQ=>"aaaaaaaagagtcaTtttttttatgactc",
+      | :SEQ_LEN=>29,
+      | :SCORES=>"IIIIIIIIIIIIII5!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>1,
+      | :HAMMING_DIST=>0}
+      |{:FOO=>"SEQ"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::AssemblePairs with :reverse_complement and ' \
+    ':overlap_min and :merge_unassembled returns correctly' do
+    @p.assemble_pairs(reverse_complement: true,
+                      overlap_min: 5, merge_unassembled: true)
+    @p.run(input: @input, output: @output2)
+    expected = <<-EXP.gsub(/\s+\|/, '')
+      |{:SEQ_NAME=>"test1/1",
+      | :SEQ=>"aaaaaaaagagtcatttttttttatgactc",
+      | :SEQ_LEN=>30,
+      | :SCORES=>"IIIIIIIIIIIIIII!!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>30}
+      |{:SEQ_NAME=>"test2/1",
+      | :SEQ=>"aaaaaaaagagGcaGttttttttatgactc",
+      | :SEQ_LEN=>30,
+      | :SCORES=>"IIIIIIIIIIIIIII!!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>30}
+      |{:SEQ_NAME=>"test3/1:overlap=7:hamming=0",
+      | :SEQ=>"aaaaaaaaGAGTCATaaaaaaaa",
+      | :SEQ_LEN=>23,
+      | :SCORES=>"IIIIIIII5555555!!!!!!!!",
+      | :OVERLAP_LEN=>7,
+      | :HAMMING_DIST=>0}
+      |{:SEQ_NAME=>"test4/1",
+      | :SEQ=>"aaaaaaaaaaaaaaaccccccccccccccc",
+      | :SEQ_LEN=>30,
+      | :SCORES=>"IIIIIIIIIIIIIII!!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>30}
+      |{:FOO=>"SEQ"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::AssemblePairs with allow_unassembled returns OK' do
+    @p.assemble_pairs(overlap_min: 100, allow_unassembled: true).
+      run(input: @input, output: @output2)
+    expected = <<-EXP.gsub(/\s+\|/, '')
+      |{:SEQ_NAME=>"test1/1",
+      | :SEQ=>"aaaaaaaagagtcat",
+      | :SEQ_LEN=>15,
+      | :SCORES=>"IIIIIIIIIIIIIII",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>15}
+      |{:SEQ_NAME=>"test1/2",
+      | :SEQ=>"gagtcataaaaaaaa",
+      | :SEQ_LEN=>15,
+      | :SCORES=>"!!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>15}
+      |{:SEQ_NAME=>"test2/1",
+      | :SEQ=>"aaaaaaaagagGcaG",
+      | :SEQ_LEN=>15,
+      | :SCORES=>"IIIIIIIIIIIIIII",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>15}
+      |{:SEQ_NAME=>"test2/2",
+      | :SEQ=>"gagtcataaaaaaaa",
+      | :SEQ_LEN=>15,
+      | :SCORES=>"!!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>15}
+      |{:SEQ_NAME=>"test3/1",
+      | :SEQ=>"aaaaaaaagagtcat",
+      | :SEQ_LEN=>15,
+      | :SCORES=>"IIIIIIIIIIIIIII",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>15}
+      |{:SEQ_NAME=>"test3/2",
+      | :SEQ=>"ttttttttatgactc",
+      | :SEQ_LEN=>15,
+      | :SCORES=>"!!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>15}
+      |{:SEQ_NAME=>"test4/1",
+      | :SEQ=>"aaaaaaaaaaaaaaa",
+      | :SEQ_LEN=>15,
+      | :SCORES=>"IIIIIIIIIIIIIII",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>15}
+      |{:SEQ_NAME=>"test4/2",
+      | :SEQ=>"ggggggggggggggg",
+      | :SEQ_LEN=>15,
+      | :SCORES=>"!!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>15}
+      |{:FOO=>"SEQ"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::AssemblePairs with allow_unassembled and ' \
+    'reverse_complement returns OK' do
+    @p.assemble_pairs(overlap_min: 100, allow_unassembled: true,
+                      reverse_complement: true)
+    @p.run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/\s+\|/, '')
+      |{:SEQ_NAME=>"test1/1",
+      | :SEQ=>"aaaaaaaagagtcat",
+      | :SEQ_LEN=>15,
+      | :SCORES=>"IIIIIIIIIIIIIII",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>15}
+      |{:SEQ_NAME=>"test1/2",
+      | :SEQ=>"ttttttttatgactc",
+      | :SEQ_LEN=>15,
+      | :SCORES=>"!!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>15}
+      |{:SEQ_NAME=>"test2/1",
+      | :SEQ=>"aaaaaaaagagGcaG",
+      | :SEQ_LEN=>15,
+      | :SCORES=>"IIIIIIIIIIIIIII",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>15}
+      |{:SEQ_NAME=>"test2/2",
+      | :SEQ=>"ttttttttatgactc",
+      | :SEQ_LEN=>15,
+      | :SCORES=>"!!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>15}
+      |{:SEQ_NAME=>"test3/1",
+      | :SEQ=>"aaaaaaaagagtcat",
+      | :SEQ_LEN=>15,
+      | :SCORES=>"IIIIIIIIIIIIIII",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>15}
+      |{:SEQ_NAME=>"test3/2",
+      | :SEQ=>"gagtcataaaaaaaa",
+      | :SEQ_LEN=>15,
+      | :SCORES=>"!!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>15}
+      |{:SEQ_NAME=>"test4/1",
+      | :SEQ=>"aaaaaaaaaaaaaaa",
+      | :SEQ_LEN=>15,
+      | :SCORES=>"IIIIIIIIIIIIIII",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>15}
+      |{:SEQ_NAME=>"test4/2",
+      | :SEQ=>"ccccccccccccccc",
+      | :SEQ_LEN=>15,
+      | :SCORES=>"!!!!!!!!!!!!!!!",
+      | :OVERLAP_LEN=>0,
+      | :HAMMING_DIST=>15}
+      |{:FOO=>"SEQ"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+end

data/test/BioDSL/commands/test_assemble_seq_idba.rb

@@ -0,0 +1,50 @@
+#!/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 AssembleSeqIdba.
+class TestAssembleSeqIdba < Test::Unit::TestCase
+  def setup
+    omit('idba_ud not found') unless BioDSL::Filesys.which('idba_ud')
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline::AssembleSeqIdba with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.assemble_seq_idba(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::AssembleSeqIdba with valid options don\'t raise' do
+    assert_nothing_raised { @p.assemble_seq_idba(cpus: 1) }
+  end
+
+  # FIXME: tests missing!
+end

data/test/BioDSL/commands/test_assemble_seq_ray.rb

@@ -0,0 +1,51 @@
+#!/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 AssembleSeqRay.
+class TestAssembleSeqRay < Test::Unit::TestCase
+  def setup
+    omit('ray not found')     unless BioDSL::Filesys.which('ray')
+    omit('mpiexec not found') unless BioDSL::Filesys.which('mpiexec')
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline::AssembleSeqRay with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.assemble_seq_ray(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::AssembleSeqRay with valid options don\'t raise' do
+    assert_nothing_raised { @p.assemble_seq_ray(cpus: 1) }
+  end
+
+  # FIXME: tests missing!
+end

data/test/BioDSL/commands/test_assemble_seq_spades.rb

@@ -0,0 +1,50 @@
+#!/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 AssembleSeqSpandes.
+class TestAssembleSeqSpades < Test::Unit::TestCase
+  def setup
+    omit('spades.py not found') unless BioDSL::Filesys.which('spades.py')
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline::AssembleSeqSpades with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.assemble_seq_spades(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::AssembleSeqSpades with OK options dont raise' do
+    assert_nothing_raised { @p.assemble_seq_spades(cpus: 1) }
+  end
+
+  # TODO: Fix missing testing here!
+end

data/test/BioDSL/commands/test_classify_seq.rb

@@ -0,0 +1,50 @@
+#!/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 ClassifySeq.
+class TestClassifySeq < Test::Unit::TestCase
+  def setup
+    @p = BP.new
+  end
+
+  test 'BioDSL::Pipeline#classify_seq with disallowed option raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.classify_seq(dir: Dir.pwd, foo: 'bar')
+    end
+  end
+
+  test 'BioDSL::Pipeline#classify_seq with allowed option dont raise' do
+    assert_nothing_raised { @p.classify_seq(dir: Dir.pwd) }
+  end
+
+  # TODO: write tests!
+end