bio 1.5.2 → 1.6.0.pre.20181210

data/lib/bio/shell/demo.rb

@@ -1,146 +0,0 @@
-#
-# = bio/shell/demo.rb - demo mode for the BioRuby shell
-#
-# Copyright::   Copyright (C) 2006
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-# $Id: demo.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
-#
-
-module Bio::Shell
-
-  private
-
-  def demo(part = nil)
-    demo = Demo.new
-    if part
-      demo.send(part)
-    else
-      demo.all
-    end
-  end
-
-  class Demo
-
-    def initialize
-      @bind = Bio::Shell.cache[:binding]
-    end
-
-    def all
-      sequence &&
-      entry &&
-      shell &&
-      pdb &&
-      true
-    end
-
-    def tutorial
-    end
-
-    def aldh2
-    end
-
-    def mito
-      run(%q[entry = getent("data/kumamushi.gb")], "Load kumamushi gene from GenBank database entry ...", false) &&
-      run(%q[disp entry], "Check the contents ...", false) &&
-      run(%q[kuma = flatparse(entry)], "Parse the database entry ...", true) &&
-      run(%q[web], "Start BioRuby on Rails...", false) &&
-      run(%q[puts kuma.entry_id], "Extract entry ID ...", false) &&
-      run(%q[puts kuma.definition], "Extract definition ...", false) &&
-      run(%q[gene = kuma.seq], "Extract DNA sequence of the gene ...", true) &&
-      run(%q[doublehelix(gene)], "Show the sequence in ascii art ...", false) &&
-      run(%q[seqstat(gene)], "Statistics of the gene ...", false) &&
-      run(%q[config :color], "Change to color mode...", false) &&
-      run(%q[seqstat(gene)], "Statistics of the gene ...", false) &&
-      #run(%q[codontable], "Codontalble ...", false) &&
-      run(%q[protein = gene.translate], "Translate DNA into protein ...", true) &&
-      run(%q[comp = protein.composition], "Composition of the amino acids ...", false) &&
-      run(%q[pp comp], "Check the composition ...", false) &&
-      run(%q[puts protein.molecular_weight], "Molecular weight ...", false) &&
-      run(%q[midifile("data/kumamushi.mid", gene)], "Gene to music ...", false) &&
-      run(%q[`open "data/kumamushi.mid"`], "Let's listen ...", false) &&
-      true
-    end
-
-    def sequence
-      run(%q[dna = getseq("atgc" * 100)], "Generating DNA sequence ...", true) &&
-      run(%q[doublehelix dna], "Double helix representation", false) &&
-      run(%q[protein = dna.translate], "Translate DNA into Protein ...", true) &&
-      run(%q[protein.molecular_weight], "Calculating molecular weight ...", true) &&
-      run(%q[protein.composition], "Amino acid composition ...", true) &&
-      true
-    end
-
-    def entry
-      run(%q[kuma = getobj("gb:AF237819")], "Obtain an entry from GenBank database", false) &&
-      run(%q[kuma.definition], "Definition of the entry", true) &&
-      run(%q[kuma.naseq], "Sequence of the entry", true) &&
-      run(%q[kuma.naseq.translate], "Translate the sequence to protein", true) &&
-      run(%q[midifile("data/AF237819.mid", kuma.naseq)], "Generate gene music ...", false) &&
-      true
-    end
-
-    def shell
-      run(%q[pwd], "Show current working directory ...", false) &&
-      run(%q[dir], "Show directory contents ...", false) &&
-      run(%q[dir "shell/session"], "Show directory contents ...", false) &&
-      true
-    end
-
-    def pdb
-      run(%q[ent_1bl8 = getent("pdb:1bl8")], "Retrieving PDB entry 1BL8 ...", false) &&
-      run(%q[head ent_1bl8], "Head part of the entry ...", false) &&
-      run(%q[savefile("1bl8.pdb", ent_1bl8)], "Saving the original entry in file ...", false) &&
-      run(%q[disp "data/1bl8.pdb"], "Look through the entire entry ...", false) &&
-      run(%q[pdb_1bl8 = flatparse(ent_1bl8)], "Parsing the entry ...", false) &&
-      run(%q[pdb_1bl8.entry_id], "Showing the entry ID ...", true) &&
-      run(%q[pdb_1bl8.each_heterogen { |heterogen| p heterogen.resName }], "Showing each heterogen object ...", false) &&
-      true
-    end
-
-    def pdb_hetdic
-#      run(%q[het_dic = open("http://deposit.pdb.org/het_dictionary.txt").read],
-#          "Retrieving the het_dic database ...", false) &&
-#      run(%q[savefile("data/het_dictionary.txt", het_dic)],
-#          "Saving the file ... ", false) &&
-      run(%q[het_dic.size], "Bytes of the file ...", true) &&
-      run(%q[disp "data/het_dictionary.txt"], "Take a look on the contents ...", true) &&
-      run(%q[flatindex("het_dic", "data/het_dictionary.txt")],
-          "Creating index to make the seaarchable database ...", false) &&
-      run(%q[ethanol = flatsearch("het_dic", "EOH")], "Search an ethanol entry ...", true) &&
-      run(%q[osake = flatparse(ethanol)], "Parse the entry ...", true) &&
-      run(%q[osake.conect], "Showing connect table (conect) of the molecule ...", true) &&
-      true
-    end
-
-    private
-
-    def run(cmd, msg, echo)
-      comment(msg)
-      splash(cmd)
-      result = eval(cmd, @bind)
-      if echo
-        pp result
-      end
-      continue?
-    end
-
-    def comment(msg)
-      puts "### #{msg}"
-    end
-
-    def splash(msg)
-      Bio::Shell.splash_message_action("bioruby> #{msg}")
-      print "bioruby> #{msg}"
-      gets
-    end
-
-    def continue?
-      Bio::Shell.ask_yes_or_no("Continue? [y/n] ")
-    end
-
-  end
-
-end
-

data/lib/bio/shell/interface.rb

@@ -1,217 +0,0 @@
-#
-# = bio/shell/interface.rb - core user interface of the BioRuby shell
-#
-# Copyright::   Copyright (C) 2005
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-#
-
-module Bio::Shell
-
-  private
-
-  ### work space
-
-  def ls
-    bind = Bio::Shell.cache[:binding]
-    list = eval("local_variables", bind).reject { |x|
-      eval(x, bind).nil?
-    }
-    puts list.inspect
-    return list
-  end
-
-  def rm(name)
-    bind = Bio::Shell.cache[:binding]
-    list = eval("local_variables", bind).reject { |x|
-      eval(x, bind).nil?
-    }
-    begin
-      if list.include?(name.to_s)
-        eval("#{name} = nil", bind)
-      else
-        raise
-      end
-    rescue
-      warn "Usage: rm :var or rm 'var' (rm var is not valid)"
-    end
-  end
-
-  ### script
-
-  def script(mode = nil)
-    Bio::Shell.script(mode)
-  end
-
-  ### object
-
-  def reload_object
-    Bio::Shell.load_object
-  end
-
-  ### plugin
-
-  def reload_plugin
-    Bio::Shell.load_plugin
-  end
-
-  ### config
-
-  def config(mode = :show, *opts)
-    case mode
-    when :show, "show"
-      Bio::Shell.config_show
-    when :echo, "echo"
-      Bio::Shell.config_echo
-    when :color, "color"
-      Bio::Shell.config_color
-    when :splash, "splash"
-      Bio::Shell.config_splash
-    when :pager, "pager"
-      Bio::Shell.config_pager(*opts)
-    when :message, "message"
-      Bio::Shell.config_message(*opts)
-    else
-      puts "Invalid mode (#{mode}) - :show, :echo, :color, :splash, :massage"
-    end
-  end
-
-  def reload_config
-    Bio::Shell.load_config
-  end
-
-  ### pager
-
-  def pager(cmd = nil)
-    unless Bio::Shell.config[:pager]
-      cmd ||= ENV['PAGER']
-    end
-    Bio::Shell.config_pager(cmd)
-    puts "Pager is set to '#{cmd ? cmd : 'off'}'"
-  end
-
-  def disp(*objs)
-    # The original idea is from http://sheepman.parfait.ne.jp/20050215.html
-    if cmd = Bio::Shell.config[:pager]
-      pg = IO.popen(cmd, "w")
-      begin
-        stdout_save = STDOUT.clone
-        STDOUT.reopen(pg)
-        objs.each do |obj|
-          if obj.is_a?(String)
-            if File.exist?(obj)
-              system("#{cmd} #{obj}")
-            else
-              obj.display
-            end
-          else
-            pp obj
-          end
-        end
-      ensure
-        STDOUT.reopen(stdout_save)
-        stdout_save.close
-        pg.close
-      end
-    else
-      objs.each do |obj|
-        if obj.is_a?(String)
-          obj.display
-        else
-          pp obj
-        end
-      end
-    end
-  end
-
-  def head(arg, num = 10)
-    str = ""
-    if File.exist?(arg)
-      File.open(arg) do |file|
-        num.times do
-          if line = file.gets
-            str << line
-          end
-        end
-      end
-    else
-      arg.to_s.each_with_index do |line, i|
-        break if i >= num
-        str << line
-      end
-    end
-    puts str
-    return str
-  end
-
-  ### file save
-
-  def savefile(file, *objs)
-    datadir = Bio::Shell.data_dir
-    message = "Save file '#{file}' in '#{datadir}' directory? [y/n] "
-    if ! file[/^#{datadir}/] and Bio::Shell.ask_yes_or_no(message)
-      file = File.join(datadir, file)
-    end
-    if File.exist?(file)
-      message = "Overwrite existing '#{file}' file? [y/n] "
-      if ! Bio::Shell.ask_yes_or_no(message)
-        puts " ... save aborted."
-        return
-      end
-    end
-    begin
-      print "Saving file (#{file}) ... "
-      File.open(file, "w") do |f|
-        objs.each do |obj|
-          f.puts obj.to_s
-        end
-      end
-      puts "done"
-    rescue
-      warn "Error: Failed to save (#{file}) : #{$!}"
-    end
-  end
-
-  ### file system
-
-  def cd(dir = ENV['HOME'])
-    if dir
-      Dir.chdir(dir)
-    end
-    puts Dir.pwd.inspect
-  end
-
-  def pwd
-    puts Dir.pwd.inspect
-  end
-
-  def dir(file = nil)
-    if file
-      if File.directory?(file)
-        files = Dir.glob("#{file}/*")
-      else
-        files = Dir.glob(file)
-      end
-    else
-      files = Dir.glob("*")
-    end
-    if files
-      str  = "   UGO  Date                                   Byte  File\n"
-      str << "------  ------------------------------  -----------  ------------\n"
-      files.sort.each { |f|
-        stat = File.lstat(f)
-        mode = format("%6o", stat.mode)
-        date = stat.mtime
-        byte = stat.size
-        name = f.inspect
-        str << format("%s  %30s%13d  %s\n", mode, date, byte, name)
-      }
-      puts str
-      return files.sort
-    end
-  end
-
-end
-
-

data/lib/bio/shell/irb.rb

@@ -1,94 +0,0 @@
-#
-# = bio/shell/irb.rb - CUI for the BioRuby shell
-#
-# Copyright::   Copyright (C) 2006
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-#
-
-module Bio::Shell
-
-  class Irb
-
-    def initialize
-      require 'irb'
-      begin
-        require 'irb/completion'
-        Bio::Shell.cache[:readline] = true
-      rescue LoadError
-        Bio::Shell.cache[:readline] = false
-      end
-      IRB.setup(nil)
-      setup_irb
-      start_irb
-    end
-
-    def start_irb
-      Bio::Shell.cache[:irb] = IRB::Irb.new
-
-      # needed for method completion
-      IRB.conf[:MAIN_CONTEXT] = Bio::Shell.cache[:irb].context
-
-      # store binding for evaluation
-      Bio::Shell.cache[:binding] = IRB.conf[:MAIN_CONTEXT].workspace.binding
-
-      # overwrite gets to store history with time stamp
-      io = IRB.conf[:MAIN_CONTEXT].io
-      io.class.class_eval do
-        alias_method :irb_original_gets, :gets
-      end
-
-      def io.gets
-        line = irb_original_gets
-        if line
-          Bio::Shell.store_history(line)
-        end
-        return line
-      end
-
-      if File.exist?("./config/boot.rb")
-        require "./config/boot"
-        require "./config/environment"
-        #require 'commands/console'
-      end
-    end
-
-    def setup_irb
-      # set application name
-      IRB.conf[:AP_NAME] = 'bioruby'
-
-      # change prompt for bioruby
-      $_ = Bio::Shell.colors
-      IRB.conf[:PROMPT][:BIORUBY_COLOR] = {
-        :PROMPT_I => "bio#{$_[:ruby]}ruby#{$_[:none]}> ",
-        :PROMPT_S => "bio#{$_[:ruby]}ruby#{$_[:none]}%l ",
-        :PROMPT_C => "bio#{$_[:ruby]}ruby#{$_[:none]}+ ",
-        :RETURN   => "  ==> %s\n"
-      }
-      IRB.conf[:PROMPT][:BIORUBY] = {
-        :PROMPT_I => "bioruby> ",
-        :PROMPT_S => "bioruby%l ",
-        :PROMPT_C => "bioruby+ ",
-        :RETURN   => "  ==> %s\n"
-      }
-      if Bio::Shell.config[:color]
-        IRB.conf[:PROMPT_MODE] = :BIORUBY_COLOR
-      else
-        IRB.conf[:PROMPT_MODE] = :BIORUBY
-      end
-
-      # echo mode (uncomment to off by default)
-      #IRB.conf[:ECHO] = Bio::Shell.config[:echo] || false
-
-      # irb/input-method.rb >= v1.5 (not in 1.8.2)
-      #IRB.conf[:SAVE_HISTORY] = 100000
-
-      # not nicely works
-      #IRB.conf[:AUTO_INDENT] = true
-    end
-
-  end # Irb
-
-end
-