bio 1.4.3.0001 → 1.5.0

data/test/unit/bio/io/test_togows.rb

@@ -5,7 +5,6 @@
 #               Naohisa Goto <ng@bioruby.org>
 # License::     The Ruby License
 #
-#  $Id:$
 #
 
 # loading helper routine for testing bioruby
@@ -59,7 +58,9 @@ module Bio
       a_and_q = {
         '/ab/cde/fghi' => [ 'ab', 'cde', 'fghi' ],
         '/a+b/a%2Bb/a%2Fb/a%26b/a%3Bb/a%2Cb/a%3Bb' =>
-        [ 'a b', 'a+b', 'a/b', 'a&b', 'a;b', 'a,b', 'a;b' ]
+        [ 'a b', 'a+b', 'a/b', 'a&b', 'a;b', 'a,b', 'a;b' ],
+        '/123,456/789%2C012,&345' =>
+        [ '123', :",", '456', '789,012', :",", :"&", '345' ]
       }
       count = 0
       a_and_q.each do |k,v|

data/test/unit/bio/sequence/test_dblink.rb

@@ -54,7 +54,7 @@ module Bio
       assert_equal('Z14088', xref.id)
       assert_equal([ 'CAA78466.1', '-', 'mRNA' ],
                    xref.secondary_ids)
-      end
+    end
   end #class
 
 end #module Bio

data/test/unit/bio/sequence/test_na.rb

@@ -65,6 +65,7 @@ module Bio
       fcomp = @obj.forward_complement
       assert_equal(str_fcomp, @obj.forward_complement)
       assert_equal(str, @obj)
+      assert_not_equal(fcomp.__id__, @obj.forward_complement.__id__)
       assert_equal(str_fcomp, @obj.forward_complement!)
       assert_equal(str_fcomp, @obj)
     end
@@ -72,9 +73,10 @@ module Bio
     def test_reverse_complement
       str       = 'atgcatgcatgcatgcaaaa'
       str_rcomp = 'tacgtacgtacgtacgtttt'.reverse
-      rcomp = @obj.forward_complement
+      rcomp = @obj.reverse_complement
       assert_equal(str_rcomp, @obj.reverse_complement)
       assert_equal(str, @obj)
+      assert_not_equal(rcomp.__id__, @obj.reverse_complement.__id__)
       assert_equal(str_rcomp, @obj.reverse_complement!)
       assert_equal(str_rcomp, @obj)
     end

data/test/unit/bio/test_alignment.rb

@@ -6,7 +6,6 @@
 #              2005 Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id:$
 #
 
 # loading helper routine for testing bioruby
@@ -178,7 +177,7 @@ module Bio
         'a' => [ 'a' ],
         'c' => [ 'c' ],
         'g' => [ 'g' ],
-        't' => [ 't' ],
+#        't' => [ 't' ],
         't' => [ 't', 'u' ],
         'm' => [ 'a', 'c' ],
         'r' => [ 'a', 'g' ],

data/test/unit/bio/test_command.rb

@@ -344,11 +344,12 @@ module Bio
     end
 
     def test_make_cgi_params_by_string
-      string = "type1=bp&type2=bp&downstream=&upstream=&format=fasta&options=similarity&options=gene&action=export&_format=Text&output=txt&submit=Continue%20%3E%3E"
-      # In this case, only URI escaping is performed.
+      ##Before BioRuby 1.4.3.0001, only URI escaping was performed.
+      #string = "type1=bp&type2=bp&downstream=&upstream=&format=fasta&options=similarity&options=gene&action=export&_format=Text&output=txt&submit=Continue%20%3E%3E"
       query = " type1=bp&type2=bp&downstream=&upstream=&format=fasta&options=similarity&options=gene&action=export&_format=Text&output=txt&submit=Continue >> "
-      result = Bio::Command.make_cgi_params(query)
-      assert_equal(string, result)
+      assert_raise(TypeError) {
+        Bio::Command.make_cgi_params(query)
+      }
     end
 
   end

data/test/unit/bio/test_db.rb

@@ -4,7 +4,6 @@
 # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id:$
 #
 
 # loading helper routine for testing bioruby
@@ -21,7 +20,10 @@ module Bio
     def setup
       
      @obj = Bio::DB.new
-      @obj.instance_eval { @orig = {"TAG" => "TAG value1\n    value2"} }
+      @obj.instance_eval {
+        @orig = {"TAG" => "TAG value1\n    value2"}
+        @tagsize = nil
+      }
     end
 
     def test_open

data/test/unit/bio/test_pathway.rb

@@ -43,18 +43,33 @@ module Bio
     end
 
     class TestRelation < Test::Unit::TestCase
+	def setup
+	    @r1 = Relation.new('a', 'b', 1)
+	    @r2 = Relation.new('b', 'a', 1)
+	    @r3 = Relation.new('b', 'a', 2)
+	    @r4 = Relation.new('a', 'b', 1)
+	end
+
 	def test_comparison_operator
-	    r1 = Relation.new('a', 'b', 1)
-	    r2 = Relation.new('b', 'a', 1)
-	    r3 = Relation.new('b', 'a', 2)
-	    r4 = Relation.new('a', 'b', 1)
-	    assert(r1 === r2, "r1 === r2 not true, === not symmetric wrt nodes")
-	    assert(!(r1 === r3), "r1 === r3 not false, === does not take edge into account")
-	    assert(r1 === r4, "r1 === r4 not true, === is not reflexive wrt nodes")
-	    assert_equal([r1, r3], [ r1, r2, r3, r4 ].uniq, "uniq did not have expected effect")
-	    assert(r1.eql?(r2), "r1 not eql r2")
-	    assert(!r3.eql?(r2), "r3 eql to r2")
+	    assert(@r1 === @r2, "@r1 === @r2 not true, === not symmetric wrt nodes")
+	    assert(!(@r1 === @r3), "@r1 === @r3 not false, === does not take edge into account")
+	    assert(@r1 === @r4, "@r1 === @r4 not true, === is not reflexive wrt nodes")
+	    assert(@r1.eql?(@r2), "@r1 not eql @r2")
+	    assert(!@r3.eql?(@r2), "@r3 eql to @r2")
 	end
+
+        def test_uniq
+            a =  [ @r1, @r2, @r3, @r4 ].uniq
+            # Array#uniq does not guarantee that the first value is always
+            # chosen, though the "bug" is fixed.
+            # (https://bugs.ruby-lang.org/issues/9340 )
+            # (https://github.com/bioruby/bioruby/issues/92 )
+            # #assert_equal([@r1, @r3], a, "uniq did not have expected effect")
+            assert_equal(2, a.size)
+	    assert(@r1 === a[0])
+	    assert(@r3 === a[1])
+	end
+
     end
 
     class TestSampleGraph < Test::Unit::TestCase

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

@@ -63,7 +63,7 @@ module Bio
       target = "G" * 9
       assert_equal(false, @obj.reynolds?(target))
       target = "aaaaAaaaaaaUaaAaaaaaAaa"
-      assert_equal(true, @obj.reynolds?(target))
+      assert_equal(8, @obj.reynolds?(target))
     end
 
     def test_uitei
@@ -111,23 +111,23 @@ module Bio
     end
 
     def test_target
-      assert_equal("gcggacguaaggaguauuccugu", @obj.target)
+      assert_equal("uucggugcggacguaaggaguau", @obj.target)
     end
 
     def test_sense
-      assert_equal("ggacguaaggaguauuccugu", @obj.sense)
+      assert_equal("cggugcggacguaaggaguau", @obj.sense)
     end
 
     def test_antisense
-      assert_equal("aggaauacuccuuacguccgc", @obj.antisense)
+      assert_equal("acuccuuacguccgcaccgaa", @obj.antisense)
     end
 
     def test_start
-      assert_equal(9, @obj.start)
+      assert_equal(3, @obj.start)
     end
 
     def test_stop
-      assert_equal(32, @obj.stop)
+      assert_equal(26, @obj.stop)
     end
 
     def test_rule
@@ -135,19 +135,19 @@ module Bio
     end
 
     def test_gc_percent
-      assert_equal(52.0, @obj.gc_percent)
+      assert_equal(57.0, @obj.gc_percent)
     end
 
     def test_report
 report =<<END
 ### siRNA
-Start: 9
-Stop:  32
+Start: 3
+Stop:  26
 Rule:  uitei
-GC %:  52
-Target:    GCGGACGUAAGGAGUAUUCCUGU
-Sense:       GGACGUAAGGAGUAUUCCUGU
-Antisense: CGCCUGCAUUCCUCAUAAGGA
+GC %:  57
+Target:    UUCGGUGCGGACGUAAGGAGUAU
+Sense:       CGGUGCGGACGUAAGGAGUAU
+Antisense: AAGCCACGCCUGCAUUCCUCA
 END
       assert_equal(report, @obj.report)
     end
@@ -172,7 +172,7 @@ END
 
     def test_top_strand
       @obj.design
-      assert_equal("caccggacguaaggaguauuccugugtgtgctgtccacaggaauacuccuuacgucc", @obj.top_strand)
+      assert_equal("caccgcggugcggacguaaggaguaugtgtgctgtccauacuccuuacguccgcaccg", @obj.top_strand)
     end
 
     def test_top_strand_class
@@ -186,7 +186,7 @@ END
 
     def test_bottom_strand
       @obj.design
-      assert_equal("aaaaggacguaaggaguauuccuguggacagcacacacaggaauacuccuuacgucc", @obj.bottom_strand)
+      assert_equal("aaaacggugcggacguaaggaguauggacagcacacauacuccuuacguccgcaccgc", @obj.bottom_strand)
     end
 
     def test_bottom_strand_class
@@ -207,11 +207,11 @@ END
     end
 
     def test_blocK_it
-      assert_equal("aaaaggacguaaggaguauuccuguggacagcacacacaggaauacuccuuacgucc", @obj.block_it)
+      assert_equal("aaaacggugcggacguaaggaguauggacagcacacauacuccuuacguccgcaccgc", @obj.block_it)
     end
 
     def test_blocK_it_BLOCK_iT
-      assert_equal("aaaaggacguaaggaguauuccuguggacagcacacacaggaauacuccuuacgucc", @obj.block_it)
+      assert_equal("aaaacggugcggacguaaggaguauggacagcacacauacuccuuacguccgcaccgc", @obj.block_it)
     end
 
     def test_blocK_it_BLOCK_IT
@@ -219,7 +219,7 @@ END
     end
 
     def test_blocK_it_piGene
-      assert_equal("aaaaggacguaaggaguauuccuguggacagcacacacaggaauacuccuuacgucc", @obj.block_it('piGENE'))
+      assert_equal("aaaacggugcggacguaaggaguauggacagcacacauacuccuuacguccgcaccgc", @obj.block_it('piGENE'))
     end
 
     def test_blocK_it_
@@ -229,10 +229,10 @@ END
     def test_report
       report =<<END
 ### shRNA
-Top strand shRNA (57 nt):
-  5'-CACCGGACGUAAGGAGUAUUCCUGUGTGTGCTGTCCACAGGAAUACUCCUUACGUCC-3'
-Bottom strand shRNA (57 nt):
-      3'-CCUGCAUUCCUCAUAAGGACACACACGACAGGUGUCCUUAUGAGGAAUGCAGGAAAA-5'
+Top strand shRNA (58 nt):
+  5'-CACCGCGGUGCGGACGUAAGGAGUAUGTGTGCTGTCCAUACUCCUUACGUCCGCACCG-3'
+Bottom strand shRNA (58 nt):
+      3'-CGCCACGCCUGCAUUCCUCAUACACACGACAGGUAUGAGGAAUGCAGGCGUGGCAAAA-5'
 END
       #@obj.design
       @obj.block_it

metadata

@@ -1,1455 +1,681 @@
 --- !ruby/object:Gem::Specification
-name: !binary |-
-  Ymlv
+name: bio
 version: !ruby/object:Gem::Version
-  version: !binary |-
-    MS40LjMuMDAwMQ==
-  prerelease: 
+  version: 1.5.0
 platform: ruby
 authors:
-- !binary |-
-  QmlvUnVieSBwcm9qZWN0
+- BioRuby project
 autorequire: 
-bindir: !binary |-
-  Ymlu
+bindir: bin
 cert_chain: []
-date: 2013-05-24 00:00:00.000000000 Z
+date: 2015-07-01 00:00:00.000000000 Z
 dependencies: []
-description: !binary |-
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-  b2d5ICsgaW5mb3JtYXRpb24gc2NpZW5jZSku
-email: !binary |-
-  c3RhZmZAYmlvcnVieS5vcmc=
+description: BioRuby is a library for bioinformatics (biology + information science).
+email: staff@bioruby.org
 executables:
-- !binary |-
-  YmlvcnVieQ==
-- !binary |-
-  YnJfYmlvZmV0Y2gucmI=
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-- !binary |-
-  YnJfYmlvZ2V0c2VxLnJi
-- !binary |-
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+- bioruby
+- br_biofetch.rb
+- br_bioflat.rb
+- br_biogetseq.rb
+- br_pmfetch.rb
 extensions: []
 extra_rdoc_files:
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-  S05PV05fSVNTVUVTLnJkb2M=
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+- KNOWN_ISSUES.rdoc
+- README.rdoc
+- README_DEV.rdoc
+- RELEASE_NOTES.rdoc
+- doc/Changes-1.3.rdoc
+- doc/RELEASE_NOTES-1.4.0.rdoc
+- doc/RELEASE_NOTES-1.4.1.rdoc
+- doc/RELEASE_NOTES-1.4.2.rdoc
+- doc/RELEASE_NOTES-1.4.3.rdoc
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+- ChangeLog
+- GPL
+- KNOWN_ISSUES.rdoc
+- LEGAL
+- LGPL
+- README.rdoc
+- README_DEV.rdoc
+- RELEASE_NOTES.rdoc
+- Rakefile
+- bin/bioruby
+- bin/br_biofetch.rb
+- bin/br_bioflat.rb
+- bin/br_biogetseq.rb
+- bin/br_pmfetch.rb
+- bioruby.gemspec
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+- doc/Tutorial.rd
+- doc/Tutorial.rd.html
+- doc/Tutorial.rd.ja
+- doc/Tutorial.rd.ja.html
+- doc/bioruby.css
+- etc/bioinformatics/seqdatabase.ini
+- gemfiles/Gemfile.travis-jruby1.8
+- gemfiles/Gemfile.travis-jruby1.9
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+- test/data/KEGG/ko00312.pathway
+- test/data/KEGG/map00030.pathway
+- test/data/KEGG/map00052.pathway
+- test/data/KEGG/rn00250.pathway
+- test/data/KEGG/test.kgml
+- test/data/SOSUI/sample.report
+- test/data/TMHMM/sample.report
+- test/data/aaindex/DAYM780301
+- test/data/aaindex/PRAM900102
+- test/data/bl2seq/cd8a_cd8b_blastp.bl2seq
+- test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq
+- test/data/blast/2.2.15.blastp.m7
+- test/data/blast/b0002.faa
+- test/data/blast/b0002.faa.m0
+- test/data/blast/b0002.faa.m7
+- test/data/blast/b0002.faa.m8
+- test/data/blast/blastp-multi.m7
+- test/data/clustalw/example1-seqnos.aln
+- test/data/clustalw/example1.aln
+- test/data/command/echoarg2.bat
+- test/data/command/echoarg2.sh
+- test/data/embl/AB090716.embl
+- test/data/embl/AB090716.embl.rel89
+- test/data/fasta/EFTU_BACSU.fasta
+- test/data/fasta/example1.txt
+- test/data/fasta/example2.txt
+- test/data/fastq/README.txt
+- test/data/fastq/error_diff_ids.fastq
+- test/data/fastq/error_double_qual.fastq
+- test/data/fastq/error_double_seq.fastq
+- test/data/fastq/error_long_qual.fastq
+- test/data/fastq/error_no_qual.fastq
+- test/data/fastq/error_qual_del.fastq
+- test/data/fastq/error_qual_escape.fastq
+- test/data/fastq/error_qual_null.fastq
+- test/data/fastq/error_qual_space.fastq
+- test/data/fastq/error_qual_tab.fastq
+- test/data/fastq/error_qual_unit_sep.fastq
+- test/data/fastq/error_qual_vtab.fastq
+- test/data/fastq/error_short_qual.fastq
+- test/data/fastq/error_spaces.fastq
+- test/data/fastq/error_tabs.fastq
+- test/data/fastq/error_trunc_at_plus.fastq
+- test/data/fastq/error_trunc_at_qual.fastq
+- test/data/fastq/error_trunc_at_seq.fastq
+- test/data/fastq/error_trunc_in_plus.fastq
+- test/data/fastq/error_trunc_in_qual.fastq
+- test/data/fastq/error_trunc_in_seq.fastq
+- test/data/fastq/error_trunc_in_title.fastq
+- test/data/fastq/illumina_full_range_as_illumina.fastq
+- test/data/fastq/illumina_full_range_as_sanger.fastq
+- test/data/fastq/illumina_full_range_as_solexa.fastq
+- test/data/fastq/illumina_full_range_original_illumina.fastq
+- test/data/fastq/longreads_as_illumina.fastq
+- test/data/fastq/longreads_as_sanger.fastq
+- test/data/fastq/longreads_as_solexa.fastq
+- test/data/fastq/longreads_original_sanger.fastq
+- test/data/fastq/misc_dna_as_illumina.fastq
+- test/data/fastq/misc_dna_as_sanger.fastq
+- test/data/fastq/misc_dna_as_solexa.fastq
+- test/data/fastq/misc_dna_original_sanger.fastq
+- test/data/fastq/misc_rna_as_illumina.fastq
+- test/data/fastq/misc_rna_as_sanger.fastq
+- test/data/fastq/misc_rna_as_solexa.fastq
+- test/data/fastq/misc_rna_original_sanger.fastq
+- test/data/fastq/sanger_full_range_as_illumina.fastq
+- test/data/fastq/sanger_full_range_as_sanger.fastq
+- test/data/fastq/sanger_full_range_as_solexa.fastq
+- test/data/fastq/sanger_full_range_original_sanger.fastq
+- test/data/fastq/solexa_full_range_as_illumina.fastq
+- test/data/fastq/solexa_full_range_as_sanger.fastq
+- test/data/fastq/solexa_full_range_as_solexa.fastq
+- test/data/fastq/solexa_full_range_original_solexa.fastq
+- test/data/fastq/wrapping_as_illumina.fastq
+- test/data/fastq/wrapping_as_sanger.fastq
+- test/data/fastq/wrapping_as_solexa.fastq
+- test/data/fastq/wrapping_original_sanger.fastq
+- test/data/gcg/pileup-aa.msf
+- test/data/genbank/CAA35997.gp
+- test/data/genbank/SCU49845.gb
+- test/data/genscan/sample.report
+- test/data/go/selected_component.ontology
+- test/data/go/selected_gene_association.sgd
+- test/data/go/selected_wikipedia2go
+- test/data/iprscan/merged.raw
+- test/data/iprscan/merged.txt
+- test/data/litdb/1717226.litdb
+- test/data/medline/20146148_modified.medline
+- test/data/meme/db
+- test/data/meme/mast
+- test/data/meme/mast.out
+- test/data/meme/meme.out
+- test/data/paml/codeml/control_file.txt
+- test/data/paml/codeml/models/aa.aln
+- test/data/paml/codeml/models/aa.dnd
+- test/data/paml/codeml/models/aa.ph
+- test/data/paml/codeml/models/alignment.phy
+- test/data/paml/codeml/models/results0-3.txt
+- test/data/paml/codeml/models/results7-8.txt
+- test/data/paml/codeml/output.txt
+- test/data/paml/codeml/rates
+- test/data/phyloxml/apaf.xml
+- test/data/phyloxml/bcl_2.xml
+- test/data/phyloxml/made_up.xml
+- test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml
+- test/data/phyloxml/phyloxml_examples.xml
+- test/data/pir/CRAB_ANAPL.pir
+- test/data/prosite/prosite.dat
+- test/data/refseq/nm_126355.entret
+- test/data/rpsblast/misc.rpsblast
+- test/data/sanger_chromatogram/test_chromatogram_abif.ab1
+- test/data/sanger_chromatogram/test_chromatogram_scf_v2.scf
+- test/data/sanger_chromatogram/test_chromatogram_scf_v3.scf
+- test/data/sim4/complement-A4.sim4
+- test/data/sim4/simple-A4.sim4
+- test/data/sim4/simple2-A4.sim4
+- test/data/soft/GDS100_partial.soft
+- test/data/soft/GSE3457_family_partial.soft
+- test/data/uniprot/p53_human.uniprot
+- test/functional/bio/sequence/test_output_embl.rb
+- test/functional/bio/test_command.rb
+- test/network/bio/appl/blast/test_remote.rb
+- test/network/bio/appl/test_blast.rb
+- test/network/bio/appl/test_pts1.rb
+- test/network/bio/io/test_pubmed.rb
+- test/network/bio/io/test_togows.rb
+- test/network/bio/test_command.rb
+- test/runner.rb
+- test/unit/bio/appl/bl2seq/test_report.rb
+- test/unit/bio/appl/blast/test_ncbioptions.rb
+- test/unit/bio/appl/blast/test_report.rb
+- test/unit/bio/appl/blast/test_rpsblast.rb
+- test/unit/bio/appl/clustalw/test_report.rb
+- test/unit/bio/appl/gcg/test_msf.rb
+- test/unit/bio/appl/genscan/test_report.rb
+- test/unit/bio/appl/hmmer/test_report.rb
+- test/unit/bio/appl/iprscan/test_report.rb
+- test/unit/bio/appl/mafft/test_report.rb
+- test/unit/bio/appl/meme/mast/test_report.rb
+- test/unit/bio/appl/meme/test_mast.rb
+- test/unit/bio/appl/meme/test_motif.rb
+- test/unit/bio/appl/paml/codeml/test_rates.rb
+- test/unit/bio/appl/paml/codeml/test_report.rb
+- test/unit/bio/appl/paml/codeml/test_report_single.rb
+- test/unit/bio/appl/paml/test_codeml.rb
+- test/unit/bio/appl/sim4/test_report.rb
+- test/unit/bio/appl/sosui/test_report.rb
+- test/unit/bio/appl/targetp/test_report.rb
+- test/unit/bio/appl/test_blast.rb
+- test/unit/bio/appl/test_fasta.rb
+- test/unit/bio/appl/test_pts1.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/biosql/tc_biosql.rb
+- test/unit/bio/db/biosql/ts_suite_biosql.rb
+- test/unit/bio/db/embl/test_common.rb
+- test/unit/bio/db/embl/test_embl.rb
+- test/unit/bio/db/embl/test_embl_rel89.rb
+- test/unit/bio/db/embl/test_embl_to_bioseq.rb
+- test/unit/bio/db/embl/test_uniprot.rb
+- test/unit/bio/db/embl/test_uniprotkb.rb
+- test/unit/bio/db/embl/test_uniprotkb_new_part.rb
+- test/unit/bio/db/fasta/test_defline.rb
+- test/unit/bio/db/fasta/test_defline_misc.rb
+- test/unit/bio/db/fasta/test_format_qual.rb
+- test/unit/bio/db/genbank/test_common.rb
+- test/unit/bio/db/genbank/test_genbank.rb
+- test/unit/bio/db/genbank/test_genpept.rb
+- test/unit/bio/db/kegg/test_compound.rb
+- test/unit/bio/db/kegg/test_drug.rb
+- test/unit/bio/db/kegg/test_enzyme.rb
+- test/unit/bio/db/kegg/test_genes.rb
+- test/unit/bio/db/kegg/test_genome.rb
+- test/unit/bio/db/kegg/test_glycan.rb
+- test/unit/bio/db/kegg/test_kgml.rb
+- test/unit/bio/db/kegg/test_module.rb
+- test/unit/bio/db/kegg/test_orthology.rb
+- test/unit/bio/db/kegg/test_pathway.rb
+- test/unit/bio/db/kegg/test_reaction.rb
+- test/unit/bio/db/pdb/test_pdb.rb
+- test/unit/bio/db/sanger_chromatogram/test_abif.rb
+- test/unit/bio/db/sanger_chromatogram/test_scf.rb
+- test/unit/bio/db/test_aaindex.rb
+- test/unit/bio/db/test_fasta.rb
+- test/unit/bio/db/test_fastq.rb
+- test/unit/bio/db/test_gff.rb
+- test/unit/bio/db/test_go.rb
+- test/unit/bio/db/test_lasergene.rb
+- test/unit/bio/db/test_litdb.rb
+- test/unit/bio/db/test_medline.rb
+- test/unit/bio/db/test_nbrf.rb
+- test/unit/bio/db/test_newick.rb
+- test/unit/bio/db/test_nexus.rb
+- test/unit/bio/db/test_phyloxml.rb
+- test/unit/bio/db/test_phyloxml_writer.rb
+- test/unit/bio/db/test_prosite.rb
+- test/unit/bio/db/test_qual.rb
+- test/unit/bio/db/test_rebase.rb
+- test/unit/bio/db/test_soft.rb
+- test/unit/bio/io/flatfile/test_autodetection.rb
+- test/unit/bio/io/flatfile/test_buffer.rb
+- test/unit/bio/io/flatfile/test_splitter.rb
+- test/unit/bio/io/test_fastacmd.rb
+- test/unit/bio/io/test_flatfile.rb
+- test/unit/bio/io/test_togows.rb
+- test/unit/bio/sequence/test_aa.rb
+- test/unit/bio/sequence/test_common.rb
+- test/unit/bio/sequence/test_compat.rb
+- test/unit/bio/sequence/test_dblink.rb
+- test/unit/bio/sequence/test_na.rb
+- test/unit/bio/sequence/test_quality_score.rb
+- test/unit/bio/sequence/test_sequence_masker.rb
+- test/unit/bio/shell/plugin/test_seq.rb
+- 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_map.rb
+- test/unit/bio/test_pathway.rb
+- test/unit/bio/test_reference.rb
+- test/unit/bio/test_sequence.rb
+- test/unit/bio/test_shell.rb
+- test/unit/bio/test_tree.rb
+- test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb
+- test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb
+- test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb
+- test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb
+- test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb
+- test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb
+- test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb
+- test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb
+- test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb
+- test/unit/bio/util/restriction_enzyme/test_analysis.rb
+- test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb
+- test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb
+- test/unit/bio/util/restriction_enzyme/test_double_stranded.rb
+- test/unit/bio/util/restriction_enzyme/test_single_strand.rb
+- test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb
+- test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb
+- test/unit/bio/util/restriction_enzyme/test_string_formatting.rb
+- test/unit/bio/util/test_color_scheme.rb
+- test/unit/bio/util/test_contingency_table.rb
+- test/unit/bio/util/test_restriction_enzyme.rb
+- test/unit/bio/util/test_sirna.rb
+homepage: http://bioruby.org/
+licenses:
+- Ruby
+metadata: {}
 post_install_message: 
 rdoc_options:
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+- "--main"
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+- "--title"
+- BioRuby API documentation
+- "--exclude"
+- "\\.yaml\\z"
+- "--line-numbers"
+- "--inline-source"
 require_paths:
-- !binary |-
-  bGli
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 required_ruby_version: !ruby/object:Gem::Requirement
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   requirements:
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     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
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+  - - ">="
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 requirements: []
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 signing_key: 
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+specification_version: 4
+summary: Bioinformatics library
 test_files: []