bio 1.0.0 → 1.1.0

data/lib/bio/shell/demo.rb

@@ -3,9 +3,9 @@
 #
 # Copyright::   Copyright (C) 2006
 #               Toshiaki Katayama <k@bioruby.org>
-# License::     Ruby's
+# License::     The Ruby License
 #
-# $Id: demo.rb,v 1.1 2006/02/27 09:33:22 k Exp $
+# $Id: demo.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
 #
 
 module Bio::Shell
@@ -24,7 +24,7 @@ module Bio::Shell
   class Demo
 
     def initialize
-      @bind = IRB.conf[:MAIN_CONTEXT].workspace.binding
+      @bind = Bio::Shell.cache[:binding]
     end
 
     def all
@@ -38,8 +38,11 @@ module Bio::Shell
     def tutorial
     end
 
+    def aldh2
+    end
+
     def mito
-      run(%q[entry = ent("data/kumamushi.gb")], "Load kumamushi gene from GenBank database entry ...", false) &&
+      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) &&
@@ -61,7 +64,7 @@ module Bio::Shell
     end
 
     def sequence
-      run(%q[dna = seq("atgc" * 100)], "Generating DNA sequence ...", true) &&
+      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) &&
@@ -70,7 +73,7 @@ module Bio::Shell
     end
 
     def entry
-      run(%q[kuma = obj("gb:AF237819")], "Obtain an entry from GenBank database", false) &&
+      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) &&
@@ -81,15 +84,15 @@ module Bio::Shell
     def shell
       run(%q[pwd], "Show current working directory ...", false) &&
       run(%q[dir], "Show directory contents ...", false) &&
-      run(%q[dir "session"], "Show directory contents ...", false) &&
+      run(%q[dir "shell/session"], "Show directory contents ...", false) &&
       true
     end
 
     def pdb
-      run(%q[ent_1bl8 = ent("pdb:1bl8")], "Retrieving PDB entry 1BL8 ...", false) &&
+      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[less "data/1bl8.pdb"], "Look through the entire entry ...", 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) &&
@@ -97,17 +100,17 @@ module Bio::Shell
     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 = 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[less "data/het_dictionary.txt"], "Take a look on the contents ...", 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[sake.conect], "Showing connect table (conect) of the molecule ...", true) &&
+      run(%q[osake.conect], "Showing connect table (conect) of the molecule ...", true) &&
       true
     end
 

data/lib/bio/shell/interface.rb

@@ -3,9 +3,9 @@
 #
 # Copyright::   Copyright (C) 2005
 #               Toshiaki Katayama <k@bioruby.org>
-# License::     Ruby's
+# License::     The Ruby License
 #
-# $Id: interface.rb,v 1.14 2006/02/27 09:36:35 k Exp $
+# $Id: interface.rb,v 1.18 2007/06/26 08:38:38 k Exp $
 #
 
 module Bio::Shell
@@ -15,20 +15,22 @@ module Bio::Shell
   ### work space
 
   def ls
-    list = eval("local_variables", conf.workspace.binding).reject { |x|
-      eval(x, conf.workspace.binding).nil?
+    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)
-    list = eval("local_variables", conf.workspace.binding).reject { |x|
-      eval(x, conf.workspace.binding).nil?
+    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", conf.workspace.binding)
+        eval("#{name} = nil", bind)
       else
         raise
       end
@@ -147,7 +149,7 @@ module Bio::Shell
   ### file save
 
   def savefile(file, *objs)
-    datadir = Bio::Shell.datadir
+    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 = datadir + file
@@ -196,18 +198,18 @@ module Bio::Shell
       files = Dir.glob("*")
     end
     if files
-      str  = "   UGO  Date                                 Byte  File\n"
-      str << "------  ----------------------------  -----------  ------------\n"
+      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  %s%13d  %s\n", mode, date, byte, name)
+        str << format("%s  %30s%13d  %s\n", mode, date, byte, name)
       }
       puts str
-      return str
+      return files.sort
     end
   end
 

data/lib/bio/shell/irb.rb

@@ -0,0 +1,95 @@
+#
+# = bio/shell/irb.rb - CUI for the BioRuby shell
+#
+# Copyright::   Copyright (C) 2006
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: irb.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
+#
+
+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.exists?("./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
+

data/lib/bio/shell/object.rb

@@ -4,13 +4,14 @@
 # Copyright::   Copyright (C) 2006
 #               Nobuya Tanaka <t@chemruby.org>,
 #               Toshiaki Katayama <k@bioruby.org>
-# License::     Ruby's
+# License::     The Ruby License
 #
-# $Id: object.rb,v 1.1 2006/02/27 09:16:13 k Exp $
+# $Id: object.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
 #
 
-require 'cgi'
 require 'pp'
+require 'cgi'
+require 'yaml'
 
 ### Object extention
 
@@ -18,35 +19,53 @@ class Object
   # Couldn't work for Fixnum (Marshal)
   attr_accessor :memo
 
-  # *TODO*
-  def to_html
-    if self.is_a?(String)
-      "<pre>" + self + "</pre>"
+  def output(format = :yaml)
+    case format
+    when :yaml
+      self.to_yaml
+    when :html
+      format_html
+    when :inspect
+      format_pp
+    when :png
+      # *TODO*
+    when :svg
+      # *TODO*
+    when :graph
+      # *TODO* (Gruff, RSRuby etc.)
     else
-      str = ""
-      PP.pp(self, str)
-      "<pre>" + str + "</pre>"
-      #"<pre>" + CGI.escapeHTML(str) + "</pre>"
-      #self.inspect
-      #"<pre>" + self.inspect + "</pre>"
-      #"<pre>" + self.to_s + "</pre>"
+      #self.inspect.to_s.fold(80)
+      self.to_s
     end
   end
+
+  private
+
+  def format_html
+    "<pre>#{CGI.escapeHTML(format_pp)}</pre>"
+  end
+
+  def format_pp
+    str = ""
+    PP.pp(self, str)
+    return str
+  end
+
 end
 
-=begin
-module Bio
-  class DB
-    def to_html
-      html = ""
-      html += "<table>"
-      @data.each do |k, v|
-        html += "<tr><td>#{k}</td><td>#{v}</td></tr>"
-      end
-      html += "</table>"
+class Hash
+
+  private
+
+  def format_html
+    html = ""
+    html += "<table>"
+    @data.each do |k, v|
+      html += "<tr><td>#{k}</td><td>#{v}</td></tr>"
     end
+    html += "</table>"
+    return html
   end
+
 end
-=end
 
- 

data/lib/bio/shell/plugin/blast.rb

@@ -0,0 +1,42 @@
+#
+# = bio/shell/plugin/blast.rb - plugin for BLAST services
+#
+# Copyright::   Copyright (C) 2006
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: blast.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
+#
+
+module Bio::Shell
+
+  private
+
+  # GenomeNet
+
+  def keggblast(query)
+    server = Bio::Blast.remote("blastp", "genes", "", "genomenet_tab")
+
+    if query[/^>/]
+      data = Bio::FastaFormat.new(query)
+      desc = data.definition
+      tmp = getseq(data.seq)
+    else
+      desc = "query"
+      tmp = getseq(query)
+    end
+    
+    if tmp.respond_to?(:translate)
+      aaseq = tmp.translate
+    else
+      aaseq = tmp
+    end
+
+    fasta = aaseq.to_fasta(desc, 60)
+    result = server.query(fasta)
+    puts server.output
+    return result
+  end
+
+end
+

data/lib/bio/shell/plugin/codon.rb

@@ -3,9 +3,9 @@
 #
 # Copyright::   Copyright (C) 2005
 #               Toshiaki Katayama <k@bioruby.org>
-# License::     Ruby's
+# License::     The Ruby License
 #
-# $Id: codon.rb,v 1.13 2006/02/09 20:48:53 k Exp $
+# $Id: codon.rb,v 1.16 2007/04/05 23:35:41 trevor Exp $
 #
 
 module Bio::Shell
@@ -35,24 +35,24 @@ module Bio::Shell
     attr_reader :table
 
     def setup_colors
-      esc_seq = Bio::Shell.esc_seq
+      c = Bio::Shell.colors
 
       @colors = {
-        :text		=> esc_seq[:none],
-        :aa		=> esc_seq[:green],
-        :start		=> esc_seq[:red],
-        :stop		=> esc_seq[:red],
-        :basic		=> esc_seq[:cyan],
-        :polar		=> esc_seq[:blue],
-        :acidic		=> esc_seq[:magenta],
-        :nonpolar	=> esc_seq[:yellow],
+        :text		=> c[:none],
+        :aa		=> c[:green],
+        :start		=> c[:red],
+        :stop		=> c[:red],
+        :basic		=> c[:cyan],
+        :polar		=> c[:blue],
+        :acidic		=> c[:magenta],
+        :nonpolar	=> c[:yellow],
       }
     end
 
     def generate_mono_text
       @table.each do |codon, aa|
         if aa == '*'
-          code = "STOP"
+          code = 'STOP'
           aa = '' unless @cuhash
         else
           code = @aacode[aa]
@@ -78,11 +78,19 @@ module Bio::Shell
         property, = @@properties.detect {|key, list| list.include?(aa)}
 
         if aa == '*'
-          color_code = "#{@colors[:stop]}STOP"
           if @cuhash
+            color_code = "#{@colors[:stop]}STOP"
             color_aa = "#{@colors[:stop]}#{aa}"
           else
-            color_aa = ''
+            color_code = "#{@colors[:stop]}STP"
+            case codon
+            when 'tga'
+              color_aa = "#{@colors[:text]}U"
+            when 'tag'
+              color_aa = "#{@colors[:text]}O"
+            else
+              color_aa = "#{@colors[:text]}*"
+            end
           end
         else
           color_code = "#{@colors[property]}#{@aacode[aa]}"