BioDSL 1.0.0

data/test/BioDSL/test_fasta.rb

@@ -0,0 +1,154 @@
+#!/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 FastaTest < Test::Unit::TestCase
+  def setup
+    @file = Tempfile.new("fasta")
+  end
+
+  def teardown
+    File.unlink("#{@file.path}.gz")  if File.exist? "#{@file.path}.gz"  
+    File.unlink("#{@file.path}.bz2") if File.exist? "#{@file.path}.bz2"  
+    @file.close
+    @file.unlink
+  end
+
+  test "BioDSL::Fasta#read with non-existing file raises" do
+    assert_raise(Errno::ENOENT) { BioDSL::Fasta.read("dasf") }
+  end
+
+  test "BioDSL::Fasta#read with empty files return empty" do
+    assert_equal([], BioDSL::Fasta.read(@file))
+  end
+
+  test "BioDSL::Fasta#read with two entries return correctly" do
+    File.open(@file, 'w') do |ios|
+ios.puts <<EOD
+>test1
+atcg
+>test2
+gtT
+EOD
+    end
+
+    @file.close
+
+    assert_equal([">test1\natcg\n", ">test2\ngtT\n"], BioDSL::Fasta.read(@file).map { |e| e.to_fasta } )
+  end
+
+  test "BioDSL::Fasta#read from gzip with two entries return correctly" do
+    File.open(@file, 'w') do |ios|
+ios.puts <<EOD
+>test1
+atcg
+>test2
+gtT
+EOD
+    end
+
+    @file.close
+
+    `gzip #{@file.path}`
+
+    assert_equal([">test1\natcg\n", ">test2\ngtT\n"], BioDSL::Fasta.read("#{@file.path}.gz").map { |e| e.to_fasta } )
+  end
+
+  test "BioDSL::Fasta#read from bzip2 with two entries return correctly" do
+    File.open(@file, 'w') do |ios|
+ios.puts <<EOD
+>test1
+atcg
+>test2
+gtT
+EOD
+    end
+
+    @file.close
+
+    `bzip2 #{@file.path}`
+
+    assert_equal([">test1\natcg\n", ">test2\ngtT\n"], BioDSL::Fasta.read("#{@file.path}.bz2").map { |e| e.to_fasta } )
+  end
+
+  test "BioDSL::Fasta#read with two entries and white space return correctly" do
+    File.open(@file, 'w') do |ios|
+ios.puts <<EOD
+
+>test1
+
+at
+
+cg
+
+>test2
+
+gt
+
+T
+
+EOD
+    end
+
+    @file.close
+
+    assert_equal([">test1\natcg\n", ">test2\ngtT\n"], BioDSL::Fasta.read(@file).map { |e| e.to_fasta } )
+  end
+
+  test "BioDSL::Fasta#read with content and missing seq_name raises" do
+    File.open(@file, 'w') do |ios|
+      ios.puts "tyt"
+    end
+
+    @file.close
+
+    assert_raise(BioDSL::FastaError) { BioDSL::Fasta.read(@file) }
+  end
+
+  test "BioDSL::Fasta#read with content before first entry raises" do
+    File.open(@file, 'w') do |ios|
+      ios.puts "foo\n>bar\natcg"
+    end
+
+    @file.close
+
+    assert_raise(BioDSL::FastaError) { BioDSL::Fasta.read(@file) }
+  end
+
+  test "BioDSL::Fasta#read with content and truncated seq_name raises" do
+    File.open(@file, 'w') do |ios|
+      ios.puts ">\ntyt"
+    end
+
+    @file.close
+
+    assert_raise(BioDSL::FastaError) { BioDSL::Fasta.read(@file) }
+  end
+end

data/test/BioDSL/test_fastq.rb

@@ -0,0 +1,46 @@
+#!/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 FastqTest < Test::Unit::TestCase
+  def setup
+    @io    = StringIO.new("@test1\nATCG\n+\nABCD\n@test2\natcg\n+test2\n@ABG\n")
+    @fastq = BioDSL::Fastq.new(@io)
+  end
+
+  test "#next_entry obtains the correct seq_name" do
+    assert_equal("test1", @fastq.next_entry.seq_name)
+  end
+
+  test "#next_entry with two entries obtain correct sequences" do
+    assert_equal("ATCG", @fastq.next_entry.seq)
+    assert_equal("atcg", @fastq.next_entry.seq)
+  end
+end

data/test/BioDSL/test_filesys.rb

@@ -0,0 +1,145 @@
+#!/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 FilesysTest < Test::Unit::TestCase
+  def setup
+    @zcat = BioDSL::Filesys::which('gzcat') || BioDSL::Filesys::which('zcat')
+
+    @tmpdir     = Dir.mktmpdir("BioDSL")
+    @file       = File.join(@tmpdir, 'test.txt')
+    file_gzip   = File.join(@tmpdir, 'test_gzip.txt')
+    file_bzip2  = File.join(@tmpdir, 'test_bzip2.txt')
+    @file_gzip  = File.join(@tmpdir, 'test_gzip.txt.gz')
+    @file_bzip2 = File.join(@tmpdir, 'test_bzip2.txt.bz2')
+
+    File.open(@file, 'w')      { |ios| ios << "foobar" }
+    File.open(file_gzip, 'w')  { |ios| ios << "foobar" }
+    File.open(file_bzip2, 'w') { |ios| ios << "foobar" }
+
+    `gzip #{file_gzip}`
+    `bzip2 #{file_bzip2}`
+  end
+
+  def teardown
+    FileUtils.rm_r @tmpdir
+  end
+
+
+  test "#which with non-existing executable returns nil" do
+    assert_nil(BioDSL::Filesys.which("__env__"))
+  end
+
+  test "#which with existing executable returns correctly" do
+    assert_equal("/usr/bin/env", BioDSL::Filesys.which("env"))
+  end
+
+  test "#tmpfile returns correctly" do
+    assert_equal(@tmpdir, BioDSL::Filesys.tmpfile(@tmpdir).match(/^#{@tmpdir}/).to_s)
+  end
+
+  test "#open in read mode returns correctly" do
+    ios = BioDSL::Filesys.open(@file)
+    assert_equal("foobar", ios.read)
+    ios.close
+  end
+
+  test "#open in read mode with block context returns correctly" do
+    BioDSL::Filesys.open(@file) { |ios| assert_equal("foobar", ios.read) }
+  end
+
+  test "#open in write mode outputs correctly" do
+    ios = BioDSL::Filesys.open(@file, 'w')
+    ios.write "foobar"
+    ios.close
+    File.open(@file) { |ios2| assert_equal("foobar", ios2.read) }
+  end
+
+  test "#open in write mode with block context outputs correctly" do
+    BioDSL::Filesys.open(@file, 'w') { |ios| ios.write "foobar" }
+    File.open(@file) { |ios| assert_equal("foobar", ios.read) }
+  end
+
+  test "#open gzip in read mode returns correctly" do
+    ios = BioDSL::Filesys.open(@file_gzip)
+    assert_equal("foobar", ios.read)
+    ios.close
+  end
+
+  test "#open gzip in read mode with block context returns correctly" do
+    BioDSL::Filesys.open(@file_gzip) { |ios| assert_equal("foobar", ios.read) }
+  end
+
+  test "#open gzip in write mode outputs correctly" do
+    ios = BioDSL::Filesys.open(@file, 'w', compress: :gzip)
+    ios.write "foobar"
+    ios.close
+    result = `#{@zcat} #{@file}`
+    assert_equal("foobar", result)
+  end
+
+  test "#open gzip in write mode with block context outputs correctly" do
+    BioDSL::Filesys.open(@file, 'w', compress: :gzip) { |ios| ios.write "foobar" }
+    result = `#{@zcat} #{@file}`
+    assert_equal("foobar", result)
+  end
+
+  test "#open bzip2 in read mode returns correctly" do
+    ios = BioDSL::Filesys.open(@file_bzip2)
+    assert_equal("foobar", ios.read)
+    ios.close
+  end
+
+  test "#open bzip2 in read mode with block context returns correctly" do
+    BioDSL::Filesys.open(@file_bzip2) { |ios| assert_equal("foobar", ios.read) }
+  end
+
+  test "#open bzip2 in write mode outputs correctly" do
+    ios = BioDSL::Filesys.open(@file, 'w', compress: :bzip2)
+    ios.write "foobar"
+    ios.close
+    result = `bzcat #{@file}`
+    assert_equal("foobar", result)
+  end
+
+  test "#open bzip2 in write mode with block context outputs correctly" do
+    BioDSL::Filesys.open(@file, 'w', compress: :bzip2) { |ios| ios.write "foobar" }
+    result = `bzcat #{@file}`
+    assert_equal("foobar", result)
+  end
+
+  test "#open if eof? returns correctly" do
+    ios = BioDSL::Filesys.open(@file)
+    assert_equal(false, ios.eof?)
+    ios.read
+    assert_equal(true, ios.eof?)
+    ios.close
+  end
+end

data/test/BioDSL/test_fork.rb

@@ -0,0 +1,85 @@
+#!/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 TestFork < Test::Unit::TestCase 
+  def setup
+    @obj = {foo: "bar"}
+  end
+
+  test "BioDSL::Fork.new without block raises" do
+    assert_raise(ArgumentError) { BioDSL::Fork.new }
+  end
+
+  test "BioDSL::Fork.read with no running fork raises" do
+    parent = BioDSL::Fork.new do |child|
+    end
+
+    assert_raise(BioDSL::ForkError) { parent.read }
+  end
+
+  test "BioDSL::Fork.write with no running fork raises" do
+    parent = BioDSL::Fork.new do |child|
+    end
+
+    assert_raise(BioDSL::ForkError) { parent.write @obj }
+  end
+
+  test "BioDSL::Fork.wait with no running fork raises" do
+    parent = BioDSL::Fork.new do |child|
+    end
+
+    assert_raise(BioDSL::ForkError) { parent.wait }
+  end
+
+  test "BioDSL::Fork.wait with running fork don't raise" do
+    parent = BioDSL::Fork.execute do |child|
+    end
+
+    assert_nothing_raised { parent.wait }
+  end
+
+  test "BioDSL::Fork IPC returns correctly" do
+    parent = BioDSL::Fork.execute do |child|
+      obj = child.read
+      obj[:child] = true
+      child.write obj
+    end
+
+    parent.write @obj
+    parent.output.close
+
+    result = parent.read
+
+    parent.wait
+
+    assert_equal({foo: "bar", child: true}, result)
+  end
+end

data/test/BioDSL/test_math.rb

@@ -0,0 +1,41 @@
+#!/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 MathTest < Test::Unit::TestCase
+  test "BioDSL::Math#dist_point2point returns correctly" do
+    assert_equal(1.5, BioDSL::Math.dist_point2point(1.0, 1.0, 1.0, 2.5))
+  end
+
+  test "BioDSL::Math#dist_point2line returns correctly" do
+    assert_equal(1.5, BioDSL::Math.dist_point2line( 3, 3, 0, 4.5, 5, 4.5))
+  end
+end
+

data/test/BioDSL/test_mummer.rb

@@ -0,0 +1,79 @@
+#!/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 Mummer.
+class TestMummer < Test::Unit::TestCase
+  def setup
+    omit('mummer not found') unless BioDSL::Filesys.which('mummer')
+
+    @entry1 = BioDSL::Seq.new(seq_name: 'test1', seq: 'ctagcttcaacctagctag')
+    @entry2 = BioDSL::Seq.new(seq_name: 'test2', seq: 'ctagcttcaGacctagctag')
+  end
+
+  test 'Mummer.each_mem with bad :length_min fails' do
+    assert_raise(BioDSL::MummerError) do
+      BioDSL::Mummer.each_mem(@entry1, @entry2, length_min: 0)
+    end
+
+    assert_raise(BioDSL::MummerError) do
+      BioDSL::Mummer.each_mem(@entry1, @entry2, length_min: 5.5)
+    end
+  end
+
+  test 'Mummer.each_mem with bad :direction fails' do
+    assert_raise(BioDSL::MummerError) do
+      BioDSL::Mummer.each_mem(@entry1, @entry2, direction: 'up')
+    end
+  end
+
+  test 'Mummer#each_mem returns OK' do
+    mems     = BioDSL::Mummer.each_mem(@entry1, @entry2, length_min: 9)
+    expected = <<-END.gsub(/^\s+\|/, '')
+      |[#<struct BioDSL::Mummer::Match
+      |  q_id="test2",
+      |  s_id="test1",
+      |  dir="forward",
+      |  s_beg=0,
+      |  q_beg=0,
+      |  hit_len=9>,
+      | #<struct BioDSL::Mummer::Match
+      |  q_id="test2",
+      |  s_id="test1",
+      |  dir="forward",
+      |  s_beg=9,
+      |  q_beg=10,
+      |  hit_len=10>]
+    END
+
+    assert_equal(Enumerator, mems.class)
+    assert_equal(expected.gsub("\n", '').gsub('  ', ' '), mems.to_a.to_s)
+  end
+end