BioDSL 1.0.0

data/test/BioDSL/commands/test_write_fastq.rb

@@ -0,0 +1,166 @@
+#!/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'
+
+# rubocop: disable ClassLength
+
+# Test class for WriteFastq.
+class TestWriteFastq < Test::Unit::TestCase
+  def setup
+    @zcat = BioDSL::Filesys.which('gzcat') ||
+            BioDSL::Filesys.which('zcat')
+
+    @tmpdir = Dir.mktmpdir('BioDSL')
+    @file   = File.join(@tmpdir, 'test.fq')
+    @file2  = File.join(@tmpdir, 'test.fq')
+
+    setup_data
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  def setup_data
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    @output.write(SEQ_NAME: 'test1', SEQ: 'atcg', SEQ_LEN: 4, SCORES: '!!II')
+    @output.write(SEQ_NAME: 'test2', SEQ: 'gtac', SEQ_LEN: 4, SCORES: '!!II')
+    @output.close
+  end
+
+  def teardown
+    FileUtils.rm_r @tmpdir
+  end
+
+  test 'BioDSL::Pipeline::WriteFastq with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.write_fastq(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::WriteFastq with invalid encoding raises' do
+    assert_raise(BioDSL::OptionError) { @p.write_fastq(encoding: 'foo') }
+  end
+
+  test 'BioDSL::Pipeline::WriteFastq with valid encoding dont raise' do
+    assert_nothing_raised { @p.write_fastq(encoding: :base_33) }
+    assert_nothing_raised { @p.write_fastq(encoding: :base_64) }
+  end
+
+  test 'BioDSL::Pipeline::WriteFastq to stdout outputs correctly' do
+    result = capture_stdout { @p.write_fastq.run(input: @input) }
+    expected = "@test1\natcg\n+\n!!II\n@test2\ngtac\n+\n!!II\n"
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteFastq status outputs correctly' do
+    capture_stdout { @p.write_fastq.run(input: @input) }
+    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(8, @p.status.first[:residues_out])
+  end
+
+  test 'BioDSL::Pipeline::WriteFastq to stdout with base 64 encoding ' \
+    'outputs correctly' do
+    result = capture_stdout do
+      @p.write_fastq(encoding: :base_64).run(input: @input)
+    end
+    expected = "@test1\natcg\n+\n@@hh\n@test2\ngtac\n+\n@@hh\n"
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteFastq to file outputs correctly' do
+    @p.write_fastq(output: @file).run(input: @input, output: @output2)
+    result = File.open(@file).read
+    expected = "@test1\natcg\n+\n!!II\n@test2\ngtac\n+\n!!II\n"
+    assert_equal(expected, result)
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteFastq to existing file raises' do
+    `touch #{@file}`
+    assert_raise(BioDSL::OptionError) { @p.write_fastq(output: @file) }
+  end
+
+  test 'BioDSL::Pipeline::WriteFastq to existing file with :force ' \
+    'outputs OK' do
+    `touch #{@file}`
+    @p.write_fastq(output: @file, force: true).run(input: @input)
+    result = File.open(@file).read
+    expected = "@test1\natcg\n+\n!!II\n@test2\ngtac\n+\n!!II\n"
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteFastq with gzipped data and no output ' \
+    'file raises' do
+    assert_raise(BioDSL::OptionError) { @p.write_fastq(gzip: true) }
+  end
+
+  test 'BioDSL::Pipeline::WriteFastq w. bzip2ed data and no ' \
+    'output file raises' do
+    assert_raise(BioDSL::OptionError) { @p.write_fastq(bzip2: true) }
+  end
+
+  test 'BioDSL::Pipeline::WriteFastq to file outputs gzipped data OK' do
+    @p.write_fastq(output: @file, gzip: true).run(input: @input)
+    result = `#{@zcat} #{@file}`
+    expected = "@test1\natcg\n+\n!!II\n@test2\ngtac\n+\n!!II\n"
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteFastq to file outputs bzip2ed data OK' do
+    @p.write_fastq(output: @file, bzip2: true).run(input: @input)
+    result = `bzcat #{@file}`
+    expected = "@test1\natcg\n+\n!!II\n@test2\ngtac\n+\n!!II\n"
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteFastq w. both gzip and bzip2 output raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.write_fastq(output: @file, gzip: true, bzip2: true)
+    end
+  end
+
+  test 'BioDSL::Pipeline::WriteFastq with flux outputs correctly' do
+    @p.write_fastq(output: @file).run(input: @input, output: @output2)
+    result = File.open(@file).read
+    expected = "@test1\natcg\n+\n!!II\n@test2\ngtac\n+\n!!II\n"
+    assert_equal(expected, result)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"test1", :SEQ=>"atcg", :SEQ_LEN=>4, :SCORES=>"!!II"}
+      |{:SEQ_NAME=>"test2", :SEQ=>"gtac", :SEQ_LEN=>4, :SCORES=>"!!II"}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+end

data/test/BioDSL/commands/test_write_table.rb

@@ -0,0 +1,411 @@
+#!/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'
+
+# rubocop: disable ClassLength
+
+# Test class for WriteTable.
+class TestWriteTable < Test::Unit::TestCase
+  def setup
+    @zcat = BioDSL::Filesys.which('gzcat') ||
+            BioDSL::Filesys.which('zcat')
+
+    @tmpdir = Dir.mktmpdir('BioDSL')
+    @file   = File.join(@tmpdir, 'test.fna')
+    @file2  = File.join(@tmpdir, 'test.fna')
+
+    setup_data
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  def setup_data
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    @output.write(ORGANISM: 'Human', COUNT: 23_524, SEQ: 'ATACGTCAG')
+    @output.write(ORGANISM: 'Dog',   COUNT: 2442,   SEQ: 'AGCATGAC')
+    @output.write(ORGANISM: 'Mouse', COUNT: 234,    SEQ: 'GACTG')
+    @output.write(ORGANISM: 'Cat',   COUNT: 2_342,  SEQ: 'AAATGCA')
+
+    @output.close
+  end
+
+  def teardown
+    FileUtils.rm_r @tmpdir
+  end
+
+  test 'BioDSL::Pipeline::WriteTable with invalid options raises' do
+    assert_raise(BioDSL::OptionError) { @p.write_table(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::WriteTable with valid options dont raise' do
+    assert_nothing_raised { @p.write_table(keys: [:SEQ]) }
+  end
+
+  test 'BioDSL::Pipeline::WriteTable to stdout outputs correctly' do
+    result = capture_stdout { @p.write_table.run(input: @input) }
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |Human\t23524\tATACGTCAG
+      |Dog\t2442\tAGCATGAC
+      |Mouse\t234\tGACTG
+      |Cat\t2342\tAAATGCA
+    EXP
+
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable status outputs correctly' do
+    capture_stdout { @p.write_table.run(input: @input) }
+
+    assert_equal(4, @p.status.first[:records_in])
+    assert_equal(4, @p.status.first[:records_out])
+  end
+
+  test 'BioDSL::Pipeline::WriteTable with :keys outputs correctly' do
+    result = capture_stdout do
+      @p.write_table(keys: [:SEQ, 'COUNT']).run(input: @input)
+    end
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |ATACGTCAG\t23524
+      |AGCATGAC\t2442
+      |GACTG\t234
+      |AAATGCA\t2342
+    EXP
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable with :skip outputs correctly' do
+    result = capture_stdout do
+      @p.write_table(skip: [:SEQ, 'COUNT']).run(input: @input)
+    end
+
+    expected = "Human\nDog\nMouse\nCat\n"
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable with :header outputs correctly' do
+    result = capture_stdout { @p.write_table(header: true).run(input: @input) }
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |#ORGANISM\tCOUNT\tSEQ
+      |Human\t23524\tATACGTCAG
+      |Dog\t2442\tAGCATGAC
+      |Mouse\t234\tGACTG
+      |Cat\t2342\tAAATGCA
+    EXP
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable with :delimiter outputs correctly' do
+    result = capture_stdout do
+      @p.write_table(delimiter: ';').run(input: @input)
+    end
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |Human;23524;ATACGTCAG
+      |Dog;2442;AGCATGAC
+      |Mouse;234;GACTG
+      |Cat;2342;AAATGCA
+    EXP
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable w. :delimiter and :pretty raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.write_table(delimiter: ';', pretty: true)
+    end
+  end
+
+  test 'BioDSL::Pipeline::WriteTable with :commify and :pretty raises' do
+    assert_raise(BioDSL::OptionError) { @p.write_table(commify: true) }
+  end
+
+  test 'BioDSL::Pipeline::WriteTable with :pretty outputs correctly' do
+    result = capture_stdout { @p.write_table(pretty: true).run(input: @input) }
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |+-------+-------+-----------+
+      || Human | 23524 | ATACGTCAG |
+      || Dog   |  2442 | AGCATGAC  |
+      || Mouse |   234 | GACTG     |
+      || Cat   |  2342 | AAATGCA   |
+      |+-------+-------+-----------+
+    EXP
+
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable with :pretty and :header outputs OK' do
+    result = capture_stdout do
+      @p.write_table(pretty: true, header: true).run(input: @input)
+    end
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |+----------+-------+-----------+
+      || ORGANISM | COUNT | SEQ       |
+      |+----------+-------+-----------+
+      || Human    | 23524 | ATACGTCAG |
+      || Dog      |  2442 | AGCATGAC  |
+      || Mouse    |   234 | GACTG     |
+      || Cat      |  2342 | AAATGCA   |
+      |+----------+-------+-----------+
+    EXP
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable w. :pretty and :commify outputs OK' do
+    result = capture_stdout do
+      @p.write_table(pretty: true, commify: true).run(input: @input)
+    end
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |+-------+--------+-----------+
+      || Human | 23,524 | ATACGTCAG |
+      || Dog   |  2,442 | AGCATGAC  |
+      || Mouse |    234 | GACTG     |
+      || Cat   |  2,342 | AAATGCA   |
+      |+-------+--------+-----------+
+    EXP
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable w. :pretty and :commify and floats ' \
+    'outputs correctly' do
+    input, output   = BioDSL::Stream.pipe
+
+    output.write(ORGANISM: 'Human', COUNT: 23_524, SEQ: 'ATACGTCAG')
+    output.write(ORGANISM: 'Dog',   COUNT: 244.1,  SEQ: 'AGCATGAC')
+    output.write(ORGANISM: 'Mouse', COUNT: 234,    SEQ: 'GACTG')
+    output.write(ORGANISM: 'Cat',   COUNT: 2_342,  SEQ: 'AAATGCA')
+
+    output.close
+
+    p = BioDSL::Pipeline.new
+
+    result = capture_stdout do
+      p.write_table(pretty: true, commify: true).run(input: input)
+    end
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |+-------+--------+-----------+
+      || Human | 23,524 | ATACGTCAG |
+      || Dog   |  244.1 | AGCATGAC  |
+      || Mouse |    234 | GACTG     |
+      || Cat   |  2,342 | AAATGCA   |
+      |+-------+--------+-----------+
+    EXP
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable with V<num> keys are output OK' do
+    input, output   = BioDSL::Stream.pipe
+
+    output.write(V1: 'Human', V2: 23_524, V0: 'ATACGTCAG')
+    output.write(V1: 'Dog',   V2: 244.1,  V0: 'AGCATGAC')
+    output.write(V1: 'Mouse', V2: 234,    V0: 'GACTG')
+    output.write(V1: 'Cat',   V2: 2_342,  V0: 'AAATGCA')
+
+    output.close
+
+    p = BioDSL::Pipeline.new
+
+    result = capture_stdout { p.write_table.run(input: input) }
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |ATACGTCAG\tHuman\t23524
+      |AGCATGAC\tDog\t244.1
+      |GACTG\tMouse\t234
+      |AAATGCA\tCat\t2342
+    EXP
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable to file outputs correctly' do
+    @p.write_table(output: @file).run(input: @input, output: @output2)
+    result = File.open(@file).read
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |Human\t23524\tATACGTCAG
+      |Dog\t2442\tAGCATGAC
+      |Mouse\t234\tGACTG
+      |Cat\t2342\tAAATGCA
+    EXP
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable to file with :first outputs OK' do
+    @p.write_table(output: @file, first: 1).run(input: @input, output: @output2)
+    result = File.open(@file).read
+    expected = "Human\t23524\tATACGTCAG\n"
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable to file with :last outputs correctly' do
+    @p.write_table(output: @file, last: 1).run(input: @input, output: @output2)
+    result = File.open(@file).read
+    expected = "Cat\t2342\tAAATGCA\n"
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable to file with :pretty outputs OK' do
+    @p.write_table(output: @file, pretty: true, header: true, commify: true).
+      run(input: @input, output: @output2)
+
+    result = File.open(@file).read
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |+----------+--------+-----------+
+      || ORGANISM | COUNT  | SEQ       |
+      |+----------+--------+-----------+
+      || Human    | 23,524 | ATACGTCAG |
+      || Dog      |  2,442 | AGCATGAC  |
+      || Mouse    |    234 | GACTG     |
+      || Cat      |  2,342 | AAATGCA   |
+      |+----------+--------+-----------+
+    EXP
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable to file with :pretty and :first ' \
+    'outputs correctly' do
+    @p.write_table(output: @file, pretty: true, header: true,
+                   commify: true, first: 1).run(input: @input, output: @output2)
+
+    result = File.open(@file).read
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |+----------+--------+-----------+
+      || ORGANISM | COUNT  | SEQ       |
+      |+----------+--------+-----------+
+      || Human    | 23,524 | ATACGTCAG |
+      |+----------+--------+-----------+
+    EXP
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable to file with :pretty and :last ' \
+    'outputs correctly' do
+    @p.write_table(output: @file, pretty: true, header: true,
+                   commify: true, last: 1).run(input: @input, output: @output2)
+
+    result = File.open(@file).read
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |+----------+-------+---------+
+      || ORGANISM | COUNT | SEQ     |
+      |+----------+-------+---------+
+      || Cat      | 2,342 | AAATGCA |
+      |+----------+-------+---------+
+    EXP
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable to existing file raises' do
+    `touch #{@file}`
+    assert_raise(BioDSL::OptionError) { @p.write_table(output: @file) }
+  end
+
+  test 'BioDSL::Pipeline::WriteTable to existing file w. :force outputs ' \
+    'OK' do
+    `touch #{@file}`
+    @p.write_table(output: @file, force: true).run(input: @input)
+    result = File.open(@file).read
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |Human\t23524\tATACGTCAG
+      |Dog\t2442\tAGCATGAC
+      |Mouse\t234\tGACTG
+      |Cat\t2342\tAAATGCA
+    EXP
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable with gzipped data and no output ' \
+    ' file raises' do
+    assert_raise(BioDSL::OptionError) { @p.write_table(gzip: true) }
+  end
+
+  test 'BioDSL::Pipeline::WriteTable with bzip2ed data and no output ' \
+    'file raises' do
+    assert_raise(BioDSL::OptionError) { @p.write_table(bzip2: true) }
+  end
+
+  test 'BioDSL::Pipeline::WriteTable to file outputs gzipped data OK' do
+    @p.write_table(output: @file, gzip: true).run(input: @input)
+    result = `#{@zcat} #{@file}`
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |Human\t23524\tATACGTCAG
+      |Dog\t2442\tAGCATGAC
+      |Mouse\t234\tGACTG
+      |Cat\t2342\tAAATGCA
+    EXP
+
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable to file outputs bzip2ed data OK' do
+    @p.write_table(output: @file, bzip2: true).run(input: @input)
+    result = `bzcat #{@file}`
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |Human\t23524\tATACGTCAG
+      |Dog\t2442\tAGCATGAC
+      |Mouse\t234\tGACTG
+      |Cat\t2342\tAAATGCA
+    EXP
+
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteTable with both gzip and bzip2 output ' \
+    'raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.write_table(output: @file, gzip: true, bzip2: true)
+    end
+  end
+
+  test 'BioDSL::Pipeline::WriteTable with flux outputs correctly' do
+    @p.write_table(output: @file).run(input: @input, output: @output2)
+    result = File.open(@file).read
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |Human\t23524\tATACGTCAG
+      |Dog\t2442\tAGCATGAC
+      |Mouse\t234\tGACTG
+      |Cat\t2342\tAAATGCA
+    EXP
+
+    assert_equal(expected, result)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:ORGANISM=>"Human", :COUNT=>23524, :SEQ=>"ATACGTCAG"}
+      |{:ORGANISM=>"Dog", :COUNT=>2442, :SEQ=>"AGCATGAC"}
+      |{:ORGANISM=>"Mouse", :COUNT=>234, :SEQ=>"GACTG"}
+      |{:ORGANISM=>"Cat", :COUNT=>2342, :SEQ=>"AAATGCA"}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+end