bio 1.4.2 → 1.4.3

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

@@ -143,7 +143,7 @@ module Bio
       @obj[3,1] = 's'
       @obj[4,1] = 'y'
       @obj[5,1] = 'w'
-      assert_equal(/a[atgcyrwskmbdhvn][agr][gcw][tcy][atw]gcatgcatgcaaaa/, @obj.to_re)
+      assert_equal(/a[atgcyrwskmbdhvn][agr][gcs][tcy][atw]gcatgcatgcaaaa/, @obj.to_re)
     end
 
     def test_names

data/test/unit/bio/test_command.rb

@@ -21,6 +21,11 @@ require 'bio/command'
 
 module Bio
   class TestCommand < Test::Unit::TestCase
+
+    def windows_platform?
+      Bio::Command.module_eval { windows_platform? }
+    end
+    private :windows_platform?
     
     def test_command_constants
       assert(Bio::Command::UNSAFE_CHARS_UNIX)
@@ -51,8 +56,8 @@ module Bio
       assert_equal("bio_ruby.123@456:789",
                    Bio::Command.escape_shell(str))
       str = "bio\'\"r u\"b\\y123@456:789"
-      case RUBY_PLATFORM
-      when /mswin32|bccwin32/
+      if windows_platform?
+        # mswin32, bccwin32, mingw32, etc.
         assert_equal("\"bio'\"\"r u\"\"b\\y123@456:789\"",
                      Bio::Command.escape_shell(str))
       else
@@ -64,8 +69,8 @@ module Bio
     def test_make_command_line
       ary = [ "ruby", 
         "test.rb", "atgcatgc", "bio\'\"r u\"b\\y123@456:789" ]
-      case RUBY_PLATFORM
-      when /mswin32|bccwin32/
+      if windows_platform?
+        # mswin32, bccwin32, mingw32, etc.
         assert_equal("ruby" + 
                        " test.rb atgcatgc" + 
                        " \"bio'\"\"r u\"\"b\\y123@456:789\"",

data/test/unit/bio/test_sequence.rb

@@ -192,11 +192,11 @@ module Bio
     # Test Sequence::NA#to_re
 
     def test_dna_to_re
-      assert_equal(/atgc[agr][tcy][acm][tgk][atgrwkd][atcwmyh][agcmrsv][tgcyskb][gcw][atw][atgcyrwskmbdhvn]/, Sequence::NA.new('atgcrymkdhvbswn').to_re)
+      assert_equal(/atgc[agr][tcy][acm][tgk][atgrwkd][atcwmyh][agcmrsv][tgcyskb][gcs][atw][atgcyrwskmbdhvn]/, Sequence::NA.new('atgcrymkdhvbswn').to_re)
     end
 
     def test_rna_to_re
-      assert_equal(/augc[agr][ucy][acm][ugk][augrwkd][aucwmyh][agcmrsv][ugcyskb][gcw][auw][augcyrwskmbdhvn]/, Sequence::NA.new('augcrymkdhvbswn').to_re)
+      assert_equal(/augc[agr][ucy][acm][ugk][augrwkd][aucwmyh][agcmrsv][ugcyskb][gcs][auw][augcyrwskmbdhvn]/, Sequence::NA.new('augcrymkdhvbswn').to_re)
     end
 
     # Test Sequence::NA#names

data/test/unit/bio/test_tree.rb

@@ -780,20 +780,20 @@ module Bio
     end
 
     def test_total_distance
-      assert_equal("0.7777", sprintf("%.15g", @tree.total_distance))
+      assert_equal("0.7777", sprintf("%.4f", @tree.total_distance))
     end
 
     def test_distance_matrix
       mat = @tree.distance_matrix([ @mouse, @rat, @human, @chimpanzee ])
       assert_instance_of(Matrix, mat)
-      assert_equal([ "0",      "0.2093", "0.6149", "0.6266" ],
-                   mat.row(0).map { |x| sprintf("%.15g", x) }.to_a)
-      assert_equal([ "0.2093", "0",      "0.6306", "0.6423" ],
-                   mat.row(1).map { |x| sprintf("%.15g", x) }.to_a)
-      assert_equal([ "0.6149", "0.6306", "0",      "0.0889" ],
-                   mat.row(2).map { |x| sprintf("%.15g", x) }.to_a)
-      assert_equal([ "0.6266", "0.6423", "0.0889", "0" ],
-                   mat.row(3).map { |x| sprintf("%.15g", x) }.to_a)
+      assert_equal([ "0.0000", "0.2093", "0.6149", "0.6266" ],
+                   mat.row(0).map { |x| sprintf("%.4f", x) }.to_a)
+      assert_equal([ "0.2093", "0.0000", "0.6306", "0.6423" ],
+                   mat.row(1).map { |x| sprintf("%.4f", x) }.to_a)
+      assert_equal([ "0.6149", "0.6306", "0.0000", "0.0889" ],
+                   mat.row(2).map { |x| sprintf("%.4f", x) }.to_a)
+      assert_equal([ "0.6266", "0.6423", "0.0889", "0.0000" ],
+                   mat.row(3).map { |x| sprintf("%.4f", x) }.to_a)
     end
      
     def test_adjacency_matrix
@@ -842,9 +842,9 @@ module Bio
       }
       assert_equal(@tree, ret)
       distance_mouse_node1 = @tree.get_edge(@mouse, node1).distance
-      assert_equal("0.0123", sprintf("%.15g", distance_mouse_node1))
+      assert_equal("0.0123", sprintf("%.4f", distance_mouse_node1))
       distance_node1_rodents = @tree.get_edge(node1, @rodents).distance
-      assert_equal("0.0845", sprintf("%.15g", distance_node1_rodents))
+      assert_equal("0.0845", sprintf("%.4f", distance_node1_rodents))
     end
   end #class TestTree2
 

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

@@ -15,7 +15,7 @@ load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
 
 # libraries needed for the tests
 require 'test/unit'
-require 'bio/util/restriction_enzyme.rb'
+require 'bio/util/restriction_enzyme'
 
 module Bio; module TestRestrictionEnzyme #:nodoc:
 

metadata

@@ -1,670 +1,1441 @@
 --- !ruby/object:Gem::Specification
-name: bio
+name: !binary |-
+  Ymlv
 version: !ruby/object:Gem::Version
-  version: 1.4.2
+  version: !binary |-
+    MS40LjM=
   prerelease: 
 platform: ruby
 authors:
-- BioRuby project
-autorequire: bio
-bindir: bin
+- !binary |-
+  QmlvUnVieSBwcm9qZWN0
+autorequire: 
+bindir: !binary |-
+  Ymlu
 cert_chain: []
-date: 2011-08-26 00:00:00.000000000 Z
+date: 2012-08-21 00:00:00.000000000 Z
 dependencies: []
-description: BioRuby is a library for bioinformatics (biology + information science).
-email: staff@bioruby.org
+description: !binary |-
+  QmlvUnVieSBpcyBhIGxpYnJhcnkgZm9yIGJpb2luZm9ybWF0aWNzIChiaW9s
+  b2d5ICsgaW5mb3JtYXRpb24gc2NpZW5jZSku
+email: !binary |-
+  c3RhZmZAYmlvcnVieS5vcmc=
 executables:
-- bioruby
-- br_biofetch.rb
-- br_bioflat.rb
-- br_biogetseq.rb
-- br_pmfetch.rb
+- !binary |-
+  YmlvcnVieQ==
+- !binary |-
+  YnJfYmlvZmV0Y2gucmI=
+- !binary |-
+  YnJfYmlvZmxhdC5yYg==
+- !binary |-
+  YnJfYmlvZ2V0c2VxLnJi
+- !binary |-
+  YnJfcG1mZXRjaC5yYg==
 extensions: []
 extra_rdoc_files:
-- ChangeLog
-- 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
+- !binary |-
+  Q2hhbmdlTG9n
+- !binary |-
+  S05PV05fSVNTVUVTLnJkb2M=
+- !binary |-
+  TEVHQUw=
+- !binary |-
+  UkVBRE1FLnJkb2M=
+- !binary |-
+  UkVBRE1FX0RFVi5yZG9j
+- !binary |-
+  UkVMRUFTRV9OT1RFUy5yZG9j
+- !binary |-
+  ZG9jL0NoYW5nZXMtMS4zLnJkb2M=
+- !binary |-
+  ZG9jL1JFTEVBU0VfTk9URVMtMS40LjAucmRvYw==
+- !binary |-
+  ZG9jL1JFTEVBU0VfTk9URVMtMS40LjEucmRvYw==
+- !binary |-
+  ZG9jL1JFTEVBU0VfTk9URVMtMS40LjIucmRvYw==
 files:
-- COPYING
-- COPYING.ja
-- 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
-- bioruby.gemspec.erb
-- doc/ChangeLog-before-1.3.1
-- doc/Changes-0.7.rd
-- doc/Changes-1.3.rdoc
-- doc/KEGG_API.rd
-- doc/KEGG_API.rd.ja
-- doc/RELEASE_NOTES-1.4.0.rdoc
-- doc/RELEASE_NOTES-1.4.1.rdoc
-- doc/Tutorial.rd
-- doc/Tutorial.rd.html
-- doc/Tutorial.rd.ja
-- doc/Tutorial.rd.ja.html
-- doc/bioruby.css
-- etc/bioinformatics/seqdatabase.ini
-- extconf.rb
-- lib/bio.rb
-- lib/bio/alignment.rb
-- lib/bio/appl/bl2seq/report.rb
-- lib/bio/appl/blast.rb
-- lib/bio/appl/blast/ddbj.rb
-- lib/bio/appl/blast/format0.rb
-- lib/bio/appl/blast/format8.rb
-- lib/bio/appl/blast/genomenet.rb
-- lib/bio/appl/blast/ncbioptions.rb
-- lib/bio/appl/blast/remote.rb
-- lib/bio/appl/blast/report.rb
-- lib/bio/appl/blast/rexml.rb
-- lib/bio/appl/blast/rpsblast.rb
-- lib/bio/appl/blast/wublast.rb
-- lib/bio/appl/blast/xmlparser.rb
-- lib/bio/appl/blat/report.rb
-- lib/bio/appl/clustalw.rb
-- lib/bio/appl/clustalw/report.rb
-- lib/bio/appl/emboss.rb
-- lib/bio/appl/fasta.rb
-- lib/bio/appl/fasta/format10.rb
-- lib/bio/appl/gcg/msf.rb
-- lib/bio/appl/gcg/seq.rb
-- lib/bio/appl/genscan/report.rb
-- lib/bio/appl/hmmer.rb
-- lib/bio/appl/hmmer/report.rb
-- lib/bio/appl/iprscan/report.rb
-- lib/bio/appl/mafft.rb
-- lib/bio/appl/mafft/report.rb
-- lib/bio/appl/meme/mast.rb
-- lib/bio/appl/meme/mast/report.rb
-- lib/bio/appl/meme/motif.rb
-- lib/bio/appl/muscle.rb
-- lib/bio/appl/paml/baseml.rb
-- lib/bio/appl/paml/baseml/report.rb
-- lib/bio/appl/paml/codeml.rb
-- lib/bio/appl/paml/codeml/rates.rb
-- lib/bio/appl/paml/codeml/report.rb
-- lib/bio/appl/paml/common.rb
-- lib/bio/appl/paml/common_report.rb
-- lib/bio/appl/paml/yn00.rb
-- lib/bio/appl/paml/yn00/report.rb
-- lib/bio/appl/phylip/alignment.rb
-- lib/bio/appl/phylip/distance_matrix.rb
-- lib/bio/appl/probcons.rb
-- lib/bio/appl/psort.rb
-- lib/bio/appl/psort/report.rb
-- lib/bio/appl/pts1.rb
-- lib/bio/appl/sim4.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/tcoffee.rb
-- lib/bio/appl/tmhmm/report.rb
-- lib/bio/command.rb
-- lib/bio/compat/features.rb
-- lib/bio/compat/references.rb
-- lib/bio/data/aa.rb
-- lib/bio/data/codontable.rb
-- lib/bio/data/na.rb
-- lib/bio/db.rb
-- lib/bio/db/aaindex.rb
-- lib/bio/db/biosql/biosql_to_biosequence.rb
-- lib/bio/db/biosql/sequence.rb
-- lib/bio/db/embl/common.rb
-- lib/bio/db/embl/embl.rb
-- lib/bio/db/embl/embl_to_biosequence.rb
-- lib/bio/db/embl/format_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/fantom.rb
-- lib/bio/db/fasta.rb
-- lib/bio/db/fasta/defline.rb
-- lib/bio/db/fasta/fasta_to_biosequence.rb
-- lib/bio/db/fasta/format_fasta.rb
-- lib/bio/db/fasta/format_qual.rb
-- lib/bio/db/fasta/qual.rb
-- lib/bio/db/fasta/qual_to_biosequence.rb
-- lib/bio/db/fastq.rb
-- lib/bio/db/fastq/fastq_to_biosequence.rb
-- lib/bio/db/fastq/format_fastq.rb
-- lib/bio/db/genbank/common.rb
-- lib/bio/db/genbank/ddbj.rb
-- lib/bio/db/genbank/format_genbank.rb
-- lib/bio/db/genbank/genbank.rb
-- lib/bio/db/genbank/genbank_to_biosequence.rb
-- lib/bio/db/genbank/genpept.rb
-- lib/bio/db/genbank/refseq.rb
-- lib/bio/db/gff.rb
-- lib/bio/db/go.rb
-- lib/bio/db/kegg/brite.rb
-- lib/bio/db/kegg/common.rb
-- lib/bio/db/kegg/compound.rb
-- lib/bio/db/kegg/drug.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/module.rb
-- lib/bio/db/kegg/orthology.rb
-- lib/bio/db/kegg/pathway.rb
-- lib/bio/db/kegg/reaction.rb
-- lib/bio/db/kegg/taxonomy.rb
-- lib/bio/db/lasergene.rb
-- lib/bio/db/litdb.rb
-- lib/bio/db/medline.rb
-- lib/bio/db/nbrf.rb
-- lib/bio/db/newick.rb
-- lib/bio/db/nexus.rb
-- lib/bio/db/pdb.rb
-- lib/bio/db/pdb/atom.rb
-- lib/bio/db/pdb/chain.rb
-- lib/bio/db/pdb/chemicalcomponent.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/db/phyloxml/phyloxml.xsd
-- lib/bio/db/phyloxml/phyloxml_elements.rb
-- lib/bio/db/phyloxml/phyloxml_parser.rb
-- lib/bio/db/phyloxml/phyloxml_writer.rb
-- lib/bio/db/prosite.rb
-- lib/bio/db/rebase.rb
-- lib/bio/db/sanger_chromatogram/abif.rb
-- lib/bio/db/sanger_chromatogram/chromatogram.rb
-- lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb
-- lib/bio/db/sanger_chromatogram/scf.rb
-- lib/bio/db/soft.rb
-- lib/bio/db/transfac.rb
-- lib/bio/feature.rb
-- lib/bio/io/biosql/ar-biosql.rb
-- lib/bio/io/biosql/biosql.rb
-- lib/bio/io/biosql/config/database.yml
-- lib/bio/io/das.rb
-- lib/bio/io/dbget.rb
-- lib/bio/io/ddbjrest.rb
-- lib/bio/io/ddbjxml.rb
-- lib/bio/io/ebisoap.rb
-- lib/bio/io/ensembl.rb
-- lib/bio/io/fastacmd.rb
-- lib/bio/io/fetch.rb
-- lib/bio/io/flatfile.rb
-- lib/bio/io/flatfile/autodetection.rb
-- lib/bio/io/flatfile/bdb.rb
-- lib/bio/io/flatfile/buffer.rb
-- lib/bio/io/flatfile/index.rb
-- lib/bio/io/flatfile/indexer.rb
-- lib/bio/io/flatfile/splitter.rb
-- lib/bio/io/higet.rb
-- lib/bio/io/hinv.rb
-- lib/bio/io/keggapi.rb
-- lib/bio/io/ncbirest.rb
-- lib/bio/io/ncbisoap.rb
-- lib/bio/io/pubmed.rb
-- lib/bio/io/registry.rb
-- lib/bio/io/soapwsdl.rb
-- lib/bio/io/sql.rb
-- lib/bio/io/togows.rb
-- lib/bio/location.rb
-- lib/bio/map.rb
-- lib/bio/pathway.rb
-- lib/bio/reference.rb
-- lib/bio/sequence.rb
-- lib/bio/sequence/aa.rb
-- lib/bio/sequence/adapter.rb
-- lib/bio/sequence/common.rb
-- lib/bio/sequence/compat.rb
-- lib/bio/sequence/dblink.rb
-- lib/bio/sequence/format.rb
-- lib/bio/sequence/format_raw.rb
-- lib/bio/sequence/generic.rb
-- lib/bio/sequence/na.rb
-- lib/bio/sequence/quality_score.rb
-- lib/bio/sequence/sequence_masker.rb
-- lib/bio/shell.rb
-- lib/bio/shell/core.rb
-- lib/bio/shell/demo.rb
-- lib/bio/shell/interface.rb
-- lib/bio/shell/irb.rb
-- lib/bio/shell/object.rb
-- lib/bio/shell/plugin/blast.rb
-- lib/bio/shell/plugin/codon.rb
-- lib/bio/shell/plugin/das.rb
-- lib/bio/shell/plugin/emboss.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/ncbirest.rb
-- lib/bio/shell/plugin/obda.rb
-- lib/bio/shell/plugin/psort.rb
-- lib/bio/shell/plugin/seq.rb
-- lib/bio/shell/plugin/soap.rb
-- lib/bio/shell/plugin/togows.rb
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml
-- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif
-- lib/bio/shell/script.rb
-- lib/bio/shell/setup.rb
-- lib/bio/shell/web.rb
-- lib/bio/tree.rb
-- lib/bio/util/color_scheme.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
-- lib/bio/util/contingency_table.rb
-- lib/bio/util/restriction_enzyme.rb
-- lib/bio/util/restriction_enzyme/analysis.rb
-- lib/bio/util/restriction_enzyme/analysis_basic.rb
-- lib/bio/util/restriction_enzyme/cut_symbol.rb
-- lib/bio/util/restriction_enzyme/dense_int_array.rb
-- lib/bio/util/restriction_enzyme/double_stranded.rb
-- lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb
-- lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb
-- lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb
-- lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb
-- lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb
-- lib/bio/util/restriction_enzyme/enzymes.yaml
-- lib/bio/util/restriction_enzyme/range/cut_range.rb
-- lib/bio/util/restriction_enzyme/range/cut_ranges.rb
-- lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb
-- lib/bio/util/restriction_enzyme/range/sequence_range.rb
-- lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb
-- lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb
-- lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb
-- lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb
-- lib/bio/util/restriction_enzyme/single_strand.rb
-- lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
-- lib/bio/util/restriction_enzyme/single_strand_complement.rb
-- lib/bio/util/restriction_enzyme/sorted_num_array.rb
-- lib/bio/util/restriction_enzyme/string_formatting.rb
-- lib/bio/util/sirna.rb
-- lib/bio/version.rb
-- rdoc.zsh
-- sample/any2fasta.rb
-- sample/biofetch.rb
-- sample/color_scheme_na.rb
-- sample/dbget
-- sample/demo_aaindex.rb
-- sample/demo_aminoacid.rb
-- sample/demo_bl2seq_report.rb
-- sample/demo_blast_report.rb
-- sample/demo_codontable.rb
-- sample/demo_das.rb
-- sample/demo_ddbjxml.rb
-- sample/demo_fasta_remote.rb
-- sample/demo_fastaformat.rb
-- sample/demo_genbank.rb
-- sample/demo_genscan_report.rb
-- sample/demo_gff1.rb
-- sample/demo_go.rb
-- sample/demo_hmmer_report.rb
-- sample/demo_kegg_compound.rb
-- sample/demo_kegg_drug.rb
-- sample/demo_kegg_genome.rb
-- sample/demo_kegg_glycan.rb
-- sample/demo_kegg_orthology.rb
-- sample/demo_kegg_reaction.rb
-- sample/demo_kegg_taxonomy.rb
-- sample/demo_keggapi.rb
-- sample/demo_litdb.rb
-- sample/demo_locations.rb
-- sample/demo_ncbi_rest.rb
-- sample/demo_nucleicacid.rb
-- sample/demo_pathway.rb
-- sample/demo_prosite.rb
-- sample/demo_psort.rb
-- sample/demo_psort_report.rb
-- sample/demo_pubmed.rb
-- sample/demo_sequence.rb
-- sample/demo_sirna.rb
-- sample/demo_sosui_report.rb
-- sample/demo_targetp_report.rb
-- sample/demo_tmhmm_report.rb
-- sample/enzymes.rb
-- sample/fasta2tab.rb
-- sample/fastagrep.rb
-- sample/fastasort.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/na2aa.rb
-- sample/pmfetch.rb
-- sample/pmsearch.rb
-- sample/psortplot_html.rb
-- sample/ssearch2tab.rb
-- sample/tdiary.rb
-- sample/test_phyloxml_big.rb
-- sample/test_restriction_enzyme_long.rb
-- sample/tfastx2tab.rb
-- sample/vs-genes.rb
-- setup.rb
-- test/bioruby_test_helper.rb
-- test/data/HMMER/hmmpfam.out
-- test/data/HMMER/hmmsearch.out
-- test/data/KEGG/1.1.1.1.enzyme
-- test/data/KEGG/C00025.compound
-- test/data/KEGG/D00063.drug
-- test/data/KEGG/G00024.glycan
-- test/data/KEGG/G01366.glycan
-- test/data/KEGG/K02338.orthology
-- test/data/KEGG/M00118.module
-- test/data/KEGG/R00006.reaction
-- test/data/KEGG/T00005.genome
-- test/data/KEGG/T00070.genome
-- test/data/KEGG/b0529.gene
-- test/data/KEGG/ec00072.pathway
-- test/data/KEGG/hsa00790.pathway
-- test/data/KEGG/ko00312.pathway
-- test/data/KEGG/map00030.pathway
-- test/data/KEGG/map00052.pathway
-- test/data/KEGG/rn00250.pathway
-- 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.aln
-- test/data/command/echoarg2.bat
-- 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/appl/blast/test_remote.rb
-- test/functional/bio/appl/test_blast.rb
-- test/functional/bio/appl/test_pts1.rb
-- test/functional/bio/io/test_ddbjrest.rb
-- test/functional/bio/io/test_ensembl.rb
-- test/functional/bio/io/test_pubmed.rb
-- test/functional/bio/io/test_soapwsdl.rb
-- test/functional/bio/io/test_togows.rb
-- test/functional/bio/sequence/test_output_embl.rb
-- test/functional/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_sptr.rb
-- test/unit/bio/db/embl/test_uniprot.rb
-- test/unit/bio/db/embl/test_uniprot_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_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_ddbjxml.rb
-- test/unit/bio/io/test_ensembl.rb
-- test/unit/bio/io/test_fastacmd.rb
-- test/unit/bio/io/test_flatfile.rb
-- test/unit/bio/io/test_soapwsdl.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
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 licenses: []
 post_install_message: 
 rdoc_options:
-- --main
-- README.rdoc
-- --title
-- BioRuby API documentation
-- --exclude
-- \.yaml\z
-- --line-numbers
-- --inline-source
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 require_paths:
-- lib
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 required_ruby_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -678,9 +1449,11 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: bioruby
-rubygems_version: 1.8.10
+rubyforge_project: !binary |-
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+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
-summary: Bioinformatics library
+summary: !binary |-
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 test_files: []