bio 0.7.0

data/test/unit/bio/util/test_contingency_table.rb

@@ -0,0 +1,106 @@
+#
+# test/unit/bio/util/test_contingency_table.rb - Unit test for Bio::ContingencyTable
+#
+#   Copyright (C) 2005 Trevor Wennblom <trevor@corevx.com>
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library 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
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#  $Id: test_contingency_table.rb,v 1.2 2005/11/23 11:55:17 nakao Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4 , 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/util/contingency_table'
+
+module Bio
+  class TestContingencyTable < Test::Unit::TestCase
+ 
+    def lite_example(sequences, max_length, characters)
+
+      output = []
+
+      0.upto(max_length - 1) do |i|
+        (i+1).upto(max_length - 1) do |j|
+          ctable = Bio::ContingencyTable.new( characters )
+          sequences.each do |seq|
+            i_char = seq[i].chr
+            j_char = seq[j].chr
+            ctable.table[i_char][j_char] += 1
+          end
+          chi_square = ctable.chi_square
+          contingency_coefficient = ctable.contingency_coefficient
+          output << [(i+1), (j+1), chi_square, contingency_coefficient]
+        end
+      end
+
+      return output
+    end
+
+
+    def test_lite_example
+      ctable = Bio::ContingencyTable
+      allowed_letters = 'abcdefghijk'.split('')
+
+      seqs = Array.new
+      seqs << 'abcde'
+      seqs << 'abcde'
+      seqs << 'kacje'
+      seqs << 'aacae'
+      seqs << 'akcfa'
+      seqs << 'akcfe'
+
+      length_of_every_sequence = seqs[0].size  # 5 letters long
+
+      results = lite_example(seqs, length_of_every_sequence, allowed_letters)
+
+=begin
+  i           j           chi_square  contingency_coefficient
+  1           2           2.4         0.534522483824849
+  1           3           0.0         0.0
+  1           4           6.0         0.707106781186548
+  1           5           0.24        0.196116135138184
+  2           3           0.0         0.0
+  2           4           12.0        0.816496580927726
+  2           5           2.4         0.534522483824849
+  3           4           0.0         0.0
+  3           5           0.0         0.0
+  4           5           2.4         0.534522483824849
+=end
+
+
+      #assert_equal(2.4, results[0][2])
+      assert_equal('2.4', results[0][2].to_s)
+      assert_equal('0.534522483824849', results[0][3].to_s)
+
+      assert_equal('12.0', results[5][2].to_s)
+      assert_equal('0.816496580927726', results[5][3].to_s)
+
+      assert_equal('2.4', results[9][2].to_s)
+      assert_equal('0.534522483824849', results[9][3].to_s)
+
+      ctable = Bio::ContingencyTable.new
+      ctable.table['a']['t'] = 4
+      ctable.table['a']['g'] = 2
+      ctable.table['g']['t'] = 3
+      assert_equal('1.28571428571429', ctable.chi_square.to_s)
+      assert_equal(ctable.column_sum_all, ctable.row_sum_all)
+      assert_equal(ctable.column_sum_all, ctable.table_sum_all)
+    end
+
+  end
+end

data/test/unit/bio/util/test_sirna.rb

@@ -0,0 +1,258 @@
+#
+# test/unit/bio/util/test_sirna.rb - Unit test for Bio::SiRNA.
+#
+#   Copyright (C) 2005 Mitsuteru C. Nakap <n@bioruby.org>
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library 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
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#  $Id: test_sirna.rb,v 1.1 2005/11/14 14:46:06 nakao Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4 , 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/util/sirna'
+
+module Bio
+  class TestSiRNANew < Test::Unit::TestCase
+    def test_new
+      srand(1)
+      naseq = Bio::Sequence::NA.new("ACGT" * 100).randomize
+      assert(Bio::SiRNA.new(naseq))
+      assert(Bio::SiRNA.new(naseq, 21))
+      assert(Bio::SiRNA.new(naseq, 21, 60.0))
+      assert(Bio::SiRNA.new(naseq, 21, 60.0, 40.0))
+      assert_raise(ArgumentError) { Bio::SiRNA.new(naseq, 21, 60.0, 40.0, 10.0) }
+    end
+
+  end
+
+  class TestSiRNA < Test::Unit::TestCase
+    def setup
+      srand(1)
+      naseq = Bio::Sequence::NA.new("ACGT" * 100).randomize
+      @obj = Bio::SiRNA.new(naseq)
+    end
+
+    def test_antisense_size
+      assert_equal(21, @obj.antisense_size)
+    end
+
+    def test_max_gc_percent
+      assert_equal(60.0, @obj.max_gc_percent)
+    end
+
+    def test_min_gc_percent
+      assert_equal(40.0, @obj.min_gc_percent)
+    end
+
+    def test_uitei?
+      target = "aaGaa"
+      assert_equal(false, @obj.uitei?(target))
+      target = "aaAaa"
+      assert_equal(false, @obj.uitei?(target))
+      target = "G" * 9
+      assert_equal(false, @obj.uitei?(target))
+    end
+
+    def test_reynolds?
+      target = "G" * 9
+      assert_equal(false, @obj.reynolds?(target))
+      target = "aaaaAaaaaaaUaaAaaaaaAaa"
+      assert_equal(true, @obj.reynolds?(target))
+    end
+
+    def test_uitei
+      assert(@obj.uitei)
+    end
+
+    def test_reynolds
+      assert(@obj.reynolds)
+    end
+
+    def test_design
+      assert(@obj.design)
+    end
+
+
+    def test_design_uitei
+      assert(@obj.design('uitei'))
+    end
+
+    def test_design_reynolds
+      assert(@obj.design('reynolds'))
+    end
+  end
+
+  class TestSiRNAPairNew < Test::Unit::TestCase
+    def test_new
+      target = ""
+      sense = ""
+      antisense = ""
+      start = 0
+      stop = 1
+      rule = 'rule'
+      gc_percent = 60.0
+      assert_raise(ArgumentError) { Bio::SiRNA::Pair.new(target, sense, antisense, start, stop, rule) }
+      assert(Bio::SiRNA::Pair.new(target, sense, antisense, start, stop, rule, gc_percent))
+      assert_raise(ArgumentError) { Bio::SiRNA::Pair.new(target, sense, antisense, start, stop, rule, gc_percent, "") }
+    end
+  end
+
+
+  class TestSiRNAPair < Test::Unit::TestCase
+    def setup
+      srand(1)
+      naseq = Bio::Sequence::NA.new("ACGT" * 100).randomize
+      @obj = Bio::SiRNA.new(naseq).design.first
+    end
+
+    def test_target
+      assert_equal("gcggacguaaggaguauuccugu", @obj.target)
+    end
+
+    def test_sense
+      assert_equal("ggacguaaggaguauuccugu", @obj.sense)
+    end
+
+    def test_antisense
+      assert_equal("aggaauacuccuuacguccgc", @obj.antisense)
+    end
+
+    def test_start
+      assert_equal(9, @obj.start)
+    end
+
+    def test_stop
+      assert_equal(32, @obj.stop)
+    end
+
+    def test_rule
+      assert_equal("uitei", @obj.rule)
+    end
+
+    def test_gc_percent
+      assert_equal(52.0, @obj.gc_percent)
+    end
+
+    def test_report
+report =<<END
+### siRNA
+Start: 9
+Stop:  32
+Rule:  uitei
+GC %:  52
+Target:    GCGGACGUAAGGAGUAUUCCUGU
+Sense:       GGACGUAAGGAGUAUUCCUGU
+Antisense: CGCCUGCAUUCCUCAUAAGGA
+END
+      assert_equal(report, @obj.report)
+    end
+  end
+
+  class TestShRNANew < Test::Unit::TestCase
+    def test_new
+      pair = ""
+      assert(Bio::SiRNA::ShRNA.new(pair))
+      assert_raise(ArgumentError) { Bio::SiRNA::ShRNA.new }
+      assert_raise(ArgumentError) { Bio::SiRNA::ShRNA.new(pair, "") }
+    end
+  end
+
+  class TestShRNA < Test::Unit::TestCase
+    def setup
+      srand(1)
+      naseq = Bio::Sequence::NA.new("ACGT" * 100).randomize
+      sirna = Bio::SiRNA.new(naseq)
+      pairs = sirna.design
+      @obj = Bio::SiRNA::ShRNA.new(pairs.first)
+    end
+
+    def test_top_strand
+      @obj.design
+      assert_equal("caccggacguaaggaguauuccugugtgtgctgtccacaggaauacuccuuacgucc", @obj.top_strand)
+    end
+
+    def test_top_strand_class
+      @obj.design
+      assert_equal(Bio::Sequence::NA, @obj.top_strand.class)
+    end
+
+    def test_top_strand_nil
+      assert_equal(nil, @obj.top_strand)
+    end
+
+    def test_bottom_strand
+      @obj.design
+      assert_equal("aaaaggacguaaggaguauuccuguggacagcacacacaggaauacuccuuacgucc", @obj.bottom_strand)
+    end
+
+    def test_bottom_strand_class
+      @obj.design
+      assert_equal(Bio::Sequence::NA, @obj.bottom_strand.class)
+    end
+
+    def test_bottom_strand_nil
+      assert_equal(nil, @obj.bottom_strand)
+    end
+
+    def test_design
+      assert(@obj.design)
+    end
+
+    def test_design_BLOCK_IT
+      assert_raises(NotImplementedError) { @obj.design('BLOCK-IT') }
+    end
+
+    def test_blocK_it
+      assert_equal("aaaaggacguaaggaguauuccuguggacagcacacacaggaauacuccuuacgucc", @obj.block_it)
+    end
+
+    def test_blocK_it_BLOCK_iT
+      assert_equal("aaaaggacguaaggaguauuccuguggacagcacacacaggaauacuccuuacgucc", @obj.block_it)
+    end
+
+    def test_blocK_it_BLOCK_IT
+      assert_raises(NotImplementedError) { @obj.block_it('BLOCK-IT') }
+    end
+
+    def test_blocK_it_piGene
+      assert_equal("aaaaggacguaaggaguauuccuguggacagcacacacaggaauacuccuuacgucc", @obj.block_it('piGENE'))
+    end
+
+    def test_blocK_it_
+      assert_raises(NotImplementedError) { @obj.block_it("") }
+    end
+    
+    def test_report
+      report =<<END
+### shRNA
+Top strand shRNA (57 nt):
+  5'-CACCGGACGUAAGGAGUAUUCCUGUGTGTGCTGTCCACAGGAAUACUCCUUACGUCC-3'
+Bottom strand shRNA (57 nt):
+      3'-CCUGCAUUCCUCAUAAGGACACACACGACAGGUGUCCUUAUGAGGAAUGCAGGAAAA-5'
+END
+      @obj.design
+      assert_equal(report, @obj.report)
+    end
+
+    def test_report_before_design
+      assert_raises(NoMethodError) { @obj.report }
+    end
+  end
+
+end

metadata

@@ -0,0 +1,295 @@
+--- !ruby/object:Gem::Specification 
+rubygems_version: 0.8.11
+specification_version: 1
+name: bio
+version: !ruby/object:Gem::Version 
+  version: 0.7.0
+date: 2005-12-19 00:00:00 +09:00
+summary: BioRuby is a library for bioinformatics (biology + information science).
+require_paths: 
+  - lib
+email: staff@bioruby.org
+homepage: http://bioruby.org/
+rubyforge_project: 
+description: 
+autorequire: bio
+default_executable: 
+bindir: bin
+has_rdoc: false
+required_ruby_version: !ruby/object:Gem::Version::Requirement 
+  requirements: 
+    - 
+      - ">"
+      - !ruby/object:Gem::Version 
+        version: 0.0.0
+  version: 
+platform: ruby
+signing_key: 
+cert_chain: 
+authors: 
+  - BioRuby project
+files: 
+  - bin/bioruby
+  - bin/br_biofetch.rb
+  - bin/br_bioflat.rb
+  - bin/br_biogetseq.rb
+  - bin/br_pmfetch.rb
+  - doc/BioRuby.rd.ja
+  - doc/Changes-0.7.rd
+  - doc/Design.rd.ja
+  - doc/KEGG_API.rd
+  - doc/KEGG_API.rd.ja
+  - doc/TODO.rd.ja
+  - doc/Tutorial.rd
+  - doc/Tutorial.rd.ja
+  - etc/bioinformatics
+  - etc/bioinformatics/seqdatabase.ini
+  - lib/bio
+  - lib/bio.rb
+  - lib/bioruby.rb
+  - lib/bio/alignment.rb
+  - lib/bio/appl
+  - lib/bio/command.rb
+  - lib/bio/data
+  - lib/bio/db
+  - lib/bio/db.rb
+  - lib/bio/feature.rb
+  - lib/bio/io
+  - lib/bio/location.rb
+  - lib/bio/pathway.rb
+  - lib/bio/reference.rb
+  - lib/bio/sequence.rb
+  - lib/bio/shell
+  - lib/bio/shell.rb
+  - lib/bio/util
+  - lib/bio/appl/bl2seq
+  - lib/bio/appl/blast
+  - lib/bio/appl/blast.rb
+  - lib/bio/appl/blat
+  - lib/bio/appl/clustalw
+  - lib/bio/appl/clustalw.rb
+  - lib/bio/appl/emboss.rb
+  - lib/bio/appl/fasta
+  - lib/bio/appl/fasta.rb
+  - lib/bio/appl/genscan
+  - lib/bio/appl/hmmer
+  - lib/bio/appl/hmmer.rb
+  - lib/bio/appl/mafft
+  - lib/bio/appl/mafft.rb
+  - lib/bio/appl/psort
+  - lib/bio/appl/psort.rb
+  - lib/bio/appl/sim4
+  - lib/bio/appl/sim4.rb
+  - lib/bio/appl/sosui
+  - lib/bio/appl/spidey
+  - lib/bio/appl/targetp
+  - lib/bio/appl/tmhmm
+  - lib/bio/appl/bl2seq/report.rb
+  - lib/bio/appl/blast/format0.rb
+  - lib/bio/appl/blast/format8.rb
+  - lib/bio/appl/blast/report.rb
+  - lib/bio/appl/blast/rexml.rb
+  - lib/bio/appl/blast/wublast.rb
+  - lib/bio/appl/blast/xmlparser.rb
+  - lib/bio/appl/blat/report.rb
+  - lib/bio/appl/clustalw/report.rb
+  - lib/bio/appl/fasta/format10.rb
+  - lib/bio/appl/fasta/format6.rb
+  - lib/bio/appl/genscan/report.rb
+  - lib/bio/appl/hmmer/report.rb
+  - lib/bio/appl/mafft/report.rb
+  - lib/bio/appl/psort/report.rb
+  - lib/bio/appl/sim4/report.rb
+  - lib/bio/appl/sosui/report.rb
+  - lib/bio/appl/spidey/report.rb
+  - lib/bio/appl/targetp/report.rb
+  - lib/bio/appl/tmhmm/report.rb
+  - lib/bio/data/aa.rb
+  - lib/bio/data/codontable.rb
+  - lib/bio/data/na.rb
+  - lib/bio/db/aaindex.rb
+  - lib/bio/db/embl
+  - lib/bio/db/fantom.rb
+  - lib/bio/db/fasta.rb
+  - lib/bio/db/genbank
+  - lib/bio/db/gff.rb
+  - lib/bio/db/go.rb
+  - lib/bio/db/kegg
+  - lib/bio/db/litdb.rb
+  - lib/bio/db/medline.rb
+  - lib/bio/db/nbrf.rb
+  - lib/bio/db/pdb
+  - lib/bio/db/pdb.rb
+  - lib/bio/db/prosite.rb
+  - lib/bio/db/rebase.rb
+  - lib/bio/db/transfac.rb
+  - lib/bio/db/embl/common.rb
+  - lib/bio/db/embl/embl.rb
+  - lib/bio/db/embl/sptr.rb
+  - lib/bio/db/embl/swissprot.rb
+  - lib/bio/db/embl/trembl.rb
+  - lib/bio/db/embl/uniprot.rb
+  - lib/bio/db/genbank/common.rb
+  - lib/bio/db/genbank/ddbj.rb
+  - lib/bio/db/genbank/genbank.rb
+  - lib/bio/db/genbank/genpept.rb
+  - lib/bio/db/genbank/refseq.rb
+  - lib/bio/db/kegg/brite.rb
+  - lib/bio/db/kegg/cell.rb
+  - lib/bio/db/kegg/compound.rb
+  - lib/bio/db/kegg/enzyme.rb
+  - lib/bio/db/kegg/expression.rb
+  - lib/bio/db/kegg/genes.rb
+  - lib/bio/db/kegg/genome.rb
+  - lib/bio/db/kegg/glycan.rb
+  - lib/bio/db/kegg/keggtab.rb
+  - lib/bio/db/kegg/kgml.rb
+  - lib/bio/db/kegg/ko.rb
+  - lib/bio/db/kegg/reaction.rb
+  - lib/bio/db/pdb/atom.rb
+  - lib/bio/db/pdb/chain.rb
+  - lib/bio/db/pdb/model.rb
+  - lib/bio/db/pdb/pdb.rb
+  - lib/bio/db/pdb/residue.rb
+  - lib/bio/db/pdb/utils.rb
+  - lib/bio/io/brdb.rb
+  - lib/bio/io/das.rb
+  - lib/bio/io/dbget.rb
+  - lib/bio/io/ddbjxml.rb
+  - lib/bio/io/fastacmd.rb
+  - lib/bio/io/fetch.rb
+  - lib/bio/io/flatfile
+  - lib/bio/io/flatfile.rb
+  - lib/bio/io/higet.rb
+  - lib/bio/io/keggapi.rb
+  - lib/bio/io/pubmed.rb
+  - lib/bio/io/registry.rb
+  - lib/bio/io/soapwsdl.rb
+  - lib/bio/io/sql.rb
+  - lib/bio/io/flatfile/bdb.rb
+  - lib/bio/io/flatfile/index.rb
+  - lib/bio/io/flatfile/indexer.rb
+  - lib/bio/shell/core.rb
+  - lib/bio/shell/plugin
+  - lib/bio/shell/session.rb
+  - lib/bio/shell/plugin/codon.rb
+  - lib/bio/shell/plugin/entry.rb
+  - lib/bio/shell/plugin/flatfile.rb
+  - lib/bio/shell/plugin/keggapi.rb
+  - lib/bio/shell/plugin/midi.rb
+  - lib/bio/shell/plugin/obda.rb
+  - lib/bio/shell/plugin/seq.rb
+  - lib/bio/util/color_scheme
+  - lib/bio/util/color_scheme.rb
+  - lib/bio/util/contingency_table.rb
+  - lib/bio/util/sirna.rb
+  - lib/bio/util/color_scheme/buried.rb
+  - lib/bio/util/color_scheme/helix.rb
+  - lib/bio/util/color_scheme/hydropathy.rb
+  - lib/bio/util/color_scheme/nucleotide.rb
+  - lib/bio/util/color_scheme/strand.rb
+  - lib/bio/util/color_scheme/taylor.rb
+  - lib/bio/util/color_scheme/turn.rb
+  - lib/bio/util/color_scheme/zappo.rb
+  - sample/biofetch.rb
+  - sample/color_scheme_na.rb
+  - sample/dbget
+  - sample/fasta2tab.rb
+  - sample/fsplit.rb
+  - sample/gb2fasta.rb
+  - sample/gb2tab.rb
+  - sample/gbtab2mysql.rb
+  - sample/genes2nuc.rb
+  - sample/genes2pep.rb
+  - sample/genes2tab.rb
+  - sample/genome2rb.rb
+  - sample/genome2tab.rb
+  - sample/goslim.rb
+  - sample/gt2fasta.rb
+  - sample/pmfetch.rb
+  - sample/pmsearch.rb
+  - sample/psortplot_html.rb
+  - sample/ssearch2tab.rb
+  - sample/tdiary.rb
+  - sample/tfastx2tab.rb
+  - sample/vs-genes.rb
+  - test/data
+  - test/functional
+  - test/runner.rb
+  - test/unit
+  - test/data/blast
+  - test/data/embl
+  - test/data/genscan
+  - test/data/prosite
+  - test/data/refseq
+  - test/data/SOSUI
+  - test/data/TMHMM
+  - test/data/uniprot
+  - test/data/blast/eco:b0002.faa
+  - test/data/blast/eco:b0002.faa.m0
+  - test/data/blast/eco:b0002.faa.m7
+  - test/data/blast/eco:b0002.faa.m8
+  - test/data/embl/AB090716.embl
+  - test/data/genscan/sample.report
+  - test/data/prosite/prosite.dat
+  - test/data/refseq/nm_126355.entret
+  - test/data/SOSUI/sample.report
+  - test/data/TMHMM/sample.report
+  - test/data/uniprot/p53_human.uniprot
+  - test/functional/bio
+  - test/functional/bio/io
+  - test/unit/bio
+  - test/unit/bio/appl
+  - test/unit/bio/data
+  - test/unit/bio/db
+  - test/unit/bio/io
+  - test/unit/bio/shell
+  - test/unit/bio/test_alignment.rb
+  - test/unit/bio/test_command.rb
+  - test/unit/bio/test_db.rb
+  - test/unit/bio/test_feature.rb
+  - test/unit/bio/test_location.rb
+  - test/unit/bio/test_pathway.rb
+  - test/unit/bio/test_sequence.rb
+  - test/unit/bio/test_shell.rb
+  - test/unit/bio/util
+  - test/unit/bio/appl/blast
+  - test/unit/bio/appl/genscan
+  - test/unit/bio/appl/sosui
+  - test/unit/bio/appl/targetp
+  - test/unit/bio/appl/test_blast.rb
+  - test/unit/bio/appl/test_fasta.rb
+  - test/unit/bio/appl/tmhmm
+  - test/unit/bio/appl/blast/test_report.rb
+  - test/unit/bio/appl/blast/test_xmlparser.rb
+  - test/unit/bio/appl/genscan/test_report.rb
+  - test/unit/bio/appl/sosui/test_report.rb
+  - test/unit/bio/appl/targetp/test_report.rb
+  - test/unit/bio/appl/tmhmm/test_report.rb
+  - test/unit/bio/data/test_aa.rb
+  - test/unit/bio/data/test_codontable.rb
+  - test/unit/bio/data/test_na.rb
+  - test/unit/bio/db/embl
+  - test/unit/bio/db/kegg
+  - test/unit/bio/db/test_fasta.rb
+  - test/unit/bio/db/test_gff.rb
+  - test/unit/bio/db/test_prosite.rb
+  - test/unit/bio/db/embl/test_common.rb
+  - test/unit/bio/db/embl/test_embl.rb
+  - test/unit/bio/db/embl/test_sptr.rb
+  - test/unit/bio/db/embl/test_uniprot.rb
+  - test/unit/bio/db/kegg/test_genes.rb
+  - test/unit/bio/io/test_ddbjxml.rb
+  - test/unit/bio/io/test_soapwsdl.rb
+  - test/unit/bio/shell/plugin
+  - test/unit/bio/shell/plugin/test_seq.rb
+  - test/unit/bio/util/test_color_scheme.rb
+  - test/unit/bio/util/test_contingency_table.rb
+  - test/unit/bio/util/test_sirna.rb
+test_files: []
+rdoc_options: []
+extra_rdoc_files: []
+executables: []
+extensions: []
+requirements: []
+dependencies: []