bio-shell 0.0.0

data/lib/bio/shell/demo.rb

@@ -0,0 +1,146 @@
+#
+# = 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

@@ -0,0 +1,217 @@
+#
+# = 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

@@ -0,0 +1,94 @@
+#
+# = 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
+