BioDSL 1.0.0

data/test/BioDSL/commands/test_collect_otus.rb

@@ -0,0 +1,82 @@
+#!/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 CollectOtus.
+class TestCollectOtus < Test::Unit::TestCase
+  def setup
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    @output.write(one: 1, two: 2, three: 3)
+    @output.write(TYPE: 'H', S_ID: 'OTU_0', SAMPLE: 'Sample0')
+    @output.write(TYPE: 'H', S_ID: 'OTU_0', SAMPLE: 'Sample0')
+    @output.write(TYPE: 'H', S_ID: 'OTU_0', SAMPLE: 'Sample1')
+    @output.write(TYPE: 'H', S_ID: 'OTU_1', SAMPLE: 'Sample0')
+    @output.write(TYPE: 'H', S_ID: 'OTU_1', SAMPLE: 'Sample1')
+    @output.write(TYPE: 'H', S_ID: 'OTU_1', SAMPLE: 'Sample1')
+    @output.close
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline#collect_otus with disallowed option raises' do
+    assert_raise(BioDSL::OptionError) { @p.collect_otus(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline#collect_otus outputs correctly' do
+    @p.collect_otus.run(input: @input, output: @output2)
+    expected = <<-EXP.gsub(/^\s+\|/, '').delete("\n")
+      |{:one=>1, :two=>2, :three=>3}
+      |{:TYPE=>"H", :S_ID=>"OTU_0", :SAMPLE=>"Sample0"}
+      |{:TYPE=>"H", :S_ID=>"OTU_0", :SAMPLE=>"Sample0"}
+      |{:TYPE=>"H", :S_ID=>"OTU_0", :SAMPLE=>"Sample1"}
+      |{:TYPE=>"H", :S_ID=>"OTU_1", :SAMPLE=>"Sample0"}
+      |{:TYPE=>"H", :S_ID=>"OTU_1", :SAMPLE=>"Sample1"}
+      |{:TYPE=>"H", :S_ID=>"OTU_1", :SAMPLE=>"Sample1"}
+      |{:RECORD_TYPE=>"OTU", :OTU=>"OTU_0", :SAMPLE0_COUNT=>2,
+      | :SAMPLE1_COUNT=>1}
+      |{:RECORD_TYPE=>"OTU", :OTU=>"OTU_1", :SAMPLE0_COUNT=>1,
+      | :SAMPLE1_COUNT=>2}
+    EXP
+
+    assert_equal(expected, collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline#collect_otus status outputs correctly' do
+    @p.collect_otus.run(input: @input, output: @output2)
+
+    assert_equal(7, @p.status.first[:records_in])
+    assert_equal(9, @p.status.first[:records_out])
+    assert_equal(6, @p.status.first[:hits_in])
+    assert_equal(2, @p.status.first[:hits_out])
+  end
+end

data/test/BioDSL/commands/test_complement_seq.rb

@@ -0,0 +1,78 @@
+#!/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 ComplementSeq.
+class TestComplementSeq < Test::Unit::TestCase
+  def setup
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline::ComplementSeq with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.complement_seq(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::ComplementSeq of DNA returns correctly' do
+    @output.write(SEQ: 'gatcGATCGT')
+    @output.close
+    @p.complement_seq.run(input: @input, output: @output2)
+
+    expected = '{:SEQ=>"ctagCTAGCA", :SEQ_LEN=>10}'
+
+    assert_equal(expected, collect_result.chomp)
+  end
+
+  test 'BioDSL::Pipeline::ComplementSeq of RNA returns correctly' do
+    @output.write(SEQ: 'gaucGAUCGU')
+    @output.close
+    @p.complement_seq.run(input: @input, output: @output2)
+
+    expected = '{:SEQ=>"cuagCUAGCA", :SEQ_LEN=>10}'
+
+    assert_equal(expected, collect_result.chomp)
+  end
+
+  test 'BioDSL::Pipeline::ComplementSeq status returns correctly' do
+    @output.write(SEQ: 'gaucGAUCGU')
+    @output.close
+    @p.complement_seq.run(input: @input, output: @output2)
+
+    assert_equal(1, @p.status.first[:records_in])
+    assert_equal(1, @p.status.first[:records_out])
+    assert_equal(1, @p.status.first[:sequences_in])
+    assert_equal(1, @p.status.first[:sequences_out])
+    assert_equal(10, @p.status.first[:residues_in])
+    assert_equal(10, @p.status.first[:residues_out])
+  end
+end

data/test/BioDSL/commands/test_count.rb

@@ -0,0 +1,103 @@
+#!/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 Count.
+class TestCount < Test::Unit::TestCase
+  def setup
+    @tmpdir = Dir.mktmpdir('BioDSL')
+    @file   = File.join(@tmpdir, 'test.txt')
+    @file2  = File.join(@tmpdir, 'test.txt')
+
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    @output.write(SEQ_NAME: 'test1', SEQ: 'atcg', SEQ_LEN: 4)
+    @output.write(SEQ_NAME: 'test2', SEQ: 'gtac', SEQ_LEN: 4)
+    @output.close
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  def teardown
+    FileUtils.rm_r @tmpdir
+  end
+
+  test 'BioDSL::Pipeline::Count with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.count(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::Count with valid options don\'t raise' do
+    assert_nothing_raised { @p.count(output: @file) }
+  end
+
+  test 'BioDSL::Pipeline::Count to file outputs correctly' do
+    @p.count(output: @file).run(input: @input, output: @output2)
+    result = File.open(@file).read
+    expected = "#RECORD_TYPE\tCOUNT\ncount\t2\n"
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::Count to existing file raises' do
+    `touch #{@file}`
+    assert_raise(BioDSL::OptionError) { @p.count(output: @file) }
+  end
+
+  test 'BioDSL::Pipeline::Count to existing file with :force outputs OK' do
+    `touch #{@file}`
+    @p.count(output: @file, force: true).run(input: @input)
+    result = File.open(@file).read
+    expected = "#RECORD_TYPE\tCOUNT\ncount\t2\n"
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::Count with flux outputs correctly' do
+    @p.count(output: @file).run(input: @input, output: @output2)
+    result = File.open(@file).read
+    expected = "#RECORD_TYPE\tCOUNT\ncount\t2\n"
+    assert_equal(expected, result)
+
+    stream_expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"test1", :SEQ=>"atcg", :SEQ_LEN=>4}
+      |{:SEQ_NAME=>"test2", :SEQ=>"gtac", :SEQ_LEN=>4}
+      |{:RECORD_TYPE=>"count", :COUNT=>2}
+    EXP
+
+    assert_equal(stream_expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::Count status outputs correctly' do
+    @p.count.run(input: @input, output: @output2)
+
+    assert_equal(2, @p.status.first[:records_in])
+    assert_equal(3, @p.status.first[:records_out])
+  end
+end

data/test/BioDSL/commands/test_count_values.rb

@@ -0,0 +1,85 @@
+#!/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 CountValues.
+class TestCountValues < Test::Unit::TestCase
+  def setup
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    [{V0: 'HUMAN', V1: 'H1'},
+     {V0: 'HUMAN', V1: 'H2'},
+     {V0: 'HUMAN', V1: 'H3'},
+     {V0: 'DOG',   V1: 'D1'},
+     {V0: 'DOG',   V1: 'D2'},
+     {V0: 'MOUSE', V1: 'M1'}
+    ].each do |record|
+      @output.write record
+    end
+
+    @output.close
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline#count_values with disallowed option raises' do
+    assert_raise(BioDSL::OptionError) { @p.count_values(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline#count_values with allowed options don\'t raise' do
+    assert_nothing_raised { @p.count_values(keys: [:V0]) }
+  end
+
+  test 'BioDSL::Pipeline#count_values returns correctly' do
+    @p.count_values(keys: ['V0', :V1, :FOO]).
+      run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:V0=>"HUMAN", :V1=>"H1", :V0_COUNT=>3, :V1_COUNT=>1}
+      |{:V0=>"HUMAN", :V1=>"H2", :V0_COUNT=>3, :V1_COUNT=>1}
+      |{:V0=>"HUMAN", :V1=>"H3", :V0_COUNT=>3, :V1_COUNT=>1}
+      |{:V0=>"DOG", :V1=>"D1", :V0_COUNT=>2, :V1_COUNT=>1}
+      |{:V0=>"DOG", :V1=>"D2", :V0_COUNT=>2, :V1_COUNT=>1}
+      |{:V0=>"MOUSE", :V1=>"M1", :V0_COUNT=>1, :V1_COUNT=>1}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline#count_values status returns correctly' do
+    @p.count_values(keys: ['V0', :V1, :FOO]).
+      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_degap_seq.rb

@@ -0,0 +1,96 @@
+#!/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 DegapSeq.
+class TestDegapSeq < Test::Unit::TestCase
+  def setup
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline::DegapSeq with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.degap_seq(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::DegapSeq with valid options don\'t raise' do
+    assert_nothing_raised { @p.degap_seq(columns_only: true) }
+  end
+
+  test 'BioDSL::Pipeline::DegapSeq returns correctly' do
+    @output.write(SEQ: 'AT--C.G~')
+    @output.close
+    @p.degap_seq.run(input: @input, output: @output2)
+
+    expected = '{:SEQ=>"ATCG", :SEQ_LEN=>4}'
+
+    assert_equal(expected, collect_result.chomp)
+  end
+
+  test 'BioDSL::Pipeline::DegapSeq status returns correctly' do
+    @output.write(SEQ: 'AT--C.G~')
+    @output.close
+    @p.degap_seq.run(input: @input, output: @output2)
+
+    assert_equal(1, @p.status.first[:records_in])
+    assert_equal(1, @p.status.first[:records_out])
+    assert_equal(1, @p.status.first[:sequences_in])
+    assert_equal(1, @p.status.first[:sequences_out])
+    assert_equal(8, @p.status.first[:residues_in])
+    assert_equal(4, @p.status.first[:residues_out])
+  end
+
+  test 'BioDSL::Pipeline::DegapSeq with :columns_only and uneven seq ' \
+    'lengths raises' do
+    @output.write(SEQ: 'AT--C.G~')
+    @output.write(SEQ: 'AT--C.G')
+    @output.close
+    assert_raise(BioDSL::SeqError) do
+      @p.degap_seq(columns_only: true).run(input: @input, output: @output2)
+    end
+  end
+
+  test 'BioDSL::Pipeline::DegapSeq with :columns_only returns correctly' do
+    @output.write(SEQ: 'ATA-C.G~')
+    @output.write(SEQ: 'AT--C.G.')
+    @output.close
+    @p.degap_seq(columns_only: true).run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ=>"ATACG", :SEQ_LEN=>5}
+      |{:SEQ=>"AT-CG", :SEQ_LEN=>5}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+end

data/test/BioDSL/commands/test_dereplicate_seq.rb

@@ -0,0 +1,92 @@
+#!/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 DereplicateSeq.
+class TestDereplicateSeq < Test::Unit::TestCase
+  def setup
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    @output.write(SEQ_NAME: 'test1', SEQ: 'ATCG')
+    @output.write(SEQ_NAME: 'test2', SEQ: 'ATCG')
+    @output.write(SEQ_NAME: 'test3', SEQ: 'atcg')
+    @output.write(SEQ_NAME: 'test4', SEQ: 'GCTA')
+    @output.write(FISH: 'eel')
+    @output.close
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline::DereplicateSeq with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.dereplicate_seq(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::DereplicateSeq with valid options don\'t raise' do
+    assert_nothing_raised { @p.dereplicate_seq(ignore_case: true) }
+  end
+
+  test 'BioDSL::Pipeline::DereplicateSeq returns correctly' do
+    @p.dereplicate_seq.run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:FISH=>"eel"}
+      |{:SEQ_NAME=>"test1", :SEQ=>"ATCG", :SEQ_COUNT=>2}
+      |{:SEQ_NAME=>"test3", :SEQ=>"atcg", :SEQ_COUNT=>1}
+      |{:SEQ_NAME=>"test4", :SEQ=>"GCTA", :SEQ_COUNT=>1}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::DereplicateSeq status returns correctly' do
+    @p.dereplicate_seq.run(input: @input, output: @output2)
+
+    assert_equal(5,  @p.status.first[:records_in])
+    assert_equal(4,  @p.status.first[:records_out])
+    assert_equal(4,  @p.status.first[:sequences_in])
+    assert_equal(3,  @p.status.first[:sequences_out])
+    assert_equal(16, @p.status.first[:residues_in])
+    assert_equal(12, @p.status.first[:residues_out])
+  end
+
+  test 'BioDSL::Pipeline::DereplicateSeq with ignore_case returns OK' do
+    @p.dereplicate_seq(ignore_case: true).run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:FISH=>"eel"}
+      |{:SEQ_NAME=>"test1", :SEQ=>"ATCG", :SEQ_COUNT=>3}
+      |{:SEQ_NAME=>"test4", :SEQ=>"GCTA", :SEQ_COUNT=>1}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+end

data/test/BioDSL/commands/test_dump.rb

@@ -0,0 +1,109 @@
+#!/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 the dump command.
+class TestDump < Test::Unit::TestCase
+  def setup
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    @output.write(one: 1, two: 2, three: 3)
+    @output.write(SEQ_NAME: 'test1', SEQ: 'atcg', SEQ_LEN: 4)
+    @output.write(SEQ_NAME: 'test2', SEQ: 'gtac', SEQ_LEN: 4)
+    @output.close
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline#dump with disallowed option raises' do
+    assert_raise(BioDSL::OptionError) { @p.dump(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline#dump with bad first raises' do
+    assert_raise(BioDSL::OptionError) { @p.dump(first: 0) }
+  end
+
+  test 'BioDSL::Pipeline#dump with bad last raises' do
+    assert_raise(BioDSL::OptionError) { @p.dump(last: 0) }
+  end
+
+  test 'BioDSL::Pipeline#dump with first and last raises' do
+    assert_raise(BioDSL::OptionError) { @p.dump(first: 1, last: 1) }
+  end
+
+  test 'BioDSL::Pipeline#dump returns correctly' do
+    result1 = capture_stdout { @p.dump.run(input: @input, output: @output2) }
+    result2 = collect_result
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:one=>1, :two=>2, :three=>3}
+      |{:SEQ_NAME=>\"test1\", :SEQ=>\"atcg\", :SEQ_LEN=>4}
+      |{:SEQ_NAME=>\"test2\", :SEQ=>\"gtac\", :SEQ_LEN=>4}
+    EXP
+
+    assert_equal(expected, result1)
+    assert_equal(expected, result2)
+  end
+
+  test 'BioDSL::Pipeline#dump status returns correctly' do
+    capture_stdout { @p.dump.run(input: @input, output: @output2) }
+
+    assert_equal(3, @p.status.first[:records_in])
+    assert_equal(3, @p.status.first[:records_out])
+  end
+
+  test 'BioDSL::Pipeline#dump with options[first: 1] returns correctly' do
+    result1 = capture_stdout do
+      @p.dump(first: 1).run(input: @input, output: @output2)
+    end
+
+    result2 = collect_result
+
+    expected = "{:one=>1, :two=>2, :three=>3}\n"
+
+    assert_equal(expected, result1)
+    assert_equal(expected, result2)
+  end
+
+  test 'BioDSL::Pipeline#dump with options[last: 1] returns correctly' do
+    result1 = capture_stdout do
+      @p.dump(last: 1).run(input: @input, output: @output2)
+    end
+
+    result2 = collect_result
+
+    expected = "{:SEQ_NAME=>\"test2\", :SEQ=>\"gtac\", :SEQ_LEN=>4}\n"
+
+    assert_equal(expected, result1)
+    assert_equal(expected, result2)
+  end
+end