RubyGems - bio - Versions diffs - 1.5.1 → 2.0.2 - Mend

bio 1.5.1 → 2.0.2

Files changed (128) hide show

checksums.yaml +5 -5
data/.travis.yml +35 -36
data/ChangeLog +911 -2554
data/{gemfiles/Gemfile.travis-ruby2.2 → Gemfile} +0 -3
data/KNOWN_ISSUES.rdoc +10 -13
data/LEGAL +0 -10
data/README.rdoc +40 -96
data/README_DEV.rdoc +5 -5
data/RELEASE_NOTES.rdoc +118 -234
data/Rakefile +13 -43
data/appveyor.yml +29 -0
data/bioruby.gemspec +18 -81
data/bioruby.gemspec.erb +8 -28
data/doc/ChangeLog-1.5.0 +2919 -0
data/doc/RELEASE_NOTES-1.5.0.rdoc +285 -0
data/doc/Tutorial.rd +6 -108
data/doc/Tutorial.rd.html +19 -98
data/gemfiles/Gemfile.travis-jruby1.8 +3 -5
data/gemfiles/Gemfile.travis-jruby1.9 +0 -3
data/gemfiles/Gemfile.travis-rbx +0 -3
data/gemfiles/Gemfile.travis-ruby1.8 +3 -5
data/gemfiles/Gemfile.travis-ruby1.9 +0 -3
data/gemfiles/Gemfile.windows +6 -0
data/gemfiles/prepare-gemspec.rb +4 -0
data/lib/bio.rb +0 -10
data/lib/bio/appl/blast/genomenet.rb +4 -4
data/lib/bio/appl/blast/report.rb +40 -8
data/lib/bio/appl/fasta/format10.rb +2 -1
data/lib/bio/command.rb +10 -0
data/lib/bio/data/codontable.rb +99 -3
data/lib/bio/db/aaindex.rb +74 -5
data/lib/bio/db/gff.rb +3 -1
data/lib/bio/db/kegg/common.rb +14 -0
data/lib/bio/db/kegg/genes.rb +26 -0
data/lib/bio/db/kegg/pathway.rb +5 -11
data/lib/bio/db/soft.rb +2 -2
data/lib/bio/io/flatfile/autodetection.rb +5 -0
data/lib/bio/io/togows.rb +5 -5
data/lib/bio/map.rb +4 -4
data/lib/bio/sequence/format.rb +1 -0
data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +1 -1
data/lib/bio/util/sirna.rb +2 -0
data/lib/bio/version.rb +6 -8
data/sample/color_scheme_aa.rb +82 -0
data/sample/color_scheme_na.rb +5 -6
data/sample/fastq2html.cwl +23 -0
data/sample/fastq2html.rb +94 -0
data/sample/fastq2html.testdata.yaml +5 -0
data/sample/na2aa.cwl +23 -0
data/sample/na2aa.rb +11 -25
data/sample/na2aa.testdata.yaml +7 -0
data/sample/rev_comp.cwl +23 -0
data/sample/rev_comp.rb +20 -0
data/sample/rev_comp.testdata.yaml +7 -0
data/sample/test_restriction_enzyme_long.rb +1 -1
data/test/network/bio/db/kegg/test_genes_hsa7422.rb +91 -0
data/test/unit/bio/appl/blast/test_report.rb +4 -4
data/test/unit/bio/data/test_codontable.rb +3 -0
data/test/unit/bio/db/test_gff.rb +5 -0
data/test/unit/bio/test_alignment.rb +2 -2
metadata +20 -77
data/bin/bioruby +0 -47
data/bin/br_biofetch.rb +0 -71
data/bin/br_bioflat.rb +0 -293
data/bin/br_biogetseq.rb +0 -45
data/bin/br_pmfetch.rb +0 -422
data/lib/bio/appl/blast/xmlparser.rb +0 -236
data/lib/bio/db/biosql/biosql_to_biosequence.rb +0 -78
data/lib/bio/db/biosql/sequence.rb +0 -444
data/lib/bio/db/phyloxml/phyloxml.xsd +0 -582
data/lib/bio/db/phyloxml/phyloxml_elements.rb +0 -1197
data/lib/bio/db/phyloxml/phyloxml_parser.rb +0 -1001
data/lib/bio/db/phyloxml/phyloxml_writer.rb +0 -227
data/lib/bio/io/biosql/ar-biosql.rb +0 -257
data/lib/bio/io/biosql/biosql.rb +0 -39
data/lib/bio/io/biosql/config/database.yml +0 -21
data/lib/bio/io/sql.rb +0 -79
data/lib/bio/shell.rb +0 -44
data/lib/bio/shell/core.rb +0 -578
data/lib/bio/shell/demo.rb +0 -146
data/lib/bio/shell/interface.rb +0 -217
data/lib/bio/shell/irb.rb +0 -94
data/lib/bio/shell/object.rb +0 -71
data/lib/bio/shell/plugin/blast.rb +0 -42
data/lib/bio/shell/plugin/codon.rb +0 -218
data/lib/bio/shell/plugin/das.rb +0 -58
data/lib/bio/shell/plugin/emboss.rb +0 -23
data/lib/bio/shell/plugin/entry.rb +0 -137
data/lib/bio/shell/plugin/flatfile.rb +0 -101
data/lib/bio/shell/plugin/midi.rb +0 -430
data/lib/bio/shell/plugin/ncbirest.rb +0 -68
data/lib/bio/shell/plugin/obda.rb +0 -45
data/lib/bio/shell/plugin/psort.rb +0 -56
data/lib/bio/shell/plugin/seq.rb +0 -248
data/lib/bio/shell/plugin/togows.rb +0 -40
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +0 -29
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +0 -4
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +0 -27
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +0 -11
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +0 -4
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +0 -7
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +0 -368
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +0 -47
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +0 -144
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +0 -47
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +0 -8
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +0 -10
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +0 -26
data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
data/lib/bio/shell/script.rb +0 -25
data/lib/bio/shell/setup.rb +0 -108
data/lib/bio/shell/web.rb +0 -102
data/sample/test_phyloxml_big.rb +0 -205
data/setup.rb +0 -1600
data/test/data/phyloxml/apaf.xml +0 -666
data/test/data/phyloxml/bcl_2.xml +0 -2097
data/test/data/phyloxml/made_up.xml +0 -144
data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +0 -65
data/test/data/phyloxml/phyloxml_examples.xml +0 -415
data/test/unit/bio/db/biosql/tc_biosql.rb +0 -114
data/test/unit/bio/db/biosql/ts_suite_biosql.rb +0 -8
data/test/unit/bio/db/test_phyloxml.rb +0 -821
data/test/unit/bio/db/test_phyloxml_writer.rb +0 -334
data/test/unit/bio/shell/plugin/test_seq.rb +0 -187
data/test/unit/bio/test_shell.rb +0 -20

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml DELETED

@@ -1,47 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<title>BioRuby shell on Rails</title>
-<%= stylesheet_link_tag "bioruby.css" %>
-<%= javascript_include_tag :defaults %>
-</head>
-<body>
-<div id="content">
- <div id="side">
-  <div class="title">Project</div>
-  <ul>
-   <li><%= link_to "#{File.basename(project_workdir)}", "file://#{project_workdir}" %>
-  </ul>
-  <div class="title">Functions</div>
-  <ul>
-    <li><%= link_to "Console", :action => "index" %></li>
-    <li><%= link_to "History", :action => "history" %></li>
-    <li><%= link_to "Commands", :action => "commands" %></li>
-  </ul>
-  <div class="title">Local variables</div>
-  <%= render :partial => "variables" %>
-  <br>
-  <a href="http://bioruby.org/"><img src="/images/bioruby/link.gif" border=0></a>
- </div><!-- side -->
- <div id="title">
-  <p class="titletop">BioRuby shell on Rails</p>
-  <p class="titlesub">Web interface for the BioRuby library</p>
- </div><!-- title -->
- <div id="main">
-<%= yield %>
- </div><!-- main -->
-</div><!-- content -->
-</body>
-</html>

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb DELETED

@@ -1,144 +0,0 @@
-class BiorubyController < ApplicationController
-  HIDE_METHODS = Object.methods + [ "singleton_method_added" ]
-  HIDE_MODULES = [
-    Base64::Deprecated, Base64, PP::ObjectMixin, Bio::Shell,
-  ]
-  HIDE_MODULES << WEBrick if defined?(WEBrick)
-  HIDE_VARIABLES = [
-    "_", "irb", "_erbout",
-  ]
-  SECURITY_NOTICE = "For security purposes, this functionality is only available to local requests."
-  def index
-    unless local_request?
-      flash[:notice] = SECURITY_NOTICE
-    end
-  end
-  def evaluate
-    if local_request?
-      begin
-        @script = params[:script].strip
-        # write out to history
-        Bio::Shell.store_history(@script)
-        # evaluate ruby script
-        @result = eval(@script, Bio::Shell.cache[:binding])
-        # *TODO* need to handle with output of print/puts/p/pp etc. here
-        @output = nil
-      rescue
-        @result = $!
-        @output = nil
-      end
-    else
-      @result = SECURITY_NOTICE
-      @output = nil
-    end
-    @number = Bio::Shell.cache[:results].store(@script, @result, @output)
-    render :update do |page|
-      render_log(page)
-    end
-  end
-  def list_methods
-    number = params[:number].to_i
-    script, result, output = Bio::Shell.cache[:results].restore(number)
-    @class = result.class
-    @methods = (result.methods - HIDE_METHODS).sort
-    render :update do |page|
-      page.replace_html "methods_#{number}", :partial => "methods"
-      page.visual_effect :toggle_blind, "methods_#{number}", :duration => 0.5
-    end
-  end
-  def list_classes
-    number = params[:number].to_i
-    script, result, output = Bio::Shell.cache[:results].restore(number)
-    class_name = result.class
-    @class = class_name
-    @classes = []
-    loop do
-      @classes.unshift(class_name)
-      if class_name == Object
-        break
-      else
-        class_name = class_name.superclass
-      end
-    end
-    render :update do |page|
-      page.replace_html "classes_#{number}", :partial => "classes"
-      page.visual_effect :toggle_blind, "classes_#{number}", :duration => 0.5
-    end
-  end
-  def list_modules
-    number = params[:number].to_i
-    script, result, output = Bio::Shell.cache[:results].restore(number)
-    @class = result.class
-    @modules = result.class.included_modules - HIDE_MODULES
-    render :update do |page|
-      page.replace_html "modules_#{number}", :partial => "modules"
-      page.visual_effect :toggle_blind, "modules_#{number}", :duration => 0.5
-    end
-  end
-  def reload_script
-    number = params[:number].to_i
-    script, result, output = Bio::Shell.cache[:results].restore(number)
-    render :update do |page|
-      page.replace_html :script, script
-    end
-  end
-  def results
-    if Bio::Shell.cache[:results].number > 0
-      limit = params[:limit].to_i
-      max_num = Bio::Shell.cache[:results].number
-      min_num = [ max_num - limit + 1, 1 ].max
-      min_num = 1 if limit == 0
-      render :update do |page|
-        # delete all existing results in the current DOM for clean up
-        page.select(".log").each do |element|
-          #page.hide element
-          page.remove element
-        end
-        # add selected results to the current DOM
-        min_num.upto(max_num) do |@number|
-          #page.show "log_#{@number}"
-          @script, @result, @output = Bio::Shell.cache[:results].restore(@number)
-          if @script
-            render_log(page)
-          end
-        end
-      end
-    end
-  end
-  def commands
-    @bioruby_commands = Bio::Shell.private_instance_methods.sort
-  end
-  def history
-    @history = File.readlines(Bio::Shell.history_file)
-  end
-end

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb DELETED

@@ -1,47 +0,0 @@
-module BiorubyHelper
-  include Bio::Shell
-  def project_workdir
-    if Bio::Shell.cache[:savedir].match(/\.bioruby$/)
-      Bio::Shell.cache[:workdir]
-    else
-      Bio::Shell.cache[:savedir]
-    end
-  end
-  def have_results
-    Bio::Shell.cache[:results].number > 0
-  end
-  def local_variables
-    eval("local_variables", Bio::Shell.cache[:binding]) -
-      BiorubyController::HIDE_VARIABLES
-  end
-  def render_log(page)
-    page.insert_html :top, :logs, :partial => "log"
-    page.replace_html "variables", :partial => "variables"
-    page.hide "methods_#{@number}"
-    page.hide "classes_#{@number}"
-    page.hide "modules_#{@number}"
-  end
-  def reference_link(class_or_module)
-    name = class_or_module.to_s
-    case name
-    when /Bio::(.+)/
-      path = $1.split('::').join('/')
-      url = "http://bioruby.org/rdoc/classes/Bio/#{path}.html"
-    when /Chem::(.+)/
-      path = $1.split('::').join('/')
-      url = "http://chemruby.org/rdoc/classes/Chem/#{path}.html"
-    else
-      path = name.split('::').join('/')
-      url = "http://www.ruby-doc.org/core/classes/#{path}.html"
-    end
-    return "<a href='#{url}'>#{name}</a>"
-  end
-end

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml DELETED

@@ -1,8 +0,0 @@
-<div id="command">
-<h2>BioRuby shell commands</h2>
-<ul>
-  <% @bioruby_commands.each do |cmd| %>
-  <li><%= cmd %></li>
-  <% end %>
-</ul>
-</div>

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml DELETED

@@ -1,10 +0,0 @@
-<div id="history">
-<h2>Command history</h2>
-<% @history.each do |line| %>
-<%   if line[/^# /] %>
-<div class="histtime"><%= line %></div>
-<%   else %>
-<div class="histline"><%= line %></div>
-<%   end %>
-<% end %>
-</div>

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml DELETED

@@ -1,26 +0,0 @@
-<div id="console">
- <%- if flash[:notice] -%>
-  <div id="notice"><p><%= flash[:notice] %></p></div><br>
- <%- end -%>
- <% form_remote_tag(:url => {:action => "evaluate"}, :position => "top",
-      :before => %(Element.show('spinner')),
-      :complete => %(Element.hide('spinner'))) do %>
-  <img id="spinner" src="/images/bioruby/spinner.gif" style="display:none">
-  <b>BioRuby script:</b>
-  <br/>
-  <textarea id="script" name="script" rows=10 cols=80></textarea>
-  <br/>
-  <input type="submit" value="Evaluate">
-  <input type="reset" value="Clear">
-  &nbsp;&nbsp;
-  Show [
-  <%= link_to_remote "All",    :url => {:action => "results", :limit => 0} %> |
-  <%= link_to_remote "Last 5", :url => {:action => "results", :limit => 5} %> |
-  <%= link_to_remote "Previous", :url => {:action => "results", :limit => 1} %>
-  ] or <%= link_to "Hide", :action => "index" %> results<br/>
- <% end %>
-</div>
-<div id="logs">
-</div>

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif DELETED

Binary file

data/lib/bio/shell/script.rb DELETED

@@ -1,25 +0,0 @@
-#
-# = bio/shell/script.rb - script mode for the BioRuby shell
-#
-# Copyright::   Copyright (C) 2006
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-# $Id: script.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
-#
-module Bio::Shell
-  class Script
-    def initialize(script)
-      Bio::Shell.cache[:binding] = TOPLEVEL_BINDING
-      Bio::Shell.load_session
-      eval(File.read(script), TOPLEVEL_BINDING)
-      exit
-    end
-  end # Script
-end

data/lib/bio/shell/setup.rb DELETED

@@ -1,108 +0,0 @@
-#
-# = bio/shell/setup.rb - setup initial environment for the BioRuby shell
-#
-# Copyright::   Copyright (C) 2006
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-#
-require 'getoptlong'
-class Bio::Shell::Setup
-  def initialize
-    check_ruby_version
-    # command line options
-    getoptlong
-    # setup working directory
-    savedir = setup_savedir
-    # load configuration and plugins
-    Bio::Shell.configure(savedir)
-    # set default to irb mode
-    Bio::Shell.cache[:mode] = ((defined? @mode) && @mode) || :irb
-    case Bio::Shell.cache[:mode]
-    when :web
-      # setup rails server
-      Bio::Shell::Web.new
-    when :irb
-      # setup irb server
-      Bio::Shell::Irb.new
-    when :script
-      # run bioruby shell script
-      Bio::Shell::Script.new(@script)
-    end
-  end
-  def check_ruby_version
-    if RUBY_VERSION < "1.8.2"
-      raise "BioRuby shell runs on Ruby version >= 1.8.2"
-    end
-  end
-  # command line argument (working directory or bioruby shell script file)
-  def getoptlong
-    opts = GetoptLong.new
-    opts.set_options(
-      [ '--rails',   '-r',  GetoptLong::NO_ARGUMENT ],
-      [ '--web',     '-w',  GetoptLong::NO_ARGUMENT ],
-      [ '--console', '-c',  GetoptLong::NO_ARGUMENT ],
-      [ '--irb',     '-i',  GetoptLong::NO_ARGUMENT ]
-    )
-    opts.each_option do |opt, arg|
-      case opt
-      when /--rails/, /--web/
-        @mode = :web
-      when /--console/, /--irb/
-        @mode = :irb
-      end
-    end
-  end
-  def setup_savedir
-    arg = ARGV.shift
-    # Options after the '--' argument are not parsed by GetoptLong and
-    # are passed to irb or rails.  This hack preserve the first option
-    # when working directory of the project is not given.
-    if arg and arg[/^-/]
-      ARGV.unshift arg
-      arg = nil
-    end
-    if arg.nil?
-      # run in the current directory
-      if File.exist?(Bio::Shell::Core::HISTORY)
-        savedir = Dir.pwd
-      else
-        savedir = File.join(ENV['HOME'].to_s, ".bioruby")
-        install_savedir(savedir)
-      end
-    elsif File.file?(arg)
-      # run file as a bioruby shell script
-      savedir = File.join(File.dirname(arg), "..")
-      @script = arg
-      @mode = :script
-    else
-      # run in new or existing directory
-      if arg[/^#{File::SEPARATOR}/]
-        savedir = arg
-      else
-        savedir = File.join(Dir.pwd, arg)
-      end
-      install_savedir(savedir)
-    end
-    return savedir
-  end
-  def install_savedir(savedir)
-    FileUtils.makedirs(savedir)
-  end
-end # Setup

data/lib/bio/shell/web.rb DELETED

@@ -1,102 +0,0 @@
-#
-# = bio/shell/web.rb - GUI for the BioRuby shell
-#
-# Copyright::   Copyright (C) 2006
-#               Nobuya Tanaka <t@chemruby.org>,
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-# $Id: web.rb,v 1.5 2007/06/26 08:38:38 k Exp $
-#
-module Bio::Shell
-  class Web
-    def initialize
-      Bio::Shell.cache[:binding] = binding
-      Bio::Shell.cache[:results] ||= Results.new
-      install_rails
-      setup_rails
-      start_rails
-    end
-    private
-    def setup_rails
-      puts
-      puts ">>>"
-      puts ">>>  open http://localhost:3000/bioruby"
-      puts ">>>"
-      puts
-      puts '(You can change the port number by adding "-- -p 4000" option)'
-      puts
-    end
-    def install_rails
-      savedir = Bio::Shell.cache[:savedir]
-      path = File.join(savedir, "script", "generate")
-      unless File.exist?(path)
-        puts "Installing Rails application for BioRuby shell ... "
-        system("rails #{savedir}")
-        puts "done"
-      end
-      path = File.join(savedir, "app", "controllers", "bioruby_controller.rb")
-      unless File.exist?(path)
-        basedir = File.dirname(__FILE__)
-        puts "Installing Rails plugin for BioRuby shell ... "
-        FileUtils.cp_r("#{basedir}/rails/.", savedir)
-        Dir.chdir(savedir) do
-          system("./script/generate bioruby shell")
-        end
-        puts "done"
-      end
-    end
-    def start_rails
-      begin
-        Bio::Shell.cache[:rails] = Thread.new do
-          Dir.chdir(Bio::Shell.cache[:savedir]) do
-            require './config/boot'
-            require 'commands/server'
-          end
-        end
-      end
-    end
-    class Results
-      attr_accessor :number, :script, :result, :output
-      def initialize
-        @number = 0
-        @script = []
-        @result = []
-        @output = []
-      end
-      def store(script, result, output)
-        @number += 1
-        @script[@number] = script
-        @result[@number] = result
-        @output[@number] = output
-        return @number
-      end
-      def restore(number)
-        return @script[number], @result[number], @output[number]
-      end
-    end
-  end
-  private
-  # *TODO* stop irb and start rails?
-  #def web
-  #end
-end