BioDSL 1.0.0

data/test/BioDSL/commands/test_read_fasta.rb

@@ -0,0 +1,229 @@
+#!/usr/bin/env ruby
+$LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..')
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                #
+#                                                                              #
+# This program is free software; you can redistribute it and/or                #
+# modify it under the terms of the GNU General Public License                  #
+# as published by the Free Software Foundation; either version 2               #
+# of the License, or (at your option) any later version.                       #
+#                                                                              #
+# This program is distributed in the hope that it will be useful,              #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of               #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                #
+# GNU General Public License for more details.                                 #
+#                                                                              #
+# You should have received a copy of the GNU General Public License            #
+# along with this program; if not, write to the Free Software                  #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,    #
+# USA.                                                                         #
+#                                                                              #
+# http://www.gnu.org/copyleft/gpl.html                                         #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# This software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+require 'test/helper'
+
+# Test class for the read_fasta command.
+# rubocop:disable ClassLength
+class TestReadFasta < Test::Unit::TestCase
+  def setup
+    @tmpdir = Dir.mktmpdir('BioDSL')
+
+    write_fasta_data1
+    write_fasta_data2
+
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    write_stream_data
+
+    @p = BioDSL::Pipeline.new
+    @err = BioDSL::OptionError
+  end
+
+  def write_fasta_data1
+    @file = File.join(@tmpdir, 'test.fna')
+
+    File.open(@file, 'w') do |ios|
+      ios.puts <<-EOF.gsub(/^\s+\|/, '')
+        |>test1
+        |atgcagcac
+        |>test2
+        |acagcactgA
+      EOF
+    end
+  end
+
+  def write_fasta_data2
+    @file2 = File.join(@tmpdir, 'test2.fna')
+
+    File.open(@file2, 'w') do |ios|
+      ios.puts <<-EOF.gsub(/^\s+\|/, '')
+        |>test3
+        |acGTAagcac
+        |>test4
+        |aCCAgcactgA
+      EOF
+    end
+  end
+
+  def write_stream_data
+    @output.write(SEQ_NAME: 'test1', SEQ: 'atgcagcac',  SEQ_LEN: 9)
+    @output.write(SEQ_NAME: 'test2', SEQ: 'acagcactgA', SEQ_LEN: 10)
+    @output.close
+  end
+
+  def teardown
+    FileUtils.rm_r @tmpdir
+  end
+
+  test 'BioDSL::Pipeline::ReadFasta with invalid options raises' do
+    assert_raise(@err) { @p.read_fasta(foo: 'bar') }
+  end
+
+  test 'BioDSL::Pipeline::ReadFasta without required options raises' do
+    assert_raise(@err) { @p.read_fasta }
+  end
+
+  test 'BioDSL::Pipeline::ReadFasta with bad first raises' do
+    assert_raise(@err) { @p.read_fasta(input: @file, first: -1) }
+  end
+
+  test 'BioDSL::Pipeline::ReadFasta with bad last raises' do
+    assert_raise(@err) { @p.read_fasta(input: @file, last: -1) }
+  end
+
+  test 'BioDSL::Pipeline::ReadFasta with exclusive unique options raises' do
+    assert_raise(@err) { @p.read_fasta(input: @file, first: 1, last: 1) }
+  end
+
+  test 'BioDSL::Pipeline::ReadFasta with non-existing input file raises' do
+    assert_raise(@err) { @p.read_fasta(input: '___adsf') }
+  end
+
+  test 'BioDSL::Pipeline::ReadFasta returns correctly' do
+    @p.read_fasta(input: @file).run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+       |{:SEQ_NAME=>"test1", :SEQ=>"atgcagcac", :SEQ_LEN=>9}
+       |{:SEQ_NAME=>"test2", :SEQ=>"acagcactgA", :SEQ_LEN=>10}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::ReadFasta status returns correctly' do
+    @p.read_fasta(input: @file).run(output: @output2)
+
+    assert_equal(0, @p.status.first[:records_in])
+    assert_equal(2, @p.status.first[:records_out])
+    assert_equal(0, @p.status.first[:sequences_in])
+    assert_equal(2, @p.status.first[:sequences_out])
+    assert_equal(0, @p.status.first[:residues_in])
+    assert_equal(19, @p.status.first[:residues_out])
+  end
+
+  test 'BioDSL::Pipeline::ReadFasta with gzipped data returns correctly' do
+    `gzip #{@file}`
+
+    @p.read_fasta(input: "#{@file}.gz").run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"test1", :SEQ=>"atgcagcac", :SEQ_LEN=>9}
+      |{:SEQ_NAME=>"test2", :SEQ=>"acagcactgA", :SEQ_LEN=>10}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::ReadFasta with bzip2\'ed data returns correctly' do
+    `bzip2 #{@file}`
+
+    @p.read_fasta(input: "#{@file}.bz2").run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"test1", :SEQ=>"atgcagcac", :SEQ_LEN=>9}
+      |{:SEQ_NAME=>"test2", :SEQ=>"acagcactgA", :SEQ_LEN=>10}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::ReadFasta with multiple files returns correctly' do
+    @p.read_fasta(input: [@file, @file2]).run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"test1", :SEQ=>"atgcagcac", :SEQ_LEN=>9}
+      |{:SEQ_NAME=>"test2", :SEQ=>"acagcactgA", :SEQ_LEN=>10}
+      |{:SEQ_NAME=>"test3", :SEQ=>"acGTAagcac", :SEQ_LEN=>10}
+      |{:SEQ_NAME=>"test4", :SEQ=>"aCCAgcactgA", :SEQ_LEN=>11}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::ReadFasta with input glob returns correctly' do
+    @p.read_fasta(input: File.join(@tmpdir, 'test*.fna')).run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"test1", :SEQ=>"atgcagcac", :SEQ_LEN=>9}
+      |{:SEQ_NAME=>"test2", :SEQ=>"acagcactgA", :SEQ_LEN=>10}
+      |{:SEQ_NAME=>"test3", :SEQ=>"acGTAagcac", :SEQ_LEN=>10}
+      |{:SEQ_NAME=>"test4", :SEQ=>"aCCAgcactgA", :SEQ_LEN=>11}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::ReadFasta with :first returns correctly' do
+    @p.read_fasta(input: [@file, @file2], first: 3).run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"test1", :SEQ=>"atgcagcac", :SEQ_LEN=>9}
+      |{:SEQ_NAME=>"test2", :SEQ=>"acagcactgA", :SEQ_LEN=>10}
+      |{:SEQ_NAME=>"test3", :SEQ=>"acGTAagcac", :SEQ_LEN=>10}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::ReadFasta#to_s with :first returns correctly' do
+    @p.read_fasta(input: @file, first: 3)
+
+    expected = %{BP.new.read_fasta(input: "#{@file}", first: 3)}
+
+    assert_equal(expected, @p.to_s)
+  end
+
+  test 'BioDSL::Pipeline::ReadFasta with :last returns correctly' do
+    @p.read_fasta(input: [@file, @file2], last: 3).run(output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"test2", :SEQ=>"acagcactgA", :SEQ_LEN=>10}
+      |{:SEQ_NAME=>"test3", :SEQ=>"acGTAagcac", :SEQ_LEN=>10}
+      |{:SEQ_NAME=>"test4", :SEQ=>"aCCAgcactgA", :SEQ_LEN=>11}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline::ReadFasta with flux returns correctly' do
+    @p.read_fasta(input: @file2).run(input: @input, output: @output2)
+
+    expected = <<-EXP.gsub(/^\s+\|/, '')
+      |{:SEQ_NAME=>"test1", :SEQ=>"atgcagcac", :SEQ_LEN=>9}
+      |{:SEQ_NAME=>"test2", :SEQ=>"acagcactgA", :SEQ_LEN=>10}
+      |{:SEQ_NAME=>"test3", :SEQ=>"acGTAagcac", :SEQ_LEN=>10}
+      |{:SEQ_NAME=>"test4", :SEQ=>"aCCAgcactgA", :SEQ_LEN=>11}
+    EXP
+
+    assert_equal(expected, collect_result)
+  end
+end