BioDSL 1.0.0

data/test/BioDSL/commands/test_align_seq_mothur.rb

@@ -0,0 +1,99 @@
+#!/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 AlignSeqMothur.
+class TestAlignSeqMothur < Test::Unit::TestCase
+  def setup
+    require 'tempfile'
+
+    omit('mothur not found') unless BioDSL::Filesys.which('mothur')
+
+    @template = Tempfile.new('template')
+
+    write_template
+
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    @output.write(SEQ_NAME: 'test', SEQ: 'gattccgatcgatcgatcga')
+    @output.close
+
+    @p = BP.new
+  end
+
+  def write_template
+    seq_name = 'ref'
+    seq      = '--a-ttc--c-a-tcga----Ttcg-at---cCa---'
+    BioDSL::Fasta.open(@template, 'w') do |ios|
+      ios.puts BioDSL::Seq.new(seq_name: seq_name, seq: seq).to_fasta
+    end
+  end
+
+  def teardown
+    @template.close
+    @template.unlink
+  end
+
+  test 'BioDSL::Pipeline#align_seq_mothur with disallowed option raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.align_seq_mothur(template_file: @template, foo: 'bar')
+    end
+  end
+
+  test 'BioDSL::Pipeline#align_seq_mothur w. allowed option don\'t raise' do
+    assert_nothing_raised do
+      @p.align_seq_mothur(template_file: @template, cpus: 2)
+    end
+  end
+
+  test 'BioDSL::Pipeline#align_seq_mothur outputs correctly' do
+    @p.align_seq_mothur(template_file: @template.path).
+      run(input: @input, output: @output2)
+
+    expected = '{:SEQ_NAME=>"test", ' \
+      ':SEQ=>"..A-TTC--CGA-TCGA-----TCG-AT---CGA...", :SEQ_LEN=>37}'
+
+    assert_equal(expected, collect_result.chomp)
+  end
+
+  test 'BioDSL::Pipeline#align_seq_mothur status returns correctly' do
+    @p.align_seq_mothur(template_file: @template.path).
+      run(input: @input, output: @output2)
+
+    assert_equal(1, @p.status.first[:records_in])
+    assert_equal(1, @p.status.first[:records_out])
+    assert_equal(1, @p.status.first[:sequences_in])
+    assert_equal(1, @p.status.first[:sequences_in])
+    assert_equal(20, @p.status.first[:residues_in])
+    assert_equal(20, @p.status.first[:residues_in])
+  end
+end

data/test/BioDSL/commands/test_analyze_residue_distribution.rb

@@ -0,0 +1,134 @@
+#!/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 AnalyzeResidueDistribution.
+class TestAnalyzeResidueDistribution < Test::Unit::TestCase
+  def setup
+    @tmpdir = Dir.mktmpdir('BioDSL')
+    @file   = File.join(@tmpdir, 'test.plot')
+
+    @input, @output   = BioDSL::Stream.pipe
+    @input2, @output2 = BioDSL::Stream.pipe
+
+    [{SEQ: 'AGCT'},
+     {SEQ: 'AGCU'},
+     {SEQ: 'FLS*'},
+     {SEQ: '-.~'},
+     {FOO: 'BAR'}].each do |record|
+      @output.write(record)
+    end
+
+    @output.close
+
+    @p = BP.new
+  end
+
+  def teardown
+    FileUtils.rm_r @tmpdir
+  end
+
+  test 'BioDSL::Pipeline#analyze_residue_distribution with disallowed ' \
+    'option raises' do
+    assert_raise(BioDSL::OptionError) do
+      @p.analyze_residue_distribution(foo: 'bar')
+    end
+  end
+
+  test 'BioDSL::Pipeline#analyze_residue_distribution with allowed ' \
+    'options don\'t raise' do
+    assert_nothing_raised { @p.analyze_residue_distribution(percent: true) }
+  end
+
+  # rubocop:disable Metrics/LineLength
+
+  test 'BioDSL::Pipeline#analyze_residue_distribution returns correctly' do
+    @p.analyze_residue_distribution.run(input: @input, output: @output2)
+    expected = <<-EOD.gsub(/^\s*\|/, '')
+      |{:SEQ=>"AGCT"}
+      |{:SEQ=>"AGCU"}
+      |{:SEQ=>"FLS*"}
+      |{:SEQ=>"-.~"}
+      |{:FOO=>"BAR"}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"A", :V1=>2, :V2=>0, :V3=>0, :V4=>0}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"G", :V1=>0, :V2=>2, :V3=>0, :V4=>0}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"C", :V1=>0, :V2=>0, :V3=>2, :V4=>0}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"T", :V1=>0, :V2=>0, :V3=>0, :V4=>1}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"U", :V1=>0, :V2=>0, :V3=>0, :V4=>1}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"F", :V1=>1, :V2=>0, :V3=>0, :V4=>0}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"L", :V1=>0, :V2=>1, :V3=>0, :V4=>0}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"S", :V1=>0, :V2=>0, :V3=>1, :V4=>0}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"*", :V1=>0, :V2=>0, :V3=>0, :V4=>1}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"-", :V1=>1, :V2=>0, :V3=>0, :V4=>0}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>".", :V1=>0, :V2=>1, :V3=>0, :V4=>0}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"~", :V1=>0, :V2=>0, :V3=>1, :V4=>0}
+    EOD
+    assert_equal(expected, collect_result)
+  end
+
+  test 'BioDSL::Pipeline#analyze_residue_distribution with :precent returns correctly' do
+    @p.analyze_residue_distribution(percent: true).run(input: @input, output: @output2)
+    expected = <<-EOD.gsub(/^\s*\|/, '')
+      |{:SEQ=>"AGCT"}
+      |{:SEQ=>"AGCU"}
+      |{:SEQ=>"FLS*"}
+      |{:SEQ=>"-.~"}
+      |{:FOO=>"BAR"}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"A", :V1=>50, :V2=>0,  :V3=>0,  :V4=>0}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"G", :V1=>0,  :V2=>50, :V3=>0,  :V4=>0}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"C", :V1=>0,  :V2=>0,  :V3=>50, :V4=>0}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"T", :V1=>0,  :V2=>0,  :V3=>0,  :V4=>33}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"U", :V1=>0,  :V2=>0,  :V3=>0,  :V4=>33}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"F", :V1=>25, :V2=>0,  :V3=>0,  :V4=>0}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"L", :V1=>0,  :V2=>25, :V3=>0,  :V4=>0}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"S", :V1=>0,  :V2=>0,  :V3=>25, :V4=>0}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"*", :V1=>0,  :V2=>0,  :V3=>0,  :V4=>33}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"-", :V1=>25, :V2=>0,  :V3=>0,  :V4=>0}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>".", :V1=>0,  :V2=>25, :V3=>0,  :V4=>0}
+      |{:RECORD_TYPE=>"residue distribution", :V0=>"~", :V1=>0,  :V2=>0,  :V3=>25, :V4=>0}
+    EOD
+    assert_equal(expected.gsub(/  /, ' '), collect_result)
+  end
+
+  # rubocop:enable Metrics/LineLength
+
+  test 'BioDSL::Pipeline#analyze_residue_distribution status returns OK' do
+    @p.analyze_residue_distribution(percent: true).
+      run(input: @input, output: @output2)
+
+    assert_equal(5, @p.status.first[:records_in])
+    assert_equal(5, @p.status.first[:records_out])
+    assert_equal(4, @p.status.first[:sequences_in])
+    assert_equal(4, @p.status.first[:sequences_in])
+    assert_equal(15, @p.status.first[:residues_in])
+    assert_equal(15, @p.status.first[:residues_in])
+  end
+end