BioDSL 1.0.0

data/lib/BioDSL/test.rb

@@ -0,0 +1,42 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# 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 the BioDSL framework (www.BioDSL.org).        #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+# Namespace for BioDSL.
+module BioDSL
+  # Class variabel visible across the BioDSL module scope.
+  @@test = false
+
+  # Class variable getter method.
+  def self.test
+    @@test
+  end
+
+  # Class variable setter method.
+  def self.test=(x)
+    @@test = x
+  end
+end

data/lib/BioDSL/tmp_dir.rb

@@ -0,0 +1,68 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+# 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).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+module BioDSL
+  # Module to provide a temporary directory.
+  module TmpDir
+    require 'tempfile'
+
+    # Create a temporary directory in block context. The directory is deleted
+    # when the TmpDir object is garbage collected or the Ruby intepreter exits.
+    # If called with a list of filenames, these are provided as block arguments
+    # such that the files parent are the temporary directory. However, the last
+    # block argument is always the path to the temporary directory.
+    #
+    # @param files [Array] List of file names.
+    #
+    # @example
+    #   BioDSL::TmpDir.create do |dir|
+    #     puts dir
+    #       # => "<tmp_dir>"
+    #   end
+    #
+    # @example
+    #   BioDSL::TmpDir.create("foo", "bar") do |foo, bar, dir|
+    #     puts foo
+    #       # => "<tmp_dir>/foo"
+    #     puts bar
+    #       # => "<tmp_dir>/foo"
+    #     puts dir
+    #       # => "<tmp_dir>"
+    #   end
+    def self.create(*files, &block)
+      fail 'no block given' unless block
+
+      Dir.mktmpdir(nil, BioDSL::Config::TMP_DIR) do |dir|
+        paths = files.each_with_object([]) { |e, a| a << File.join(dir, e) }
+
+        if paths.empty?
+          block.call(dir)
+        else
+          block.call(paths << dir)
+        end
+      end
+    end
+  end
+end

data/lib/BioDSL/usearch.rb

@@ -0,0 +1,301 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# 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).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+# Namespace for BioDSL.
+module BioDSL
+  # Error class for all exceptions to do with Usearch.
+  class UsearchError < StandardError; end
+
+  # rubocop: disable ClassLength
+
+  # Class with methods to execute Usearch and parse the results.
+  class Usearch
+    include Enumerable
+
+    # Execute cluster_smallmem.
+    #
+    # @param options [Hash] Options Hash
+    # @option options [String] :input
+    # @option options [String] :output
+    # @option options [String] :database
+    # @option options [Float] :identity
+    # @option options [Fixnum] :cpus
+    # @option options [String] :strand
+    def self.cluster_smallmem(options)
+      usearch = new(options)
+      usearch.cluster_smallmem
+    end
+
+    # Execute cluster_otus.
+    #
+    # @param options [Hash] Options Hash
+    # @option options [String] :input
+    # @option options [String] :output
+    # @option options [String] :database
+    # @option options [Float] :identity
+    # @option options [Fixnum] :cpus
+    # @option options [String] :strand
+    def self.cluster_otus(options)
+      usearch = new(options)
+      usearch.cluster_otus
+    end
+
+    # Execute uchime_ref.
+    #
+    # @param options [Hash] Options Hash
+    # @option options [String] :input
+    # @option options [String] :output
+    # @option options [String] :database
+    # @option options [Float] :identity
+    # @option options [Fixnum] :cpus
+    # @option options [String] :strand
+    def self.uchime_ref(options)
+      usearch = new(options)
+      usearch.uchime_ref
+    end
+
+    # Execute usearch_local.
+    #
+    # @param options [Hash] Options Hash
+    # @option options [String] :input
+    # @option options [String] :output
+    # @option options [String] :database
+    # @option options [Float] :identity
+    # @option options [Fixnum] :cpus
+    # @option options [String] :strand
+    def self.usearch_global(options)
+      usearch = new(options)
+      usearch.usearch_global
+    end
+
+    # Execute usearch_local.
+    #
+    # @param options [Hash] Options Hash
+    # @option options [String] :input
+    # @option options [String] :output
+    # @option options [String] :database
+    # @option options [Float] :identity
+    # @option options [Fixnum] :cpus
+    # @option options [String] :strand
+    def self.usearch_local(options)
+      usearch = new(options)
+      usearch.usearch_local
+    end
+
+    # Open a Usearch file.
+    #
+    # @param [Array] List of open arguments.
+    #
+    # @yield [IO] stream.
+    # @return [IO] stream.
+    def self.open(*args)
+      ios = IO.open(*args)
+
+      if block_given?
+        yield ios
+      else
+        return ios
+      end
+    end
+
+    # Constructor for Usearch class.
+    #
+    # @param options [Hash] Options Hash
+    # @option options [String] :input
+    # @option options [String] :output
+    # @option options [String] :database
+    # @option options [Float] :identity
+    # @option options [Fixnum] :cpus
+    # @option options [String] :strand
+    #
+    # @return [Usearch] Class instance.
+    def initialize(options)
+      @options = options
+      @stderr  = nil
+
+      return self unless File.size(@options[:input]) == 0
+
+      fail UsearchError, %(Empty input file -> "#{@options[:input]}")
+    end
+
+    # Combose a command list and execute cluster_smallmem with this.
+    #
+    # @return [self]
+    def cluster_smallmem
+      command = []
+      command << 'usearch'
+      command << "-cluster_smallmem #{@options[:input]}"
+      command << "-id #{@options[:identity]}"
+      command << "-threads #{@options[:cpus]}" if @options[:cpus]
+      command << "-strand #{@options[:strand]}"
+
+      if @options[:align]
+        command << "-msaout #{@options[:output]}"
+      else
+        command << "-uc #{@options[:output]}"
+      end
+
+      execute(command)
+
+      self
+    end
+
+    # Combose a command list and execute cluster_otus with this.
+    #
+    # @return [self]
+    def cluster_otus
+      command = []
+      command << 'usearch'
+      command << "-cluster_otus #{@options[:input]}"
+      command << "-otus #{@options[:output]}"
+      command << "-id #{@options[:identity]}"
+      command << "-threads #{@options[:cpus]}" if @options[:cpus]
+
+      execute(command)
+
+      self
+    end
+
+    # Combose a command list and execute uchime_ref with this.
+    #
+    # @return [self]
+    def uchime_ref
+      command = []
+      command << 'usearch'
+      command << "-uchime_ref #{@options[:input]}"
+      command << "-db #{@options[:database]}"
+      command << "-strand #{@options[:strand]}"
+      command << "-threads #{@options[:cpus]}" if @options[:cpus]
+      command << "-nonchimeras #{@options[:output]}"
+
+      execute(command)
+
+      self
+    end
+
+    # Combose a command list and execute usearch_global with this.
+    #
+    # @return [self]
+    def usearch_global
+      command = []
+      command << 'usearch'
+      command << '-notrunclabels'
+      command << "-usearch_global #{@options[:input]}"
+      command << "-db #{@options[:database]}"
+      command << "-strand #{@options[:strand]}" if @options[:strand]
+      command << "-threads #{@options[:cpus]}"  if @options[:cpus]
+      command << "-id #{@options[:identity]}"
+      command << "-uc #{@options[:output]}"
+
+      execute(command)
+
+      self
+    end
+
+    # Combose a command list and execute usearch_local with this.
+    #
+    # @return [self]
+    def usearch_local
+      command = []
+      command << 'usearch'
+      command << '-notrunclabels'
+      command << "-usearch_local #{@options[:input]}"
+      command << "-db #{@options[:database]}"
+      command << "-strand #{@options[:strand]}" if @options[:strand]
+      command << "-threads #{@options[:cpus]}"  if @options[:cpus]
+      command << "-id #{@options[:identity]}"
+      command << "-uc #{@options[:output]}"
+
+      execute(command)
+
+      self
+    end
+
+    private
+
+    # Execute Usearch on a given command.
+    #
+    # @param command [Array] Usearch command list.
+    def execute(command)
+      command << '--quiet' unless @options[:verbose]
+      command_str = command.join(' ')
+
+      $stderr.puts "Running command: #{command_str}" if @options[:verbose]
+
+      Open3.popen3(command_str) do |_stdin, _stdout, stderr, wait_thr|
+        @stderr = stderr.read.split $INPUT_RECORD_SEPARATOR
+        exit_status = wait_thr.value # Process::Status object returned.
+
+        unless exit_status.success?
+          # TODO: write error message to log.
+          fail UsearchError, "Command failed: #{command_str} + \
+            #{@stderr.join $INPUT_RECORD_SEPARATOR}"
+        end
+      end
+    end
+
+    # Class for Usearch IO.
+    class IO < Filesys
+      # Parse a given type of Uclust format and yield the result.
+      #
+      # @param format [Symbol] Format type to parse.
+      def each(format = :uc)
+        case format
+        when :uc then each_uc { |e| yield e }
+        else
+          fail UsearchError, "Unknown iterator format: #{format}"
+        end
+      end
+
+      # rubocop: disable Metrics/AbcSize
+
+      # Parse each UC type record and yield the result.
+      #
+      # @yield [Hash] BioDSL record with UC result.
+      def each_uc
+        @io.each do |line|
+          fields = line.chomp.split("\t")
+          record = {TYPE:    fields[0],
+                    CLUSTER: fields[1].to_i}
+
+          case fields[0]
+          when 'C' then record[:CLUSTER_SIZE] = fields[2].to_i
+          else          record[:SEQ_LEN]      = fields[2].to_i
+          end
+
+          record[:IDENT]  = fields[3].to_f if fields[0] == 'H'
+          record[:STRAND] = fields[4]
+          record[:CIGAR]  = fields[7]
+          record[:Q_ID]   = fields[8]
+          record[:S_ID]   = fields[9] if fields[0] == 'H'
+
+          yield record
+        end
+      end
+    end
+  end
+end

data/lib/BioDSL/verbose.rb

@@ -0,0 +1,42 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# 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 the BioDSL framework (www.BioDSL.org).        #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+# Namespace for BioDSL.
+module BioDSL
+  # Class variabel visible across the BioDSL module scope.
+  @@verbose = false
+
+  # Class variable getter method.
+  def self.verbose
+    @@verbose
+  end
+
+  # Class variable setter method.
+  def self.verbose=(x)
+    @@verbose = x
+  end
+end

data/lib/BioDSL/version.rb

@@ -0,0 +1,31 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# 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 the BioDSL framework (www.BioDSL.org).        #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+# Namespace for BioDSL.
+module BioDSL
+  VERSION = '1.0.0'
+end

data/lib/BioDSL.rb

@@ -0,0 +1,81 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# 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).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+fail 'Ruby 2.0 or later required' if RUBY_VERSION < '2.0'
+
+# Commify numbers.
+class Numeric
+  def commify
+    to_s.gsub(/(^[-+]?\d+?(?=(?>(?:\d{3})+)(?!\d))|\G\d{3}(?=\d))/, '\1,')
+  end
+end
+
+# Convert string to float or integer if applicable.
+class String
+  def to_num
+    Integer(self)
+    to_i
+  rescue ArgumentError
+    begin
+      Float(self)
+      to_f
+    rescue ArgumentError
+      self
+    end
+  end
+end
+
+# Namespace for BioDSL.
+module BioDSL
+  require 'pp'
+  require 'BioDSL/cary'
+  require 'BioDSL/commands'
+  require 'BioDSL/debug'
+  require 'BioDSL/helpers'
+  require 'BioDSL/seq'
+  require 'BioDSL/config'
+  require 'BioDSL/hamming'
+  require 'BioDSL/version'
+  require 'BioDSL/filesys'
+  require 'BioDSL/csv'
+  require 'BioDSL/fork'
+  require 'BioDSL/html_report'
+  require 'BioDSL/pipeline'
+  require 'BioDSL/fasta'
+  require 'BioDSL/fastq'
+  require 'BioDSL/math'
+  require 'BioDSL/mummer'
+  require 'BioDSL/taxonomy'
+  require 'BioDSL/tmp_dir'
+  require 'BioDSL/serializer'
+  require 'BioDSL/stream'
+  require 'BioDSL/test'
+  require 'BioDSL/usearch'
+  require 'BioDSL/verbose'
+end
+
+BP = BioDSL::Pipeline # Module alias for irb short hand

data/test/BioDSL/commands/test_add_key.rb

@@ -0,0 +1,105 @@
+#!/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 AddKey.
+class TestAddKey < 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#add_key with disallowed option raises' do
+    assert_raise(BioDSL::OptionError) { @p.add_key(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline#add_key with value and prefix options raise' do
+    assert_raise(BioDSL::OptionError) do
+      @p.add_key(key: 'SEQ_NAME', value: 'foobar', prefix: 'foo')
+    end
+  end
+
+  test 'BioDSL::Pipeline#add_key with allowed options don\'t raise' do
+    assert_nothing_raised { @p.add_key(key: 'SEQ_NAME', value: 'fobar') }
+  end
+
+  test 'BioDSL::Pipeline#add_key status returns correctly' do
+    @p.add_key(key: 'SEQ_NAME', value: 'fobar').
+      run(input: @input, output: @output2)
+
+    assert_equal(3, @p.status.last[:records_in])
+    assert_equal(3, @p.status.last[:records_out])
+  end
+
+  test 'BioDSL::Pipeline#add_key with value returns correctly' do
+    @p.add_key(key: 'SEQ_NAME', value: 'fobar').
+      run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:one=>1, :two=>2, :three=>3, :SEQ_NAME=>"fobar"}
+      |{:SEQ_NAME=>"fobar", :SEQ=>"atcg", :SEQ_LEN=>4}
+      |{:SEQ_NAME=>"fobar", :SEQ=>"gtac", :SEQ_LEN=>4}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline#add_key with empty prefix returns correctly' do
+    @p.add_key(key: 'SEQ_NAME', prefix: '').run(input: @input, output: @output2)
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:one=>1, :two=>2, :three=>3, :SEQ_NAME=>"0"}
+      |{:SEQ_NAME=>"1", :SEQ=>"atcg", :SEQ_LEN=>4}
+      |{:SEQ_NAME=>"2", :SEQ=>"gtac", :SEQ_LEN=>4}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline#add_key with prefix returns correctly' do
+    @p.add_key(key: 'SEQ_NAME', prefix: 'ID_').
+      run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:one=>1, :two=>2, :three=>3, :SEQ_NAME=>"ID_0"}
+      |{:SEQ_NAME=>"ID_1", :SEQ=>"atcg", :SEQ_LEN=>4}
+      |{:SEQ_NAME=>"ID_2", :SEQ=>"gtac", :SEQ_LEN=>4}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+end