bio 0.7.1 → 1.0.0

data/lib/bio/shell/demo.rb

@@ -0,0 +1,143 @@
+#
+# = bio/shell/demo.rb - demo mode for the BioRuby shell
+#
+# Copyright::   Copyright (C) 2006
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     Ruby's
+#
+# $Id: demo.rb,v 1.1 2006/02/27 09:33:22 k 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 = IRB.conf[:MAIN_CONTEXT].workspace.binding
+    end
+
+    def all
+      sequence &&
+      entry &&
+      shell &&
+      pdb &&
+      true
+    end
+
+    def tutorial
+    end
+
+    def mito
+      run(%q[entry = ent("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 = seq("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 = obj("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 "session"], "Show directory contents ...", false) &&
+      true
+    end
+
+    def pdb
+      run(%q[ent_1bl8 = ent("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[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[less "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) &&
+      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/{session.rb → interface.rb}

@@ -1,29 +1,11 @@
 #
-# = bio/shell/session.rb - core user interface of the BioRuby shell
+# = bio/shell/interface.rb - core user interface of the BioRuby shell
 #
-# Copyright::	Copyright (C) 2005
-#		Toshiaki Katayama <k@bioruby.org>
-# License::	LGPL
+# Copyright::   Copyright (C) 2005
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     Ruby's
 #
-# $Id: session.rb,v 1.11 2005/12/07 07:50:44 k Exp $
-#
-#--
-#
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#++
+# $Id: interface.rb,v 1.14 2006/02/27 09:36:35 k Exp $
 #
 
 module Bio::Shell
@@ -37,6 +19,7 @@ module Bio::Shell
       eval(x, conf.workspace.binding).nil?
     }
     puts list.inspect
+    return list
   end
 
   def rm(name)
@@ -82,10 +65,14 @@ module Bio::Shell
       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
 
@@ -97,35 +84,46 @@ module Bio::Shell
 
   def pager(cmd = nil)
     unless Bio::Shell.config[:pager]
-      cmd = ENV['PAGER'] || cmd
+      cmd ||= ENV['PAGER']
     end
     Bio::Shell.config_pager(cmd)
     puts "Pager is set to '#{cmd ? cmd : 'off'}'"
   end
 
-  def display(*obj)
+  def disp(*objs)
     # The original idea is from http://sheepman.parfait.ne.jp/20050215.html
-    if Bio::Shell.config[:pager]
-      pg = IO.popen(Bio::Shell.config[:pager], "w")
+    if cmd = Bio::Shell.config[:pager]
+      pg = IO.popen(cmd, "w")
       begin
         stdout_save = STDOUT.clone
         STDOUT.reopen(pg)
-        puts(*obj)
+        objs.each do |obj|
+          if obj.is_a?(String)
+            if File.exists?(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
-      puts(*obj)
+      objs.each do |obj|
+        if obj.is_a?(String)
+          obj.display
+        else
+          pp obj
+        end
+      end
     end
   end
 
-  def less(file)
-    pager = Bio::Shell.config[:pager] || ENV['PAGER'] || "less"
-    system("#{pager} #{file}")
-  end
-
   def head(arg, num = 10)
     str = ""
     if File.exists?(arg)
@@ -149,16 +147,20 @@ module Bio::Shell
   ### file save
 
   def savefile(file, *objs)
+    datadir = Bio::Shell.datadir
+    message = "Save file '#{file}' in '#{datadir}' directory? [y/n] "
+    if ! file[/^#{datadir}/] and Bio::Shell.ask_yes_or_no(message)
+      file = datadir + file
+    end
     if File.exists?(file)
-      loop do
-        print "Overwrite existing #{file}? [y/n]: "
-        answer = gets
-        return if /^\s*[Nn]/.match(answer)
-        break if /^\s*[Yy]/.match(answer)
+      message = "Overwrite existing '#{file}' file? [y/n] "
+      if ! Bio::Shell.ask_yes_or_no(message)
+        puts " ... save aborted."
+        return
       end
     end
     begin
-      print "Saving data (#{file}) ... "
+      print "Saving file (#{file}) ... "
       File.open(file, "w") do |f|
         objs.each do |obj|
           f.puts obj.to_s

data/lib/bio/shell/object.rb

@@ -0,0 +1,52 @@
+#
+# = bio/shell/object.rb - Object extension for the BioRuby shell
+#
+# Copyright::   Copyright (C) 2006
+#               Nobuya Tanaka <t@chemruby.org>,
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     Ruby's
+#
+# $Id: object.rb,v 1.1 2006/02/27 09:16:13 k Exp $
+#
+
+require 'cgi'
+require 'pp'
+
+### Object extention
+
+class Object
+  # Couldn't work for Fixnum (Marshal)
+  attr_accessor :memo
+
+  # *TODO*
+  def to_html
+    if self.is_a?(String)
+      "<pre>" + self + "</pre>"
+    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>"
+    end
+  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>"
+    end
+  end
+end
+=end
+
+ 

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

@@ -1,29 +1,11 @@
 #
 # = bio/shell/plugin/codon.rb - plugin for the codon table
 #
-# Copyright::	Copyright (C) 2005
-#		Toshiaki Katayama <k@bioruby.org>
-# License::	LGPL
+# Copyright::   Copyright (C) 2005
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     Ruby's
 #
-# $Id: codon.rb,v 1.12 2005/12/19 02:34:24 k Exp $
-#
-#--
-#
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#++
+# $Id: codon.rb,v 1.13 2006/02/09 20:48:53 k Exp $
 #
 
 module Bio::Shell

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

@@ -0,0 +1,23 @@
+#
+# = bio/shell/plugin/emboss.rb - methods to use EMBOSS
+#
+# Copyright::   Copyright (C) 2005
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     Ruby's
+#
+# $Id: emboss.rb,v 1.2 2006/02/09 20:48:53 k Exp $
+#
+
+module Bio::Shell
+
+  private
+
+  def seqret(usa)
+    Bio::EMBOSS.seqret(usa)
+  end
+
+  def entret(usa)
+    Bio::EMBOSS.entret(usa)
+  end
+
+end

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

@@ -1,29 +1,11 @@
 #
 # = bio/shell/plugin/entry.rb - extract entry and sequence
 #
-# Copyright::	Copyright (C) 2005
-#		Toshiaki Katayama <k@bioruby.org>
-# License::	LGPL
+# Copyright::   Copyright (C) 2005
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     Ruby's
 #
-# $Id: entry.rb,v 1.4 2005/12/07 05:12:07 k Exp $
-#
-#--
-#
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#++
+# $Id: entry.rb,v 1.8 2006/02/27 09:37:14 k Exp $
 #
 
 module Bio::Shell
@@ -58,7 +40,7 @@ module Bio::Shell
     end
 
     if tmp and tmp.is_a?(String) and not tmp.empty?
-      seq = Bio::Sequence.auto(tmp)
+      seq = Bio::Sequence.auto(tmp).seq
     end
     return seq
   end
@@ -66,20 +48,47 @@ module Bio::Shell
   # Obtain a database entry from
   #   * IO          -- IO object (first entry only)
   #   * "filename"  -- local file (first entry only)
-  #   * "db:entry"  -- local bioflat, OBDA, KEGG API
+  #   * "db:entry"  -- local BioFlat, OBDA, EMBOSS, KEGG API
   def ent(arg)
     entry = ""
     db, entry_id = arg.to_s.strip.split(/:/)
+
+    # local file
     if arg.respond_to?(:gets) or File.exists?(arg)
+      puts "Retrieving entry from file (#{arg})"
       entry = flatfile(arg)
+
+    # BioFlat in ./.bioruby/bioflat/ or ~/.bioinformatics/.bioruby/bioflat/
     elsif Bio::Shell.find_flat_dir(db)
+      puts "Retrieving entry from local BioFlat database (#{arg})"
       entry = flatsearch(db, entry_id)
+
+    # OBDA in ~/.bioinformatics/seqdatabase.ini
     elsif obdadbs.include?(db)
+      puts "Retrieving entry from OBDA (#{arg})"
       entry = obdaentry(db, entry_id)
+
     else
-      entry = bget(arg)
+      # EMBOSS USA in ~/.embossrc
+      str = entret(arg)
+      if $?.exitstatus == 0 and str.length != 0
+        puts "Retrieving entry from EMBOSS (#{arg})"
+        entry = str
+
+      # KEGG API at http://www.genome.jp/kegg/soap/
+      else
+        puts "Retrieving entry from KEGG API (#{arg})"
+        entry = bget(arg)
+      end
     end
+
     return entry
   end
 
+  # Obtain a parsed object from sources that ent() supports.
+  def obj(arg)
+    str = ent(arg)
+    flatparse(str)
+  end
+
 end