BioDSL 1.0.0

data/test/BioDSL/commands/test_slice_seq.rb

@@ -0,0 +1,131 @@
+#!/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 SliceSeq.
+class TestSliceSeq < Test::Unit::TestCase
+  def setup
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    @output.write(FOO: 'BAR', SEQ: 'atcg')
+    @output.write(SEQ: 'atcg', SCORES: '0123')
+    @output.close
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline::SliceSeq with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.slice_seq(slice: 1, foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::SliceSeq with valid options don\'t raise' do
+    assert_nothing_raised { @p.slice_seq(slice: 1) }
+  end
+
+  test 'BioDSL::Pipeline::SliceSeq with index returns correctly' do
+    @p.slice_seq(slice: 1).run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:FOO=>"BAR", :SEQ=>"t", :SEQ_LEN=>1}
+      |{:SEQ=>"t", :SCORES=>"1", :SEQ_LEN=>1}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::SliceSeq with out of range index returns OK' do
+    @p.slice_seq(slice: 10).run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:FOO=>"BAR", :SEQ=>"", :SEQ_LEN=>0}
+      |{:SEQ=>"", :SCORES=>"", :SEQ_LEN=>0}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::SliceSeq with negative index returns correctly' do
+    @p.slice_seq(slice: -1).run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:FOO=>"BAR", :SEQ=>"g", :SEQ_LEN=>1}
+      |{:SEQ=>"g", :SCORES=>"3", :SEQ_LEN=>1}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::SliceSeq with negative out of range index ' \
+    'returns correctly' do
+    @p.slice_seq(slice: -10).run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:FOO=>"BAR", :SEQ=>"", :SEQ_LEN=>0}
+      |{:SEQ=>"", :SCORES=>"", :SEQ_LEN=>0}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::SliceSeq with range returns correctly' do
+    @p.slice_seq(slice: 1..-1).run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:FOO=>"BAR", :SEQ=>"tcg", :SEQ_LEN=>3}
+      |{:SEQ=>"tcg", :SCORES=>"123", :SEQ_LEN=>3}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::SliceSeq with out of range end range returns OK' do
+    @p.slice_seq(slice: 1..10).run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:FOO=>"BAR", :SEQ=>"tcg", :SEQ_LEN=>3}
+      |{:SEQ=>"tcg", :SCORES=>"123", :SEQ_LEN=>3}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::SliceSeq status returns OK' do
+    @p.slice_seq(slice: 1..10).run(input: @input, output: @output2)
+
+    assert_equal(2, @p.status.first[:records_in])
+    assert_equal(2, @p.status.first[:records_out])
+    assert_equal(2, @p.status.first[:sequences_in])
+    assert_equal(2, @p.status.first[:sequences_out])
+    assert_equal(8, @p.status.first[:residues_in])
+    assert_equal(6, @p.status.first[:residues_out])
+  end
+end

data/test/BioDSL/commands/test_sort.rb

@@ -0,0 +1,128 @@
+#!/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 Sort.
+class TestSort < Test::Unit::TestCase
+  def setup
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    @output.write(NAME: 'test2', COUNT: 4)
+    @output.write(NAME: 'test1', COUNT: 21)
+    @output.write(NAME: 'test2', COUNT: 2)
+    @output.write(NAME: 'test3', COUNT: 9)
+    @output.close
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline::Sort with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.sort(key: :COUNT, foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::Sort with valid options don\'t raise' do
+    assert_nothing_raised { @p.sort(key: :COUNT) }
+  end
+
+  test 'BioDSL::Pipeline::Sort alphabetical returns correctly' do
+    @p.sort(key: 'NAME').run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:NAME=>"test1", :COUNT=>21}
+      |{:NAME=>"test2", :COUNT=>4}
+      |{:NAME=>"test2", :COUNT=>2}
+      |{:NAME=>"test3", :COUNT=>9}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::Sort numerical returns correctly' do
+    @p.sort(key: :COUNT).run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:NAME=>"test2", :COUNT=>2}
+      |{:NAME=>"test2", :COUNT=>4}
+      |{:NAME=>"test3", :COUNT=>9}
+      |{:NAME=>"test1", :COUNT=>21}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::Sort reverse returns correctly' do
+    @p.sort(key: :COUNT, reverse: true).run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:NAME=>"test1", :COUNT=>21}
+      |{:NAME=>"test3", :COUNT=>9}
+      |{:NAME=>"test2", :COUNT=>4}
+      |{:NAME=>"test2", :COUNT=>2}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::Sort with block_size returns correctly' do
+    @p.sort(key: :COUNT, block_size: 60).run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:NAME=>"test2", :COUNT=>2}
+      |{:NAME=>"test2", :COUNT=>4}
+      |{:NAME=>"test3", :COUNT=>9}
+      |{:NAME=>"test1", :COUNT=>21}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::Sort with block_size and reverse returns OK' do
+    @p.sort(key: :COUNT, block_size: 30, reverse: true).
+      run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:NAME=>"test1", :COUNT=>21}
+      |{:NAME=>"test3", :COUNT=>9}
+      |{:NAME=>"test2", :COUNT=>4}
+      |{:NAME=>"test2", :COUNT=>2}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::Sort status returns OK' do
+    @p.sort(key: :COUNT).run(input: @input, output: @output2)
+
+    assert_equal(4, @p.status.first[:records_in])
+    assert_equal(4, @p.status.first[:records_out])
+  end
+end

data/test/BioDSL/commands/test_split_pair_seq.rb

@@ -0,0 +1,164 @@
+#!/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 SplitPairSeq.
+class TestSplitPairSeq < Test::Unit::TestCase
+  def setup
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    setup_output
+
+    @output.close
+
+    setup_expected
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  # rubocop: disable MethodLength
+  def setup_output
+    [
+      {SEQ_NAME: 'M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14',
+       SEQ: 'TGGGGAATATTGGACAATGGCCTGTTTGCTACCCACGCTT',
+       SEQ_LEN: 40,
+       SCORES: '<??????BDDDDDDDDGGGG?????BB<-<BDDDDDFEEF',
+       SEQ_LEN_LEFT: 20,
+       SEQ_LEN_RIGHT: 20},
+      {SEQ_NAME: 'M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14',
+       SEQ: 'TAGGGAATCTTGCACAATGGACTCTTCGCTACCCATGCTT',
+       SEQ_LEN: 40,
+       SCORES: '<???9?BBBDBDDBDDFFFF,5<??BB?DDABDBDDFFFF',
+       SEQ_LEN_LEFT: 20,
+       SEQ_LEN_RIGHT: 20},
+      {SEQ_NAME: 'M01168:16:000000000-A1R9L:1:1101:14865:2158 1:N:0:14',
+       SEQ: 'TAGGGAATCTTGCACAATGGCCTCTTCGCTACCCATGCTT',
+       SEQ_LEN: 40,
+       SCORES: '?????BBBBBDDBDDBFFFF??,<??B?BB?BBBBBFF?F',
+       SEQ_LEN_LEFT: 20,
+       SEQ_LEN_RIGHT: 20}
+    ].each do |record|
+      @output.write record
+    end
+  end
+
+  def setup_expected
+    @expected = <<-EOD.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14",
+      | :SEQ=>"TGGGGAATATTGGACAATGG",
+      | :SEQ_LEN=>20,
+      | :SCORES=>"<??????BDDDDDDDDGGGG"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14862:1868 2:N:0:14",
+      | :SEQ=>"CCTGTTTGCTACCCACGCTT",
+      | :SEQ_LEN=>20,
+      | :SCORES=>"?????BB<-<BDDDDDFEEF"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14",
+      | :SEQ=>"TAGGGAATCTTGCACAATGG",
+      | :SEQ_LEN=>20,
+      | :SCORES=>"<???9?BBBDBDDBDDFFFF"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:13906:2139 2:N:0:14",
+      | :SEQ=>"ACTCTTCGCTACCCATGCTT",
+      | :SEQ_LEN=>20,
+      | :SCORES=>",5<??BB?DDABDBDDFFFF"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14865:2158 1:N:0:14",
+      | :SEQ=>"TAGGGAATCTTGCACAATGG",
+      | :SEQ_LEN=>20,
+      | :SCORES=>"?????BBBBBDDBDDBFFFF"}
+      |{:SEQ_NAME=>"M01168:16:000000000-A1R9L:1:1101:14865:2158 2:N:0:14",
+      | :SEQ=>"CCTCTTCGCTACCCATGCTT",
+      | :SEQ_LEN=>20,
+      | :SCORES=>"??,<??B?BB?BBBBBFF?F"}
+    EOD
+  end
+
+  # rubocop: enable MethodLength
+  test 'BioDSL::Pipeline::SplitPairSeq with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.split_pair_seq(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::SplitPairSeq with bad sequence lengths raises' do
+    input, output = BioDSL::Stream.pipe
+
+    record = {
+      SEQ_NAME: 'M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14',
+      SEQ: 'TGGGGAATATTGGACAATGGCCTGTTTGCTACCCACGCTT',
+      SEQ_LEN: 40,
+      SCORES: '<??????BDDDDDDDDGGGG?????BB<-<BDDDDDFEEF',
+      SEQ_LEN_LEFT: 10,
+      SEQ_LEN_RIGHT: 20
+    }
+
+    output.write record
+    output.close
+
+    assert_raise(BioDSL::SeqError) do
+      @p.split_pair_seq.run(input: input, output: @output2)
+    end
+  end
+
+  test 'BioDSL::Pipeline::SplitPairSeq with bad sequence name raises' do
+    input, output = BioDSL::Stream.pipe
+
+    record = {
+      SEQ_NAME: 'M01168:16:000000000-A1R9L:1:1101:14862:18681:N:0:14',
+      SEQ: 'TGGGGAATATTGGACAATGGCCTGTTTGCTACCCACGCTT',
+      SEQ_LEN: 40,
+      SCORES: '<??????BDDDDDDDDGGGG?????BB<-<BDDDDDFEEF',
+      SEQ_LEN_LEFT: 20,
+      SEQ_LEN_RIGHT: 20
+    }
+
+    output.write record
+    output.close
+
+    assert_raise(RuntimeError) do
+      @p.split_pair_seq.run(input: input, output: @output2)
+    end
+  end
+
+  test 'BioDSL::Pipeline::SplitPairSeq returns correctly' do
+    @p.split_pair_seq.run(input: @input, output: @output2)
+
+    assert_equal(@expected.delete("\n"), collect_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline::SplitPairSeq status returns correctly' do
+    @p.split_pair_seq.run(input: @input, output: @output2)
+
+    assert_equal(3,   @p.status.first[:records_in])
+    assert_equal(6,   @p.status.first[:records_out])
+    assert_equal(3,   @p.status.first[:sequences_in])
+    assert_equal(6,   @p.status.first[:sequences_out])
+    assert_equal(120, @p.status.first[:residues_in])
+    assert_equal(120, @p.status.first[:residues_out])
+  end
+end

data/test/BioDSL/commands/test_split_values.rb

@@ -0,0 +1,95 @@
+#!/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 SplitValues.
+class TestSplitValues < Test::Unit::TestCase
+  def setup
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    @output.write(ID: 'FOO:count=10', SEQ: 'gataag')
+    @output.write(ID: 'FOO_10_20', SEQ: 'gataag')
+    @output.close
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline::SplitValues with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.split_values(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::SplitValues with valid options don\'t raise' do
+    assert_nothing_raised { @p.split_values(key: :ID) }
+  end
+
+  test 'BioDSL::Pipeline::SplitValues returns correctly' do
+    @p.split_values(key: :ID).run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:ID=>"FOO:count=10", :SEQ=>"gataag"}
+      |{:ID=>"FOO_10_20", :SEQ=>"gataag", :ID_0=>"FOO", :ID_1=>10, :ID_2=>20}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::SplitValues status returns correctly' do
+    @p.split_values(key: :ID).run(input: @input, output: @output2)
+
+    assert_equal(2, @p.status.first[:records_in])
+    assert_equal(2, @p.status.first[:records_out])
+  end
+
+  test 'BioDSL::Pipeline::SplitValues with :delimiter returns correctly' do
+    @p.split_values(key: 'ID', delimiter: ':count=').
+      run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:ID=>"FOO:count=10", :SEQ=>"gataag", :ID_0=>"FOO", :ID_1=>10}
+      |{:ID=>"FOO_10_20", :SEQ=>"gataag"}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::SplitValues w. :delimiter and :keys returns OK' do
+    @p.split_values(key: 'ID', keys: ['ID', :COUNT], delimiter: ':count=').
+      run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:ID=>"FOO", :SEQ=>"gataag", :COUNT=>10}
+      |{:ID=>"FOO_10_20", :SEQ=>"gataag"}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+end