BioDSL 1.0.0

data/test/BioDSL/commands/test_uclust.rb

@@ -0,0 +1,139 @@
+#!/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 Uclust.
+class TestUclust < Test::Unit::TestCase
+  def setup
+    omit('usearch not found') unless BioDSL::Filesys.which('usearch')
+  end
+
+  test 'BioDSL::Pipeline#uclust with disallowed option raises' do
+    p = BioDSL::Pipeline.new
+    assert_raise(BioDSL::OptionError) { p.uclust(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline#uclust with allowed option dont raise' do
+    p = BioDSL::Pipeline.new
+    assert_nothing_raised { p.uclust(identity: 1, strand: :both) }
+  end
+
+  test 'BioDSL::Pipeline#uclust outputs correctly' do
+    input, output   = BioDSL::Stream.pipe
+    @input2, output2 = BioDSL::Stream.pipe
+
+    output.write(one: 1, two: 2, three: 3)
+    output.write(SEQ: 'gtgtgtagctacgatcagctagcgatcgagctatatgttt')
+    output.write(SEQ: 'atcgatcgatcgatcgatcgatcgatcgtacgacgtagct')
+    output.close
+
+    p = BioDSL::Pipeline.new
+    p.uclust(identity: 0.97, strand: 'plus').run(input: input, output: output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ=>"atcgatcgatcgatcgatcgatcgatcgtacgacgtagct",
+      | :SEQ_NAME=>"2",
+      | :TYPE=>"C",
+      | :CLUSTER=>1,
+      | :CLUSTER_SIZE=>1,
+      | :STRAND=>"*",
+      | :CIGAR=>"*",
+      | :Q_ID=>"2",
+      | :RECORD_TYPE=>"uclust"}
+      |{:SEQ=>"gtgtgtagctacgatcagctagcgatcgagctatatgttt",
+      | :SEQ_NAME=>"1",
+      | :TYPE=>"C",
+      | :CLUSTER=>0,
+      | :CLUSTER_SIZE=>1,
+      | :STRAND=>"*",
+      | :CIGAR=>"*",
+      | :Q_ID=>"1",
+      | :RECORD_TYPE=>"uclust"}
+      |{:one=>1,
+      | :two=>2,
+      | :three=>3}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_sorted_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline#uclust status outputs correctly' do
+    input, output   = BioDSL::Stream.pipe
+    @input2, output2 = BioDSL::Stream.pipe
+
+    output.write(one: 1, two: 2, three: 3)
+    output.write(SEQ: 'gtgtgtagctacgatcagctagcgatcgagctatatgttt')
+    output.write(SEQ: 'atcgatcgatcgatcgatcgatcgatcgtacgacgtagct')
+    output.close
+
+    p = BioDSL::Pipeline.new
+    p.uclust(identity: 0.97, strand: 'plus').run(input: input, output: output2)
+
+    assert_equal(3, p.status.first[:records_in])
+    assert_equal(3, p.status.first[:records_out])
+    assert_equal(2, p.status.first[:sequences_in])
+    assert_equal(2, p.status.first[:sequences_out])
+    assert_equal(80, p.status.first[:residues_in])
+    assert_equal(80, p.status.first[:residues_out])
+  end
+
+  test 'BioDSL::Pipeline#uclust outputs msa correctly' do
+    input, output   = BioDSL::Stream.pipe
+    @input2, output2 = BioDSL::Stream.pipe
+
+    output.write(one: 1, two: 2, three: 3)
+    output.write(SEQ: 'gtgtgtagctacgatcagctagcgatcgagctatatgttt')
+    output.write(SEQ: 'atcgatcgatcgatcgatcgatcgatcgtacgacgtagct')
+    output.close
+
+    p = BioDSL::Pipeline.new
+    p.uclust(identity: 0.97, strand: 'plus', align: true).
+      run(input: input, output: output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:RECORD_TYPE=>"uclust",
+      | :CLUSTER=>0,
+      | :SEQ_NAME=>"*1",
+      | :SEQ=>"GTgtgtAGCTACGATCAGCTAGCGATCGAGCTATATGTTT",
+      | :SEQ_LEN=>40}
+      |{:RECORD_TYPE=>"uclust",
+      | :CLUSTER=>1,
+      | :SEQ_NAME=>"*2",
+      | :SEQ=>"ATCGATCGATCGATCGATCGATCGATCGTACGACGTAGCT",
+      | :SEQ_LEN=>40}
+      |{:one=>1,
+      | :two=>2,
+      | :three=>3}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_sorted_result.delete("\n"))
+  end
+end

data/test/BioDSL/commands/test_unique_values.rb

@@ -0,0 +1,98 @@
+#!/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 UniqueValues.
+class TestUniqueValues < 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'},
+     {FOO: 'BAR'}
+    ].each do |record|
+      @output.write record
+    end
+
+    @output.close
+
+    @p = BioDSL::Pipeline.new
+  end
+
+  test 'BioDSL::Pipeline#unique_values with disallowed option raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.unique_values(key: :V0, foo: 'bar')
+    end
+  end
+
+  test 'BioDSL::Pipeline#unique_values with allowed options dont raise' do
+    assert_nothing_raised { @p.unique_values(key: :V0) }
+  end
+
+  test 'BioDSL::Pipeline#unique_values returns correctly' do
+    @p.unique_values(key: 'V0').run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:V0=>"HUMAN", :V1=>"H1"}
+      |{:V0=>"DOG", :V1=>"D1"}
+      |{:V0=>"MOUSE", :V1=>"M1"}
+      |{:FOO=>"BAR"}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline#unique_values status returns correctly' do
+    @p.unique_values(key: 'V0').run(input: @input, output: @output2)
+
+    assert_equal(7, @p.status.first[:records_in])
+    assert_equal(4, @p.status.first[:records_out])
+  end
+
+  test 'BioDSL::Pipeline#unique_values with :invert returns correctly' do
+    @p.unique_values(key: 'V0', invert: true).
+      run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:V0=>"HUMAN", :V1=>"H2"}
+      |{:V0=>"HUMAN", :V1=>"H3"}
+      |{:V0=>"DOG", :V1=>"D2"}
+      |{:FOO=>"BAR"}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+end

data/test/BioDSL/commands/test_usearch_global.rb

@@ -0,0 +1,123 @@
+#!/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 UsearchGlobal.
+class TestUsearchGlobal < Test::Unit::TestCase
+  require 'tempfile'
+
+  def setup
+    omit('usearch not found') unless BioDSL::Filesys.which('usearch')
+
+    data = <<-DAT.gsub(/^\s+\|/, '')
+      |>test1
+      |gtgtgtagctacgatcagctagcgatcgagctatatgttt
+    DAT
+
+    @db = Tempfile.new('database')
+
+    File.open(@db, 'w') do |ios|
+      ios << data
+    end
+  end
+
+  def teardown
+    @db.close
+    @db.unlink
+  end
+
+  test 'BioDSL::Pipeline#usearch_global with disallowed option raises' do
+    p = BioDSL::Pipeline.new
+    assert_raise(BioDSL::OptionError) { p.usearch_global(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline#usearch_global with allowed option dont raise' do
+    p = BioDSL::Pipeline.new
+    assert_nothing_raised { p.usearch_global(database: @db.path, identity: 1) }
+  end
+
+  test 'BioDSL::Pipeline#usearch_global outputs correctly' do
+    input, output    = BioDSL::Stream.pipe
+    @input2, output2 = BioDSL::Stream.pipe
+
+    output.write(one: 1, two: 2, three: 3)
+    output.write(SEQ: 'gtgtgtagctacgatcagctagcgatcgagctatatgttt')
+    output.write(SEQ: 'atcgatcgatcgatcgatcgatcgatcgtacgacgtagct')
+    output.close
+
+    p = BioDSL::Pipeline.new
+    p.usearch_global(database: @db.path, identity: 0.97, strand: 'plus').
+      run(input: input, output: output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ=>"atcgatcgatcgatcgatcgatcgatcgtacgacgtagct"}
+      |{:SEQ=>"gtgtgtagctacgatcagctagcgatcgagctatatgttt"}
+      |{:TYPE=>"H",
+      | :CLUSTER=>0,
+      | :SEQ_LEN=>40,
+      | :IDENT=>100.0,
+      | :STRAND=>"+",
+      | :CIGAR=>"40M",
+      | :Q_ID=>"1",
+      | :S_ID=>"test1",
+      | :RECORD_TYPE=>"usearch"}
+      |{:TYPE=>"N",
+      | :CLUSTER=>0,
+      | :SEQ_LEN=>0,
+      | :STRAND=>".",
+      | :CIGAR=>"*",
+      | :Q_ID=>"2",
+      | :RECORD_TYPE=>"usearch"}
+      |{:one=>1, :two=>2, :three=>3}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_sorted_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline#usearch_global status outputs correctly' do
+    input, output    = BioDSL::Stream.pipe
+    @input2, output2 = BioDSL::Stream.pipe
+
+    output.write(one: 1, two: 2, three: 3)
+    output.write(SEQ: 'gtgtgtagctacgatcagctagcgatcgagctatatgttt')
+    output.write(SEQ: 'atcgatcgatcgatcgatcgatcgatcgtacgacgtagct')
+    output.close
+
+    p = BioDSL::Pipeline.new
+    p.usearch_global(database: @db.path, identity: 0.97, strand: 'plus').
+      run(input: input, output: output2)
+
+    assert_equal(3, p.status.first[:records_in])
+    assert_equal(5, p.status.first[:records_out])
+    assert_equal(2, p.status.first[:sequences_in])
+    assert_equal(2, p.status.first[:hits_out])
+  end
+end

data/test/BioDSL/commands/test_usearch_local.rb

@@ -0,0 +1,125 @@
+#!/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 UsearchLocal.
+class TestUsearchLocal < Test::Unit::TestCase
+  require 'tempfile'
+
+  def setup
+    omit('usearch not found') unless BioDSL::Filesys.which('usearch')
+
+    data = <<-DAT.gsub(/^\s+\|/, '')
+      |>test1
+      |gtgtgtagctacgatcagctagcgatcgagctatatgttt
+    DAT
+
+    @db = Tempfile.new('database')
+
+    File.open(@db, 'w') do |ios|
+      ios << data
+    end
+  end
+
+  def teardown
+    @db.close
+    @db.unlink
+  end
+
+  test 'BioDSL::Pipeline#usearch_local with disallowed option raises' do
+    p = BioDSL::Pipeline.new
+    assert_raise(BioDSL::OptionError) { p.usearch_local(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline#usearch_local with allowed option dont raise' do
+    p = BioDSL::Pipeline.new
+    assert_nothing_raised { p.usearch_local(database: @db.path, identity: 1) }
+  end
+
+  test 'BioDSL::Pipeline#usearch_local outputs correctly' do
+    input, output   = BioDSL::Stream.pipe
+    @input2, output2 = BioDSL::Stream.pipe
+
+    output.write(one: 1, two: 2, three: 3)
+    output.write(SEQ: 'gtgtgtagctacgatcagctagcgatcgagctatatgttt')
+    output.write(SEQ: 'atcgatcgatcgatcgatcgatcgatcgtacgacgtagct')
+    output.close
+
+    p = BioDSL::Pipeline.new
+    p.usearch_local(database: @db.path, identity: 0.97, strand: 'plus').
+      run(input: input, output: output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ=>"atcgatcgatcgatcgatcgatcgatcgtacgacgtagct"}
+      |{:SEQ=>"gtgtgtagctacgatcagctagcgatcgagctatatgttt"}
+      |{:TYPE=>"H",
+      | :CLUSTER=>0,
+      | :SEQ_LEN=>40,
+      | :IDENT=>100.0,
+      | :STRAND=>"+",
+      | :CIGAR=>"40M",
+      | :Q_ID=>"1",
+      | :S_ID=>"test1",
+      | :RECORD_TYPE=>"usearch"}
+      |{:TYPE=>"N",
+      | :CLUSTER=>0,
+      | :SEQ_LEN=>0,
+      | :STRAND=>".",
+      | :CIGAR=>"*",
+      | :Q_ID=>"2",
+      | :RECORD_TYPE=>"usearch"}
+      |{:one=>1,
+      | :two=>2,
+      | :three=>3}
+    EXP
+
+    assert_equal(expected.delete("\n"), collect_sorted_result.delete("\n"))
+  end
+
+  test 'BioDSL::Pipeline#usearch_local status outputs correctly' do
+    input, output   = BioDSL::Stream.pipe
+    @input2, output2 = BioDSL::Stream.pipe
+
+    output.write(one: 1, two: 2, three: 3)
+    output.write(SEQ: 'gtgtgtagctacgatcagctagcgatcgagctatatgttt')
+    output.write(SEQ: 'atcgatcgatcgatcgatcgatcgatcgtacgacgtagct')
+    output.close
+
+    p = BioDSL::Pipeline.new
+    p.usearch_local(database: @db.path, identity: 0.97, strand: 'plus').
+      run(input: input, output: output2)
+
+    assert_equal(3, p.status.first[:records_in])
+    assert_equal(5, p.status.first[:records_out])
+    assert_equal(2, p.status.first[:sequences_in])
+    assert_equal(2, p.status.first[:hits_out])
+  end
+end

data/test/BioDSL/commands/test_write_fasta.rb

@@ -0,0 +1,159 @@
+#!/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 WriteFasta.
+class TestWriteFasta < Test::Unit::TestCase
+  def setup
+    @zcat = BioDSL::Filesys.which('gzcat') ||
+            BioDSL::Filesys.which('zcat')
+
+    init_test_files
+    init_data_streams
+
+    @expected = <<-EXP.gsub(/^\s+\|/, '')
+      |>test1
+      |atcg
+      |>test2
+      |gtac
+    EXP
+
+    @p = BioDSL::Pipeline.new
+    @e = BioDSL::OptionError
+  end
+
+  def init_test_files
+    @tmpdir = Dir.mktmpdir('BioDSL')
+    @file   = File.join(@tmpdir, 'test.fna')
+    @file2  = File.join(@tmpdir, 'test.fna')
+  end
+
+  def init_data_streams
+    @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
+  end
+
+  def teardown
+    FileUtils.rm_r @tmpdir
+  end
+
+  test 'BioDSL::Pipeline::WriteFasta with invalid options raises' do
+    assert_raise(@e) { @p.write_fasta(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::WriteFasta to stdout outputs correctly' do
+    result = capture_stdout { @p.write_fasta.run(input: @input) }
+    assert_equal(@expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteFasta status outputs correctly' do
+    capture_stdout { @p.write_fasta.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::WriteFasta with :wrap outputs correctly' do
+    result = capture_stdout { @p.write_fasta(wrap: 2).run(input: @input) }
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |>test1
+      |at
+      |cg
+      |>test2
+      |gt
+      |ac
+    EXP
+
+    assert_equal(expected, result)
+  end
+
+  test 'BioDSL::Pipeline::WriteFasta to file outputs correctly' do
+    @p.write_fasta(output: @file).run(input: @input, output: @output2)
+
+    assert_equal(@expected, File.read(@file))
+  end
+
+  test 'BioDSL::Pipeline::WriteFasta to existing file raises' do
+    `touch #{@file}`
+    assert_raise(@e) { @p.write_fasta(output: @file) }
+  end
+
+  test 'BioDSL::Pipeline::WriteFasta to file with :force outputs OK' do
+    `touch #{@file}`
+    @p.write_fasta(output: @file, force: true).run(input: @input)
+
+    assert_equal(@expected, File.open(@file).read)
+  end
+
+  test 'BioDSL::Pipeline::WriteFasta with gzipdata and w/o file raises' do
+    assert_raise(@e) { @p.write_fasta(gzip: true) }
+  end
+
+  test 'BioDSL::Pipeline::WriteFasta with bzip2 data w/o file raises' do
+    assert_raise(@e) { @p.write_fasta(bzip2: true) }
+  end
+
+  test 'BioDSL::Pipeline::WriteFasta to file outputs gzipped data OK' do
+    @p.write_fasta(output: @file, gzip: true).run(input: @input)
+
+    assert_equal(@expected, `#{@zcat} #{@file}`)
+  end
+
+  test 'BioDSL::Pipeline::WriteFasta to file outputs bzip2\'ed data OK' do
+    @p.write_fasta(output: @file, bzip2: true).run(input: @input)
+
+    assert_equal(@expected, `bzcat #{@file}`)
+  end
+
+  test 'BioDSL::Pipeline::WriteFasta with gzip and bzip2 output raises' do
+    assert_raise(@e) { @p.write_fasta(output: @file, gzip: true, bzip2: true) }
+  end
+
+  test 'BioDSL::Pipeline::WriteFasta with flux outputs correctly' do
+    @p.write_fasta(output: @file).run(input: @input, output: @output2)
+
+    expected2 = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"test1", :SEQ=>"atcg", :SEQ_LEN=>4}
+      |{:SEQ_NAME=>"test2", :SEQ=>"gtac", :SEQ_LEN=>4}
+    EXP
+
+    assert_equal(@expected, File.open(@file).read)
+    assert_equal(expected2, collect_result)
+  end
+end