bio 1.2.1 → 1.3.0

data/Rakefile

@@ -0,0 +1,143 @@
+#
+# = Rakefile - helper of developement and packaging
+#
+# Copyright::   Copyright (C) 2009 Naohisa Goto <ng@bioruby.org>
+# License::     The Ruby License
+#
+
+require 'rubygems'
+require 'erb'
+require 'rake/testtask'
+require 'rake/packagetask'
+require 'rake/gempackagetask'
+require 'rake/rdoctask'
+
+load "./lib/bio/version.rb"
+BIO_VERSION_RB_LOADED = true
+
+# Version string for tar.gz, tar.bz2, or zip archive.
+# If nil, use the value in lib/bio.rb
+# Note that gem version is always determined from bioruby.gemspec.erb.
+version = ENV['BIORUBY_VERSION'] || Bio::BIORUBY_VERSION.join(".")
+version = nil if version.to_s.empty?
+extraversion = ENV['BIORUBY_EXTRA_VERSION'] || Bio::BIORUBY_EXTRA_VERSION
+extraversion = nil if extraversion.to_s.empty?
+BIORUBY_VERSION = version
+BIORUBY_EXTRA_VERSION = extraversion
+
+task :default => "test"
+
+Rake::TestTask.new do |t|
+  t.test_files = FileList["test/{unit,functional}/**/test_*.rb"]
+end
+
+# files not included in gem but included in tar archive
+tar_additional_files = []
+
+GEM_SPEC_FILE = "bioruby.gemspec"
+GEM_SPEC_TEMPLATE_FILE = "bioruby.gemspec.erb"
+
+# gets gem spec string
+gem_spec_string = ERB.new(File.read(GEM_SPEC_TEMPLATE_FILE)).result
+
+# gets gem spec object
+spec = eval(gem_spec_string)
+
+# adds notice of automatically generated file
+gem_spec_string = "# This file is automatically generated from #{GEM_SPEC_TEMPLATE_FILE} and\n# should NOT be edited by hand.\n# \n" + gem_spec_string
+
+# compares current gemspec file and newly generated gemspec string
+current_string = File.read(GEM_SPEC_FILE) rescue nil
+if current_string and current_string != gem_spec_string then
+  #Rake::Task[GEM_SPEC_FILE].invoke
+  flag_update_gemspec = true
+else
+  flag_update_gemspec = false
+end
+
+desc "Update gem spec file"
+task :gemspec => GEM_SPEC_FILE
+
+desc "Force update gem spec file"
+task :regemspec do
+  #rm GEM_SPEC_FILE, :force => true
+  Rake::Task[GEM_SPEC_FILE].execute
+end
+
+desc "Update #{GEM_SPEC_FILE}"
+file GEM_SPEC_FILE => [ GEM_SPEC_TEMPLATE_FILE, 'Rakefile',
+                        'lib/bio/version.rb' ] do |t|
+  puts "creates #{GEM_SPEC_FILE}"
+  File.open(t.name, 'w') do |w|
+    w.print gem_spec_string
+  end
+end
+
+task :package => [ GEM_SPEC_FILE ] do
+  Rake::Task[:regemspec].invoke if flag_update_gemspec
+end
+
+Rake::PackageTask.new("bioruby") do |pkg|
+  #pkg.package_dir = "./pkg"
+  pkg.need_tar_gz = true
+  pkg.package_files.import(spec.files)
+  pkg.package_files.include(*tar_additional_files)
+  pkg.version = (BIORUBY_VERSION || spec.version) + BIORUBY_EXTRA_VERSION.to_s
+end
+
+Rake::GemPackageTask.new(spec) do |pkg|
+  #pkg.package_dir = "./pkg"
+end
+
+Rake::RDocTask.new do |r|
+  r.rdoc_dir = "rdoc"
+  r.rdoc_files.include(*spec.extra_rdoc_files)
+  r.rdoc_files.import(spec.files.find_all {|x| /\Alib\/.+\.rb\z/ =~ x})
+  #r.rdoc_files.exclude /\.yaml\z"
+  opts = spec.rdoc_options.to_a.dup
+  if i = opts.index('--main') then
+    main = opts[i + 1]
+    opts.delete_at(i)
+    opts.delete_at(i)
+  else
+    main = 'README.rdoc'
+  end
+  r.main = main
+  r.options = opts
+end
+
+# Tutorial files
+TUTORIAL_RD =    'doc/Tutorial.rd'
+TUTORIAL_RD_JA = 'doc/Tutorial.rd.ja'
+
+TUTORIAL_RD_HTML    = TUTORIAL_RD    + '.html'
+TUTORIAL_RD_JA_HTML = TUTORIAL_RD_JA + '.html'
+
+HTMLFILES_TUTORIAL = [ TUTORIAL_RD_HTML, TUTORIAL_RD_JA_HTML ]
+
+# Formatting RD to html.
+def rd2html(src, dst)
+  sh "rd2 -r rd/rd2html-lib.rb --with-css=bioruby.css #{src} > #{dst}"
+end
+
+# Tutorial.rd to Tutorial.rd.html
+file TUTORIAL_RD_HTML => TUTORIAL_RD do |t|
+  rd2html(t.prerequisites[0], t.name)
+end
+
+# Tutorial.rd.ja to Tutorial.html.ja
+file TUTORIAL_RD_JA_HTML => TUTORIAL_RD_JA do |t|
+  rd2html(t.prerequisites[0], t.name)
+end
+
+desc "Update doc/Tutorial*.html"
+task :tutorial2html => HTMLFILES_TUTORIAL
+
+desc "Force update doc/Tutorial*.html"
+task :retutorial2html do
+  # safe_unlink HTMLFILES_TUTORIAL
+  HTMLFILES_TUTORIAL.each do |x|
+    Rake::Task[x].execute
+  end
+end
+

data/bin/br_bioflat.rb

@@ -41,6 +41,10 @@ Create index options:
 Options only valid for --create (or --update) --type flat:
   --sort=/path/to/sort   use external sort program (e.g. /usr/bin/sort)
   --sort=BUILTIN         use builtin sort routine
+                         (default: /usr/bin/sort or BUILTIN)
+  --env=/path/to/env     use env program to run sort (default: /usr/bin/env)
+  --env-arg=XXXXXX       argument given to the env program (default: LC_ALL=C)
+                         (multiple --env-arg=XXXXXX can be specified)
 
 Options only valid for --update:
   --renew                re-read all flatfiles and update whole index
@@ -88,7 +92,7 @@ def do_index(mode = :create)
 
     # OBDA stuff
 
-    when /^\-\-?format/
+    when /^\-\-?format$/
       args.shift
       format = nil		# throw this f*ckin' mess for auto detect :)
     when /^\-\-?location/
@@ -120,6 +124,13 @@ def do_index(mode = :create)
     when /^\-\-?no\-?te?mp/i
       options['onmemory'] = true
 
+    when /^\-\-?env\=(.*)/i
+      options['env_program'] = $1
+
+    when /^\-\-?env-arg(?:ument)?\=(.*)/i
+      options['env_program_arguments'] ||= []
+      options['env_program_arguments'].push $1
+
     when /^\-\-?primary.*\=(.*)/i
       options['primary_namespace'] = $1
 

data/bin/br_pmfetch.rb

@@ -6,15 +6,16 @@
 #               Toshiaki Katayama <k@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: br_pmfetch.rb,v 1.7 2007/04/05 23:35:39 trevor Exp $
+# $Id:$
 #
 
-PROG_VER  = '$Id: br_pmfetch.rb,v 1.7 2007/04/05 23:35:39 trevor Exp $'
+require 'bio'
+
+PROG_VER  = "Powered by BioRuby #{Bio::BIORUBY_VERSION_ID}"
 PROG_NAME = File.basename($0)
 
 
 require 'getoptlong'
-require 'bio'
 
 
 ### formatting

data/bioruby.gemspec

@@ -0,0 +1,477 @@
+# This file is automatically generated from bioruby.gemspec.erb and
+# should NOT be edited by hand.
+# 
+Gem::Specification.new do |s|
+  s.name = 'bio'
+  s.version = "1.3.0"
+
+  s.author = "BioRuby project"
+  s.email = "staff@bioruby.org"
+  s.homepage = "http://bioruby.org/"
+  s.rubyforge_project = "bioruby"
+  s.summary = "Bioinformatics library"
+  s.description = "BioRuby is a library for bioinformatics (biology + information science)."
+
+  s.platform = Gem::Platform::RUBY
+  s.files = [
+    "ChangeLog",
+    "KNOWN_ISSUES.rdoc",
+    "README.rdoc",
+    "README_DEV.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/Changes-0.7.rd",
+    "doc/Changes-1.3.rdoc",
+    "doc/KEGG_API.rd",
+    "doc/KEGG_API.rd.ja",
+    "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/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/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/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/orthology.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/prosite.rb",
+    "lib/bio/db/rebase.rb",
+    "lib/bio/db/soft.rb",
+    "lib/bio/db/transfac.rb",
+    "lib/bio/feature.rb",
+    "lib/bio/io/biosql/biodatabase.rb",
+    "lib/bio/io/biosql/bioentry.rb",
+    "lib/bio/io/biosql/bioentry_dbxref.rb",
+    "lib/bio/io/biosql/bioentry_path.rb",
+    "lib/bio/io/biosql/bioentry_qualifier_value.rb",
+    "lib/bio/io/biosql/bioentry_reference.rb",
+    "lib/bio/io/biosql/bioentry_relationship.rb",
+    "lib/bio/io/biosql/biosequence.rb",
+    "lib/bio/io/biosql/comment.rb",
+    "lib/bio/io/biosql/config/database.yml",
+    "lib/bio/io/biosql/dbxref.rb",
+    "lib/bio/io/biosql/dbxref_qualifier_value.rb",
+    "lib/bio/io/biosql/location.rb",
+    "lib/bio/io/biosql/location_qualifier_value.rb",
+    "lib/bio/io/biosql/ontology.rb",
+    "lib/bio/io/biosql/reference.rb",
+    "lib/bio/io/biosql/seqfeature.rb",
+    "lib/bio/io/biosql/seqfeature_dbxref.rb",
+    "lib/bio/io/biosql/seqfeature_path.rb",
+    "lib/bio/io/biosql/seqfeature_qualifier_value.rb",
+    "lib/bio/io/biosql/seqfeature_relationship.rb",
+    "lib/bio/io/biosql/taxon.rb",
+    "lib/bio/io/biosql/taxon_name.rb",
+    "lib/bio/io/biosql/term.rb",
+    "lib/bio/io/biosql/term_dbxref.rb",
+    "lib/bio/io/biosql/term_path.rb",
+    "lib/bio/io/biosql/term_relationship.rb",
+    "lib/bio/io/biosql/term_relationship_term.rb",
+    "lib/bio/io/biosql/term_synonym.rb",
+    "lib/bio/io/das.rb",
+    "lib/bio/io/dbget.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/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/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/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_sequence.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/tfastx2tab.rb",
+    "sample/vs-genes.rb",
+    "setup.rb",
+    "test/data/HMMER/hmmpfam.out",
+    "test/data/HMMER/hmmsearch.out",
+    "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/command/echoarg2.bat",
+    "test/data/embl/AB090716.embl",
+    "test/data/embl/AB090716.embl.rel89",
+    "test/data/fasta/example1.txt",
+    "test/data/fasta/example2.txt",
+    "test/data/genscan/sample.report",
+    "test/data/iprscan/merged.raw",
+    "test/data/iprscan/merged.txt",
+    "test/data/paml/codeml/control_file.txt",
+    "test/data/paml/codeml/output.txt",
+    "test/data/paml/codeml/rates",
+    "test/data/prosite/prosite.dat",
+    "test/data/refseq/nm_126355.entret",
+    "test/data/rpsblast/misc.rpsblast",
+    "test/data/soft/GDS100_partial.soft",
+    "test/data/soft/GSE3457_family_partial.soft",
+    "test/data/uniprot/p53_human.uniprot",
+    "test/functional/bio/appl/test_pts1.rb",
+    "test/functional/bio/io/test_ensembl.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/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/paml/codeml/test_rates.rb",
+    "test/unit/bio/appl/paml/codeml/test_report.rb",
+    "test/unit/bio/appl/paml/test_codeml.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/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/kegg/test_genes.rb",
+    "test/unit/bio/db/pdb/test_pdb.rb",
+    "test/unit/bio/db/test_aaindex.rb",
+    "test/unit/bio/db/test_fasta.rb",
+    "test/unit/bio/db/test_gff.rb",
+    "test/unit/bio/db/test_lasergene.rb",
+    "test/unit/bio/db/test_medline.rb",
+    "test/unit/bio/db/test_newick.rb",
+    "test/unit/bio/db/test_nexus.rb",
+    "test/unit/bio/db/test_prosite.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/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_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_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"
+  ]
+
+  s.has_rdoc = true
+  s.extra_rdoc_files = [ 
+    "ChangeLog",
+    "KNOWN_ISSUES.rdoc",
+    "README.rdoc",
+    "README_DEV.rdoc",
+    "doc/Changes-1.3.rdoc"
+  ]
+  s.rdoc_options << '--main' << 'README.rdoc'
+  s.rdoc_options << '--title' << 'BioRuby API documentation'
+  s.rdoc_options << '--exclude' << '\.yaml\z'
+  s.rdoc_options << '--line-numbers' << '--inline-source'
+
+  s.require_path = 'lib'
+  s.autorequire = 'bio'
+
+  s.bindir = "bin"
+  s.executables = [
+    "bioruby",
+    "br_biofetch.rb",
+    "br_bioflat.rb",
+    "br_biogetseq.rb",
+    "br_pmfetch.rb"
+  ]
+  s.default_executable = "bioruby"
+end