BioDSL 1.0.0

data/test/BioDSL/test_csv.rb

@@ -0,0 +1,514 @@
+#!/usr/bin/env ruby
+$:.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.BioDSL.org).                        #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+require 'test/helper'
+
+class StringIO
+  def get_entry
+    self.gets
+  end
+end
+
+class TestCSV < Test::Unit::TestCase 
+  require 'stringio'
+  require 'tempfile'
+
+  def setup
+    table = <<END
+
+#Organism   Sequence    Count
+Human       ATACGTCAG   23524
+Dog         AGCATGAC    2442
+Mouse       GACTG       234
+Cat         AAATGCA     2342
+
+END
+
+    table2 = <<END
+
+#Organism;Sequence;Count
+Human;ATACGTCAG;23524
+Dog;AGCATGAC;2442
+Mouse;GACTG;234
+Cat;AAATGCA;2342
+
+END
+
+    table3 = <<END
+
+Human       ATACGTCAG   5.24
+Dog         AGCATGAC    4.2
+Mouse       GACTG       3.4
+Cat         AAATGCA     3.42
+
+END
+
+    io   = StringIO.new(table)
+    @csv = BioDSL::CSV.new(io)
+
+    @table  = table
+    @table2 = table2
+    @table3 = table3
+
+    @file = Tempfile.new('foo')
+  end
+
+  def teardown
+    @file.close
+    @file.unlink
+  end
+
+  test "CSV#skip returns correctly" do
+    @csv.skip(3)
+
+    result = []
+    @csv.each_array { |array| result << array }
+
+    expected = [["Mouse", "GACTG", 234],
+                ["Cat", "AAATGCA", 2342]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_array returns correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_array(@file.path)
+    expected = [["Human", "ATACGTCAG", 23524],
+                ["Dog", "AGCATGAC", 2442],
+                ["Mouse", "GACTG", 234],
+                ["Cat", "AAATGCA", 2342]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_array with floats returns correctly" do
+    @file.write(@table3)
+    @file.rewind
+    result   = BioDSL::CSV.read_array(@file.path)
+    expected = [["Human", "ATACGTCAG", 5.24],
+                ["Dog", "AGCATGAC", 4.2],
+                ["Mouse", "GACTG", 3.4],
+                ["Cat", "AAATGCA", 3.42]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_array with include_header: true returns correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_array(@file.path, include_header: true)
+    expected = [["Organism", "Sequence", "Count"],
+                ["Human", "ATACGTCAG", 23524],
+                ["Dog", "AGCATGAC", 2442],
+                ["Mouse", "GACTG", 234],
+                ["Cat", "AAATGCA", 2342]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_array with :delimiter returns correctly" do
+    @file.write(@table2)
+    @file.rewind
+    result   = BioDSL::CSV.read_array(@file.path, delimiter: ";")
+    expected = [["Human", "ATACGTCAG", 23524],
+                ["Dog", "AGCATGAC", 2442],
+                ["Mouse", "GACTG", 234],
+                ["Cat", "AAATGCA", 2342]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_array with :delimiter and :include_header returns correctly" do
+    @file.write(@table2)
+    @file.rewind
+    result   = BioDSL::CSV.read_array(@file.path, delimiter: ";", include_header: true)
+    expected = [["Organism", "Sequence", "Count"],
+                ["Human", "ATACGTCAG", 23524],
+                ["Dog", "AGCATGAC", 2442],
+                ["Mouse", "GACTG", 234],
+                ["Cat", "AAATGCA", 2342]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_array with :select and out-of-bounds numerical value raises" do
+    @file.write(@table)
+    @file.rewind
+    assert_raise(BioDSL::CSVError) { BioDSL::CSV.read_array(@file.path, select: [3]) }
+  end
+
+  test "CSV.read_array with :select of numerical values return correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_array(@file.path, select: [2, 0])
+    expected = [[23524, "Human"],
+                [2442,  "Dog"],
+                [234,   "Mouse"],
+                [2342,  "Cat"]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_array with :select of numerical values and :include_header returns correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_array(@file.path, select: [2, 0], include_header: true)
+    expected = [["Count", "Organism"],
+                [23524, "Human"],
+                [2442,  "Dog"],
+                [234,   "Mouse"],
+                [2342,  "Cat"]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_array with :select and out-of-bounds range raises" do
+    @file.write(@table)
+    @file.rewind
+    assert_raise(BioDSL::CSVError) { BioDSL::CSV.read_array(@file.path, select: 1 .. 3) }
+  end
+
+  test "CSV.read_array with :select of range return correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_array(@file.path, select: 0 .. 1)
+    expected = [["Human", "ATACGTCAG"],
+                ["Dog", "AGCATGAC"],
+                ["Mouse", "GACTG"],
+                ["Cat", "AAATGCA"]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_array with :select of range and :include_header returns correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_array(@file.path, select: 0 .. 1, include_header: true)
+    expected = [["Organism", "Sequence"],
+                ["Human", "ATACGTCAG"],
+                ["Dog", "AGCATGAC"],
+                ["Mouse", "GACTG"],
+                ["Cat", "AAATGCA"]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_array with :select of non-numerical values and no header raises" do
+    @file.write(@table3)
+    @file.rewind
+    assert_raise(BioDSL::CSVError) { BioDSL::CSV.read_array(@file.path, select: ["Organism"]) }
+  end
+
+  test "CSV.read_array with :select of non-numerical values not matching header raises" do
+    @file.write(@table)
+    @file.rewind
+    assert_raise(BioDSL::CSVError) { BioDSL::CSV.read_array(@file.path, select: ["ount"]) }
+  end
+
+  test "CSV.read_array with :select of non-numerical values returns correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_array(@file.path, select: ["Count", :Organism])
+    expected = [[23524, "Human"],
+                [2442,  "Dog"],
+                [234,   "Mouse"],
+                [2342,  "Cat"]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_array with :select of non-numerical values and :include_header returns correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_array(@file.path, select: ["Count", :Organism], include_header: true)
+    expected = [["Count", "Organism"],
+                [23524,   "Human"],
+                [2442,    "Dog"],
+                [234,     "Mouse"],
+                [2342,    "Cat"]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_array with :reject and out-of-bounds numerical value raises" do
+    @file.write(@table)
+    @file.rewind
+    assert_raise(BioDSL::CSVError) { BioDSL::CSV.read_array(@file.path, reject: [3]) }
+  end
+
+  test "CSV.read_array with :reject of numerical values return correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_array(@file.path, reject: [2, 0])
+    expected = [["ATACGTCAG"],
+                ["AGCATGAC"],
+                ["GACTG"],
+                ["AAATGCA"]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_array with :reject of numerical values and :include_header returns correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_array(@file.path, reject: [2, 0], include_header: true)
+    expected = [["Sequence"],
+                ["ATACGTCAG"],
+                ["AGCATGAC"],
+                ["GACTG"],
+                ["AAATGCA"]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_array with :reject and out-of-bounds range raises" do
+    @file.write(@table)
+    @file.rewind
+    assert_raise(BioDSL::CSVError) { BioDSL::CSV.read_array(@file.path, reject: 1 .. 3) }
+  end
+
+  test "CSV.read_array with :reject of range return correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_array(@file.path, reject: 0 .. 1)
+    expected = [[23524],
+                [2442],
+                [234],
+                [2342]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_array with :reject of range and :include_header returns correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_array(@file.path, reject: 0 .. 1, include_header: true)
+    expected = [["Count"],
+                [23524],
+                [2442],
+                [234],
+                [2342]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_array with :reject of non-numerical values and no header raises" do
+    @file.write(@table3)
+    @file.rewind
+    assert_raise(BioDSL::CSVError) { BioDSL::CSV.read_array(@file.path, reject: ["Organism"]) }
+  end
+
+  test "CSV.read_array with :reject of non-numerical values not matching header raises" do
+    @file.write(@table)
+    @file.rewind
+    assert_raise(BioDSL::CSVError) { BioDSL::CSV.read_array(@file.path, reject: ["ount"]) }
+  end
+
+  test "CSV.read_array with :reject of non-numerical values returns correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_array(@file.path, reject: ["Count", :Organism])
+    expected = [["ATACGTCAG"],
+                ["AGCATGAC"],
+                ["GACTG"],
+                ["AAATGCA"]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_array with :reject of non-numerical values and :include_header returns correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_array(@file.path, reject: ["Count", :Organism], include_header: true)
+    expected = [["Sequence"],
+                ["ATACGTCAG"],
+                ["AGCATGAC"],
+                ["GACTG"],
+                ["AAATGCA"]]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_hash returns correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_hash(@file.path)
+    expected = [{Count: 23524, Organism: "Human", Sequence: "ATACGTCAG"},
+                {Count: 2442,  Organism: "Dog",   Sequence: "AGCATGAC"},
+                {Count: 234,   Organism: "Mouse", Sequence: "GACTG"},
+                {Count: 2342,  Organism: "Cat",   Sequence: "AAATGCA"}]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_hash with no header returns correctly" do
+    @file.write(@table3)
+    @file.rewind
+    result   = BioDSL::CSV.read_hash(@file.path)
+    expected = [{V0: "Human", V1: "ATACGTCAG", V2: 5.24},
+                {V0: "Dog",   V1: "AGCATGAC",  V2: 4.2},
+                {V0: "Mouse", V1: "GACTG",     V2: 3.4},
+                {V0: "Cat",   V1: "AAATGCA",   V2: 3.42}]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_hash with :delimiter returns correctly" do
+    @file.write(@table2)
+    @file.rewind
+    result   = BioDSL::CSV.read_hash(@file.path, delimiter: ";")
+    expected = [{:Count=>23524, :Organism=>"Human", :Sequence=>"ATACGTCAG"},
+                {:Count=>2442,  :Organism=>"Dog",   :Sequence=>"AGCATGAC"},
+                {:Count=>234,   :Organism=>"Mouse", :Sequence=>"GACTG"},
+                {:Count=>2342,  :Organism=>"Cat",   :Sequence=>"AAATGCA"}]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_hash with :select and out-of-bounds numerical value raises" do
+    @file.write(@table)
+    @file.rewind
+    assert_raise(BioDSL::CSVError) { BioDSL::CSV.read_hash(@file.path, select: [3]) }
+  end
+
+  test "CSV.read_hash with :select of numerical values return correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_hash(@file.path, select: [2, 0])
+    expected = [{:Count=>23524, :Organism=>"Human"},
+                {:Count=>2442,  :Organism=>"Dog"},
+                {:Count=>234,   :Organism=>"Mouse"},
+                {:Count=>2342,  :Organism=>"Cat"}]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_hash with :select and out-of-bounds range raises" do
+    @file.write(@table)
+    @file.rewind
+    assert_raise(BioDSL::CSVError) { BioDSL::CSV.read_hash(@file.path, select: 1 .. 3) }
+  end
+
+  test "CSV.read_hash with :select of range return correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_hash(@file.path, select: 0 .. 1)
+    expected = [{:Organism=>"Human", :Sequence=>"ATACGTCAG"},
+                {:Organism=>"Dog",   :Sequence=>"AGCATGAC"},
+                {:Organism=>"Mouse", :Sequence=>"GACTG"},
+                {:Organism=>"Cat",   :Sequence=>"AAATGCA"}]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_hash with :select of non-numerical values and no header raises" do
+    @file.write(@table3)
+    @file.rewind
+    assert_raise(BioDSL::CSVError) { BioDSL::CSV.read_hash(@file.path, select: ["Organism"]) }
+  end
+
+  test "CSV.read_hash with :select of non-numerical values not matching header raises" do
+    @file.write(@table)
+    @file.rewind
+    assert_raise(BioDSL::CSVError) { BioDSL::CSV.read_hash(@file.path, select: ["ount"]) }
+  end
+
+  test "CSV.read_hash with :select of non-numerical values returns correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_hash(@file.path, select: ["Count", :Organism])
+    expected = [{:Count=>23524, :Organism=>"Human"},
+                {:Count=>2442,  :Organism=>"Dog"},
+                {:Count=>234,   :Organism=>"Mouse"},
+                {:Count=>2342,  :Organism=>"Cat"}]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_hash with :reject and out-of-bounds numerical value raises" do
+    @file.write(@table)
+    @file.rewind
+    assert_raise(BioDSL::CSVError) { BioDSL::CSV.read_hash(@file.path, reject: [3]) }
+  end
+
+  test "CSV.read_hash with :reject of numerical values return correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_hash(@file.path, reject: [2, 0])
+    expected = [{:Sequence=>"ATACGTCAG"},
+                {:Sequence=>"AGCATGAC"},
+                {:Sequence=>"GACTG"},
+                {:Sequence=>"AAATGCA"}]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_hash with :reject and out-of-bounds range raises" do
+    @file.write(@table)
+    @file.rewind
+    assert_raise(BioDSL::CSVError) { BioDSL::CSV.read_hash(@file.path, reject: 1 .. 3) }
+  end
+
+  test "CSV.read_hash with :reject of range return correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_hash(@file.path, reject: 0 .. 1)
+    expected = [{:Count=>23524},
+                {:Count=>2442},
+                {:Count=>234},
+                {:Count=>2342}]
+
+    assert_equal(expected, result)
+  end
+
+  test "CSV.read_hash with :reject of non-numerical values and no header raises" do
+    @file.write(@table3)
+    @file.rewind
+    assert_raise(BioDSL::CSVError) { BioDSL::CSV.read_hash(@file.path, reject: ["Organism"]) }
+  end
+
+  test "CSV.read_hash with :reject of non-numerical values not matching header raises" do
+    @file.write(@table)
+    @file.rewind
+    assert_raise(BioDSL::CSVError) { BioDSL::CSV.read_hash(@file.path, reject: ["ount"]) }
+  end
+
+  test "CSV.read_hash with :reject of non-numerical values returns correctly" do
+    @file.write(@table)
+    @file.rewind
+    result   = BioDSL::CSV.read_hash(@file.path, reject: ["Count", :Organism])
+    expected = [{:Sequence=>"ATACGTCAG"},
+                {:Sequence=>"AGCATGAC"},
+                {:Sequence=>"GACTG"},
+                {:Sequence=>"AAATGCA"}]
+
+    assert_equal(expected, result)
+  end
+end

data/test/BioDSL/test_debug.rb

@@ -0,0 +1,42 @@
+#!/usr/bin/env ruby
+$:.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.BioDSL.org).                        #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+require 'test/helper'
+
+class DebugTest < Test::Unit::TestCase
+  def teardown
+    BioDSL::debug = false
+  end
+
+  test "BioDSL::debug returns correctly" do
+    BioDSL::debug = true
+    assert_equal(true, BioDSL::debug)
+  end
+end
+