BioDSL 1.0.0

data/test/BioDSL/commands/test_read_fastq.rb

@@ -0,0 +1,552 @@
+#!/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 ReadFastq.
+#
+# rubocop: disable LineLength
+# rubocop: disable ClassLength
+class TestReadFastq < Test::Unit::TestCase
+  def setup
+    @tmpdir = Dir.mktmpdir('BioDSL')
+
+    setup_file1
+    setup_file2
+    setup_file3
+    setup_file4
+    setup_file5
+    setup_file6
+    setup_data
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  def setup_file1
+    @file = File.join(@tmpdir, 'test.fq')
+
+    File.open(@file, 'w') do |ios|
+      ios.puts <<-'EOF'.gsub(/^\s+\|/, '')
+        |@base_33
+        |aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+        |+
+        |!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
+        |@base_64
+        |bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
+        |+
+        |;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
+      EOF
+    end
+  end
+
+  def setup_file2
+    @file2 = File.join(@tmpdir, 'test2.fq')
+
+    File.open(@file2, 'w') do |ios|
+      ios.puts <<-EOF.gsub(/^\s+\|/, '')
+        |@M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14
+        |TGGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCA
+        |+
+        |<??????BDDDDDDDDGGGGGGGHHIIIEHIHHFGGHFH
+        |@M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14
+        |TAGGGAATCTTGCACAATGGAGGAAACTCTGATGCAGCG
+        |+
+        |<???9?BBBDBDDBDDFFFFFFHHHIFHFHHIHHFHHHH
+      EOF
+    end
+  end
+
+  def setup_file3
+    @file3 = File.join(@tmpdir, 'test3.fq')
+
+    File.open(@file3, 'w') do |ios|
+      ios.puts <<-EOF.gsub(/^\s+\|/, '')
+        |@M01168:16:000000000-A1R9L:1:1101:14862:1868 2:N:0:14
+        |CCTGTTTGCTACCCACGCTTTCGTACCTCAGCGTCAGTA
+        |+
+        |?????BB<-<BDDDDDFEEFFFHFFHI;F;EGHHDHEF9
+        |@M01168:16:000000000-A1R9L:1:1101:13906:2139 2:N:0:14
+        |ACTCTTCGCTACCCATGCTTTCGTTCCTCAGCGTCAGTA
+        |+
+        |,5<??BB?DDABDBDDFFFFFFHFHIHFHHIIHEHEHF?
+      EOF
+    end
+  end
+
+  def setup_file4
+    @file4 = File.join(@tmpdir, 'base64.fastq')
+
+    File.open(@file4, 'w') do |ios|
+      ios.puts <<-'EOF'.gsub(/^\s+\|/, '')
+        |@base_64
+        |bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
+        |+
+        |;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
+      EOF
+    end
+  end
+
+  def setup_file5
+    @file5 = File.join(@tmpdir, 'base64_2.fastq')
+
+    File.open(@file5, 'w') do |ios|
+      ios.puts <<-'EOF'.gsub(/^\s+\|/, '')
+        |@base_64_2
+        |bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
+        |+
+        |=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|
+      EOF
+    end
+  end
+
+  def setup_file6
+    @file6 = File.join(@tmpdir, 'inconclusive.fastq')
+
+    File.open(@file6, 'w') do |ios|
+      ios.puts <<-EOF.gsub(/^\s+\|/, '')
+        |@base_base33
+        |bbbbbbbbbbbbbbbb
+        |+
+        |;<=>?@ABCDEFGHIJ
+      EOF
+    end
+  end
+
+  def setup_data
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    @output.write(SEQ_NAME: 'test1', SEQ: 'atgcagcac', SEQ_LEN: 9)
+    @output.write(SEQ_NAME: 'test2', SEQ: 'acagcactgA', SEQ_LEN: 10)
+    @output.close
+  end
+
+  def teardown
+    FileUtils.rm_r @tmpdir
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.read_fastq(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq without required options raises' do
+    assert_raise(BioDSL::OptionError) { @p.read_fastq }
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with bad first raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.read_fastq(input: @file, first: -1)
+    end
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with bad last raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.read_fastq(input: @file, last: -1)
+    end
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with exclusive unique options raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.read_fastq(input: @file, first: 1, last: 1)
+    end
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with non-existing input file raises' do
+    assert_raise(BioDSL::OptionError) { @p.read_fastq(input: '___adsf') }
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with non-existing input2 file raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.read_fastq(input: '___adsf', input2: '___xsdf')
+    end
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with uneven sized input and ' \
+    'input2 raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.read_fastq(input: [@file, @file2], input2: @file3).run
+    end
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with input and non-conclusive ' \
+    'encoding raises' do
+    assert_raise(BioDSL::SeqError) { @p.read_fastq(input: @file6).run }
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with input and input2 and ' \
+    'non-conclusive encoding raises' do
+    assert_raise(BioDSL::SeqError) do
+      @p.read_fastq(input: @file6, input2: @file6).run
+    end
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with encoding and bad value raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.read_fastq(input: @file6, encoding: :foo).run
+    end
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with encoding: :auto don\'t raise' do
+    assert_nothing_raised { @p.read_fastq(input: @file, encoding: :auto).run }
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with encoding: :base_33 don\'t raise' do
+    assert_nothing_raised do
+      @p.read_fastq(input: @file2, encoding: :base_33).run
+    end
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with encoding: :base_64 don\'t raise' do
+    assert_nothing_raised do
+      @p.read_fastq(input: @file4, encoding: :base_64).run
+    end
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq returns correctly' do
+    @p.read_fastq(input: @file).run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"base_33",
+      | :SEQ=>"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
+      | :SEQ_LEN=>94,
+      | :SCORES=>"!\\\"\\\#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"}
+      |{:SEQ_NAME=>"base_64",
+      | :SEQ=>"bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb",
+      | :SEQ_LEN=>68,
+      | :SCORES=>";<=>?@ABCDEFGHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq status returns correctly' do
+    @p.read_fastq(input: @file).run(output: @output2)
+
+    assert_equal(0,   @p.status.first[:records_in])
+    assert_equal(2,   @p.status.first[:records_out])
+    assert_equal(0,   @p.status.first[:sequences_in])
+    assert_equal(2,   @p.status.first[:sequences_out])
+    assert_equal(0,   @p.status.first[:residues_in])
+    assert_equal(162, @p.status.first[:residues_out])
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with gzipped data returns correctly' do
+    `gzip #{@file}`
+
+    @p.read_fastq(input: "#{@file}.gz").run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"base_33",
+      | :SEQ=>"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
+      | :SEQ_LEN=>94,
+      | :SCORES=>"!\\\"\\\#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"}
+      |{:SEQ_NAME=>"base_64",
+      | :SEQ=>"bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb",
+      | :SEQ_LEN=>68,
+      | :SCORES=>";<=>?@ABCDEFGHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with bzip2\'ed data returns correctly' do
+    `bzip2 #{@file}`
+
+    @p.read_fastq(input: "#{@file}.bz2").run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"base_33",
+      | :SEQ=>"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
+      | :SEQ_LEN=>94,
+      | :SCORES=>"!\\\"\\\#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"}
+      |{:SEQ_NAME=>"base_64",
+      | :SEQ=>"bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb",
+      | :SEQ_LEN=>68,
+      | :SCORES=>";<=>?@ABCDEFGHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with multiple files returns correctly' do
+    @p.read_fastq(input: [@file, @file2]).run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"base_33",
+      | :SEQ=>"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
+      | :SEQ_LEN=>94,
+      | :SCORES=>"!\\\"\\\#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"}
+      |{:SEQ_NAME=>"base_64",
+      | :SEQ=>"bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb",
+      | :SEQ_LEN=>68,
+      | :SCORES=>";<=>?@ABCDEFGHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14",
+      | :SEQ=>"TGGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCA",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"<??????BDDDDDDDDGGGGGGGHHIIIEHIHHFGGHFH"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14",
+      | :SEQ=>"TAGGGAATCTTGCACAATGGAGGAAACTCTGATGCAGCG",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"<???9?BBBDBDDBDDFFFFFFHHHIFHFHHIHHFHHHH"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with input glob returns correctly' do
+    @p.read_fastq(input: File.join(@tmpdir, 'test*.fq')).run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"base_33",
+      | :SEQ=>"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
+      | :SEQ_LEN=>94,
+      | :SCORES=>"!\\\"\\\#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"}
+      |{:SEQ_NAME=>"base_64",
+      | :SEQ=>"bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb",
+      | :SEQ_LEN=>68,
+      | :SCORES=>";<=>?@ABCDEFGHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14",
+      | :SEQ=>"TGGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCA",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"<??????BDDDDDDDDGGGGGGGHHIIIEHIHHFGGHFH"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14",
+      | :SEQ=>"TAGGGAATCTTGCACAATGGAGGAAACTCTGATGCAGCG",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"<???9?BBBDBDDBDDFFFFFFHHHIFHFHHIHHFHHHH"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14862:1868 2:N:0:14",
+      | :SEQ=>"CCTGTTTGCTACCCACGCTTTCGTACCTCAGCGTCAGTA",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"?????BB<-<BDDDDDFEEFFFHFFHI;F;EGHHDHEF9"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:13906:2139 2:N:0:14",
+      | :SEQ=>"ACTCTTCGCTACCCATGCTTTCGTTCCTCAGCGTCAGTA",
+      | :SEQ_LEN=>39,
+      | :SCORES=>",5<??BB?DDABDBDDFFFFFFHFHIHFHHIIHEHEHF?"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with :first returns correctly' do
+    @p.read_fastq(input: [@file, @file2], first: 3).run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"base_33",
+      | :SEQ=>"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
+      | :SEQ_LEN=>94,
+      | :SCORES=>"!\\\"\\\#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"}
+      |{:SEQ_NAME=>"base_64",
+      | :SEQ=>"bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb",
+      | :SEQ_LEN=>68,
+      | :SCORES=>";<=>?@ABCDEFGHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14",
+      | :SEQ=>"TGGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCA",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"<??????BDDDDDDDDGGGGGGGHHIIIEHIHHFGGHFH"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq#to_s with :first returns correctly' do
+    @p.read_fastq(input: @file, first: 3)
+
+    expected = %{BP.new.read_fastq(input: "#{@file}", first: 3)}
+
+    assert_equal(expected, @p.to_s)
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with :last returns correctly' do
+    @p.read_fastq(input: [@file, @file2], last: 3).run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"base_64",
+      | :SEQ=>"bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb",
+      | :SEQ_LEN=>68,
+      | :SCORES=>";<=>?@ABCDEFGHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14",
+      | :SEQ=>"TGGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCA",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"<??????BDDDDDDDDGGGGGGGHHIIIEHIHHFGGHFH"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14",
+      | :SEQ=>"TAGGGAATCTTGCACAATGGAGGAAACTCTGATGCAGCG",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"<???9?BBBDBDDBDDFFFFFFHHHIFHFHHIHHFHHHH"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with :input and :input2 returns OK' do
+    @p.read_fastq(input: @file2, input2: @file3, encoding: :base_33).
+      run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14",
+      | :SEQ=>"TGGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCA",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"<??????BDDDDDDDDGGGGGGGHHIIIEHIHHFGGHFH"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14862:1868 2:N:0:14",
+      | :SEQ=>"CCTGTTTGCTACCCACGCTTTCGTACCTCAGCGTCAGTA",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"?????BB<-<BDDDDDFEEFFFHFFHI;F;EGHHDHEF9"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14",
+      | :SEQ=>"TAGGGAATCTTGCACAATGGAGGAAACTCTGATGCAGCG",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"<???9?BBBDBDDBDDFFFFFFHHHIFHFHHIHHFHHHH"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:13906:2139 2:N:0:14",
+      | :SEQ=>"ACTCTTCGCTACCCATGCTTTCGTTCCTCAGCGTCAGTA",
+      | :SEQ_LEN=>39,
+      | :SCORES=>",5<??BB?DDABDBDDFFFFFFHFHIHFHHIIHEHEHF?"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq status with :input and :input2 ' \
+    'returns correctly' do
+    @p.read_fastq(input: @file2, input2: @file3, encoding: :base_33).
+      run(output: @output2)
+
+    assert_equal(156, @p.status.first[:residues_out])
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with :input and :input2 and ' \
+    ':first returns correctly' do
+    @p.read_fastq(input: @file2, input2: @file3, encoding: :base_33, first: 2).
+      run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14",
+      | :SEQ=>"TGGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCA",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"<??????BDDDDDDDDGGGGGGGHHIIIEHIHHFGGHFH"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14862:1868 2:N:0:14",
+      | :SEQ=>"CCTGTTTGCTACCCACGCTTTCGTACCTCAGCGTCAGTA",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"?????BB<-<BDDDDDFEEFFFHFFHI;F;EGHHDHEF9"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with :input and :input2 and :last ' \
+    'returns correctly' do
+    @p.read_fastq(input: @file2, input2: @file3, last: 2, encoding: :base_33).
+      run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14",
+      | :SEQ=>"TAGGGAATCTTGCACAATGGAGGAAACTCTGATGCAGCG",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"<???9?BBBDBDDBDDFFFFFFHHHIFHFHHIHHFHHHH"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:13906:2139 2:N:0:14",
+      | :SEQ=>"ACTCTTCGCTACCCATGCTTTCGTTCCTCAGCGTCAGTA",
+      | :SEQ_LEN=>39,
+      | :SCORES=>",5<??BB?DDABDBDDFFFFFFHFHIHFHHIIHEHEHF?"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with base_64 :input returns correctly' do
+    @p.read_fastq(input: @file4).run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"base_64",
+      | :SEQ=>"bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb",
+      | :SEQ_LEN=>68,
+      | :SCORES=>"!!!!!!\\\"\\\#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIIIIIIIIIIIIIIIIIIIIIII\"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with base_64 :input and :input2 ' \
+    'returns correctly' do
+    @p.read_fastq(input: @file4, input2: @file5).run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"base_64",
+      | :SEQ=>"bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb",
+      | :SEQ_LEN=>68,
+      | :SCORES=>"!!!!!!\\\"\\\#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIIIIIIIIIIIIIIIIIIIIIII\"}
+      |{:SEQ_NAME=>"base_64_2",
+      | :SEQ=>"bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb",
+      | :SEQ_LEN=>64,
+      | :SCORES=>"!!!!\\\"\\\#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIIIIIIIIIIIIIIIIIIIII\"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with base_64 :input and :input2 and ' \
+    ':reverse_complement returns correctly' do
+    @p.read_fastq(input: @file2, input2: @file3, first: 2,
+                  reverse_complement: true, encoding: :base_33).
+      run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14",
+      | :SEQ=>"TGGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCA",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"<??????BDDDDDDDDGGGGGGGHHIIIEHIHHFGGHFH"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14862:1868 2:N:0:14",
+      | :SEQ=>"TACTGACGCTGAGGTACGAAAGCGTGGGTAGCAAACAGG",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"9FEHDHHGE;F;IHFFHFFFEEFDDDDDB<-<BB?????"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::ReadFastq with flux returns correctly' do
+    @p.read_fastq(input: @file2, encoding: :base_33).
+      run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"test1",
+      | :SEQ=>"atgcagcac",
+      | :SEQ_LEN=>9}
+      |{:SEQ_NAME=>"test2",
+      | :SEQ=>"acagcactgA",
+      | :SEQ_LEN=>10}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14",
+      | :SEQ=>"TGGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCA",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"<??????BDDDDDDDDGGGGGGGHHIIIEHIHHFGGHFH"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14",
+      | :SEQ=>"TAGGGAATCTTGCACAATGGAGGAAACTCTGATGCAGCG",
+      | :SEQ_LEN=>39,
+      | :SCORES=>"<???9?BBBDBDDBDDFFFFFFHHHIFHFHHIHHFHHHH"}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_result.delete("\n"))
+  end
+end