bio 0.7.1 → 1.0.0

data/lib/bio/sequence/na.rb

@@ -0,0 +1,189 @@
+#
+# = bio/sequence/na.rb - nucleic acid sequence class
+#
+# Copyright::   Copyright (C) 2006
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     Ruby's
+#
+# $Id: na.rb,v 1.2 2006/02/06 14:13:52 k Exp $
+#
+
+require 'bio/sequence/common'
+
+module Bio
+
+  autoload :NucleicAcid, 'bio/data/na'
+  autoload :CodonTable,  'bio/data/codontable'
+
+class Sequence
+
+
+# Nucleic Acid sequence
+class NA < String
+
+  include Bio::Sequence::Common
+
+  # Generate a nucleic acid sequence object from a string.
+  def initialize(str)
+    super
+    self.downcase!
+    self.tr!(" \t\n\r",'')
+  end
+
+  # This method depends on Locations class, see bio/location.rb
+  def splicing(position)
+    mRNA = super
+    if mRNA.rna?
+      mRNA.tr!('t', 'u')
+    else
+      mRNA.tr!('u', 't')
+    end
+    mRNA
+  end
+
+  # Returns complement sequence without reversing ("atgc" -> "tacg")
+  def forward_complement
+    s = self.class.new(self)
+    s.forward_complement!
+    s
+  end
+
+  # Convert to complement sequence without reversing ("atgc" -> "tacg")
+  def forward_complement!
+    if self.rna?
+      self.tr!('augcrymkdhvbswn', 'uacgyrkmhdbvswn')
+    else
+      self.tr!('atgcrymkdhvbswn', 'tacgyrkmhdbvswn')
+    end
+    self
+  end
+
+  # Returns reverse complement sequence ("atgc" -> "gcat")
+  def reverse_complement
+    s = self.class.new(self)
+    s.reverse_complement!
+    s
+  end
+
+  # Convert to reverse complement sequence ("atgc" -> "gcat")
+  def reverse_complement!
+    self.reverse!
+    self.forward_complement!
+  end
+
+  # Aliases for short
+  alias complement reverse_complement
+  alias complement! reverse_complement!
+
+
+  # Translate into the amino acid sequence from the given frame and the
+  # selected codon table.  The table also can be a Bio::CodonTable object.
+  # The 'unknown' character is used for invalid/unknown codon (can be
+  # used for 'nnn' and/or gap translation in practice).
+  #
+  # Frame can be 1, 2 or 3 for the forward strand and -1, -2 or -3
+  # (4, 5 or 6 is also accepted) for the reverse strand.
+  def translate(frame = 1, table = 1, unknown = 'X')
+    if table.is_a?(Bio::CodonTable)
+      ct = table
+    else
+      ct = Bio::CodonTable[table]
+    end
+    naseq = self.dna
+    case frame
+    when 1, 2, 3
+      from = frame - 1
+    when 4, 5, 6
+      from = frame - 4
+      naseq.complement!
+    when -1, -2, -3
+      from = -1 - frame
+      naseq.complement!
+    else
+      from = 0
+    end
+    nalen = naseq.length - from
+    nalen -= nalen % 3
+    aaseq = naseq[from, nalen].gsub(/.{3}/) {|codon| ct[codon] or unknown}
+    return Bio::Sequence::AA.new(aaseq)
+  end
+
+  # Returns counts of the each codon in the sequence by Hash.
+  def codon_usage
+    hash = Hash.new(0)
+    self.window_search(3, 3) do |codon|
+      hash[codon] += 1
+    end
+    return hash
+  end
+
+  # Calculate the ratio of GC / ATGC bases in percent.
+  def gc_percent
+    count = self.composition
+    at = count['a'] + count['t'] + count['u']
+    gc = count['g'] + count['c']
+    gc = 100 * gc / (at + gc)
+    return gc
+  end
+
+  # Show abnormal bases other than 'atgcu'.
+  def illegal_bases
+    self.scan(/[^atgcu]/).sort.uniq
+  end
+
+  # Estimate the weight of this biological string molecule.
+  def molecular_weight
+    if self.rna?
+      Bio::NucleicAcid.weight(self, true)
+    else
+      Bio::NucleicAcid.weight(self)
+    end
+  end
+
+  # Convert the universal code string into the regular expression.
+  def to_re
+    if self.rna?
+      Bio::NucleicAcid.to_re(self.dna, true)
+    else
+      Bio::NucleicAcid.to_re(self)
+    end
+  end
+
+  # Convert the self string into the list of the names of the each base.
+  def names
+    array = []
+    self.each_byte do |x|
+      array.push(Bio::NucleicAcid.names[x.chr.upcase])
+    end
+    return array
+  end
+
+  # Output a DNA string by substituting 'u' to 't'.
+  def dna
+    self.tr('u', 't')
+  end
+
+  def dna!
+    self.tr!('u', 't')
+  end
+
+  # Output a RNA string by substituting 't' to 'u'.
+  def rna
+    self.tr('t', 'u')
+  end
+
+  def rna!
+    self.tr!('t', 'u')
+  end
+
+  def rna?
+    self.index('u')
+  end
+  protected :rna?
+
+end # NA
+
+end # Sequence
+
+end # Bio
+

data/lib/bio/shell.rb

@@ -1,29 +1,11 @@
 #
 # = bio/shell.rb - Loading all BioRuby shell features
 #
-# Copyright::	Copyright (C) 2005
-#		Toshiaki Katayama <k@bioruby.org>
-# License::	LGPL
+# Copyright::   Copyright (C) 2005, 2006
+#               Toshiaki Katayama <k@bioruby.org>
+# License:      Ruby's
 #
-# $Id: shell.rb,v 1.11 2005/12/07 05:12:06 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: shell.rb,v 1.15 2006/02/27 09:34:23 k Exp $
 #
 
 require 'bio'
@@ -34,7 +16,10 @@ require 'pp'
 module Bio::Shell
 
   require 'bio/shell/core'
-  require 'bio/shell/session'
+  require 'bio/shell/interface'
+  require 'bio/shell/object'
+  require 'bio/shell/web'
+  require 'bio/shell/demo'
   require 'bio/shell/plugin/entry'
   require 'bio/shell/plugin/seq'
   require 'bio/shell/plugin/midi'
@@ -42,6 +27,7 @@ module Bio::Shell
   require 'bio/shell/plugin/flatfile'
   require 'bio/shell/plugin/obda'
   require 'bio/shell/plugin/keggapi'
+  require 'bio/shell/plugin/emboss'
 
   extend Ghost
   extend Private

data/lib/bio/shell/core.rb

@@ -1,44 +1,25 @@
 #
 # = bio/shell/core.rb - internal methods for the BioRuby shell
 #
-# Copyright::	Copyright (C) 2005
-#		Toshiaki Katayama <k@bioruby.org>
-# License::	LGPL
+# Copyright::   Copyright (C) 2005, 2006
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     Ruby's
 #
-# $Id: core.rb,v 1.16 2005/12/07 10:54:23 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: core.rb,v 1.21 2006/02/27 09:09:57 k Exp $
 #
 
+
 module Bio::Shell::Ghost
 
+  SAVEDIR = "session/"
   CONFIG  = "config"
   OBJECT  = "object"
   HISTORY = "history"
   SCRIPT  = "script.rb"
   PLUGIN  = "plugin/"
+  DATADIR = "data/"
   BIOFLAT = "bioflat/"
 
-  SITEDIR = "/etc/bioinformatics/bioruby/"
-  USERDIR = "#{ENV['HOME']}/.bioinformatics/bioruby/"
-  SAVEDIR = ".bioruby/"
-
   MARSHAL = [ Marshal::MAJOR_VERSION, Marshal::MINOR_VERSION ]
 
   MESSAGE = "...BioRuby in the shell..."
@@ -55,6 +36,14 @@ module Bio::Shell::Ghost
     :n => "\e[00m",  :none    => "\e[00m",  :reset => "\e[00m",
   }
 
+  def history
+    SAVEDIR + HISTORY
+  end
+
+  def datadir
+    DATADIR
+  end
+
   def esc_seq
     ESC_SEQ
   end
@@ -76,48 +65,19 @@ module Bio::Shell::Ghost
   # A hash to store temporal (per session) configurations
   attr_accessor :cache
 
-  def load
+  def load_session
     load_object
     load_history
     opening_splash
   end
 
-  def save
+  def save_session
     closing_splash
-    save_history
-    save_object
-    save_config
-  end
-
-  #--
-  # *TODO* How to prevent terminal collapse and suppress loading messages?
-  #++
-  def load_thread
-    message = ''
-    begin
-      t1 = Thread.new do
-        require 'stringio'
-        sio = StringIO.new('')
-        begin
-          stdout_save = STDOUT.clone
-          STDOUT.reopen(sio)
-          load_object
-          load_history
-        ensure
-          STDOUT.reopen(stdout_save)
-          stdout_save.close
-          message = sio.read
-          sio.close
-        end
-      end
-      t2 = Thread.new do
-        opening_splash
-      end
-      t1.join
-      t2.join
-    rescue
+    if create_save_dir_ask
+      #save_history	# changed to use our own...
+      save_object
+      save_config
     end
-    puts message
   end
 
   ### setup
@@ -135,36 +95,44 @@ module Bio::Shell::Ghost
   end
 
   def create_save_dir
-    dir = ask_save_dir
-    create_real_dir(dir)
-    create_real_dir(dir + PLUGIN)
-    create_real_dir(dir + BIOFLAT)
-    return dir
+    create_real_dir(SAVEDIR)
+    create_real_dir(DATADIR)
+    create_real_dir(PLUGIN)
   end
 
-  # 1. ask to save in SAVEDIR directory in the current directory
-  # 2. otherwise save in USERDIR directory
-  # 3. remember the choice in @cache[:savedir] once per session
-  def ask_save_dir
-    if @cache[:savedir]
-      dir = @cache[:savedir]
-    else
-      dir = SAVEDIR
-      if ! File.directory?(dir)
-        loop do
-          print "Save in \"#{dir}\" directory? [y/n]: "
-          answer = gets
-          if /^\s*[Yy]/.match(answer)
-            break
-          elsif /^\s*[Nn]/.match(answer)
-            dir = USERDIR
-            break
-          end
-        end
+  def create_save_dir_ask
+    if File.directory?(SAVEDIR)
+      @cache[:save] = true
+    end
+    if @cache[:save].nil?
+      if ask_yes_or_no("Save session in '#{SAVEDIR}' directory? [y/n] ")
+        create_real_dir(SAVEDIR)
+        create_real_dir(DATADIR)
+        create_real_dir(PLUGIN)
+#       create_real_dir(BIOFLAT)
+        @cache[:save] = true
+      else
+        @cache[:save] = false
+      end
+    end
+    return @cache[:save]
+  end
+
+  def ask_yes_or_no(message)
+    loop do
+      print "#{message}"
+      answer = gets
+      if answer.nil?
+        # readline support might be broken
+        return false
+      elsif /^\s*[Nn]/.match(answer)
+        return false
+      elsif /^\s*[Yy]/.match(answer)
+        return true
+      else
+        # loop
       end
-      @cache[:savedir] = dir
     end
-    return dir
   end
 
   def create_real_dir(dir)
@@ -174,7 +142,7 @@ module Bio::Shell::Ghost
         Dir.mkdir(dir)
         puts "done"
       rescue
-        warn "Error: Failed to create #{dir} : #{$!}"
+        warn "Error: Failed to create directory (#{dir}) : #{$!}"
       end
     end
   end
@@ -182,16 +150,18 @@ module Bio::Shell::Ghost
   ### bioflat
 
   def create_flat_dir(dbname)
-    if prefix = create_save_dir
-      return prefix + BIOFLAT + dbname.to_s.strip
-    else
-      return nil
+    dir = BIOFLAT + dbname.to_s.strip
+    unless File.directory?(BIOFLAT)
+      Dir.mkdir(BIOFLAT)
     end
+    unless File.directory?(dir)
+      Dir.mkdir(dir)
+    end
+    return dir
   end
 
   def find_flat_dir(dbname)
-    dir = SAVEDIR + BIOFLAT + dbname.to_s.strip
-    dir = USERDIR + BIOFLAT + dbname.to_s.strip unless File.exists?(dir)
+    dir = BIOFLAT + dbname.to_s.strip
     if File.exists?(dir)
       return dir
     else
@@ -202,8 +172,6 @@ module Bio::Shell::Ghost
   ### config
 
   def load_config
-    load_config_file(SITEDIR + CONFIG)
-    load_config_file(USERDIR + CONFIG)
     load_config_file(SAVEDIR + CONFIG)
   end
 
@@ -218,8 +186,7 @@ module Bio::Shell::Ghost
   end
 
   def save_config
-    dir = create_save_dir
-    save_config_file(dir + CONFIG)
+    save_config_file(SAVEDIR + CONFIG)
   end
 
   def save_config_file(file)
@@ -265,17 +232,23 @@ module Bio::Shell::Ghost
     @config[:pager] = cmd
   end
 
+  def config_splash
+    flag = ! @config[:splash]
+    @config[:splash] = flag
+    puts "Splash #{flag ? 'on' : 'off'}"
+    opening_splash
+  end
+
   def config_message(str = nil)
     str ||= MESSAGE
     @config[:message] = str
+    opening_splash
   end
 
   ### plugin
 
   def load_plugin
-    load_plugin_dir(SITEDIR + PLUGIN)
-    load_plugin_dir(USERDIR + PLUGIN)
-    load_plugin_dir(SAVEDIR + PLUGIN)
+    load_plugin_dir(PLUGIN)
   end
 
   def load_plugin_dir(dir)
@@ -291,8 +264,6 @@ module Bio::Shell::Ghost
   ### object
 
   def load_object
-    load_object_file(SITEDIR + OBJECT)
-    load_object_file(USERDIR + OBJECT)
     load_object_file(SAVEDIR + OBJECT)
   end
 
@@ -318,8 +289,7 @@ module Bio::Shell::Ghost
   end
   
   def save_object
-    dir = create_save_dir
-    save_object_file(dir + OBJECT)
+    save_object_file(SAVEDIR + OBJECT)
   end
 
   def save_object_file(file)
@@ -358,8 +328,6 @@ module Bio::Shell::Ghost
 
   def load_history
     if @cache[:readline]
-      load_history_file(SITEDIR + HISTORY)
-      load_history_file(USERDIR + HISTORY)
       load_history_file(SAVEDIR + HISTORY)
     end
   end
@@ -368,7 +336,9 @@ module Bio::Shell::Ghost
     if File.exists?(file)
       print "Loading history (#{file}) ... "
       File.open(file).each do |line|
-        Readline::HISTORY.push line.chomp
+        #Readline::HISTORY.push line.chomp
+	date, hist = line.chomp.split("\t")
+        Readline::HISTORY.push hist if hist
       end
       puts "done"
     end
@@ -376,8 +346,7 @@ module Bio::Shell::Ghost
   
   def save_history
     if @cache[:readline]
-      dir = create_save_dir
-      save_history_file(dir + HISTORY)
+      save_history_file(SAVEDIR + HISTORY)
     end
   end
 
@@ -428,10 +397,20 @@ module Bio::Shell::Ghost
 
   def save_script
     if @script_begin and @script_end and @script_begin <= @script_end
-      dir = create_save_dir
-      save_script_file(dir + SCRIPT)
+      if File.exists?(SCRIPT)
+        message = "Overwrite script file (#{SCRIPT})? [y/n] "
+      else
+        message = "Save script file (#{SCRIPT})? [y/n] "
+      end
+      if ask_yes_or_no(message)
+        save_script_file(SCRIPT)
+      else
+        puts " ... save aborted."
+      end 
+    elsif @script_begin and @script_end and @script_begin - @script_end == 1
+      puts " ... script aborted."
     else
-      puts "Error: script range #{@script_begin}..#{@script_end} is invalid"
+      puts "Error: Script range #{@script_begin}..#{@script_end} is invalid"
     end
   end
 
@@ -439,10 +418,10 @@ module Bio::Shell::Ghost
     begin
       print "Saving script (#{file}) ... "
         File.open(file, "w") do |f|
-        f.print "#!/usr/bin/env ruby\n\n"
-        f.print "require 'bioruby'\n\n"
+        f.puts "#!/usr/bin/env bioruby"
+        f.puts
         f.puts Readline::HISTORY.to_a[@script_begin..@script_end]
-        f.print "\n\n"
+        f.puts
       end
       puts "done"
     rescue
@@ -465,8 +444,25 @@ module Bio::Shell::Ghost
     return str.sub(/R u b y/) { "#{ruby}R u b y#{none}" }
   end
 
-  def splash_message_action
-    s = splash_message
+  def splash_message_action(message = nil)
+    s = message || splash_message
+    l = s.length
+    x = " "
+    0.step(l,2) do |i|
+      l1 = l-i;  l2 = l1/2;  l4 = l2/2
+      STDERR.print "#{s[0,i]}#{x*l1}#{s[i,1]}\r"
+      sleep(0.001)
+      STDERR.print "#{s[0,i]}#{x*l2}#{s[i,1]}#{x*(l1-l2)}\r"
+      sleep(0.002)
+      STDERR.print "#{s[0,i]}#{x*l4}#{s[i,1]}#{x*(l2-l4)}\r"
+      sleep(0.004)
+      STDERR.print "#{s[0,i+1]}#{x*l4}\r"
+      sleep(0.008)
+    end
+  end
+
+  def splash_message_action_color(message = nil)
+    s = message || splash_message
     l = s.length
     c = ESC_SEQ
     x = " "
@@ -484,28 +480,37 @@ module Bio::Shell::Ghost
   end
 
   def opening_splash
-    print "\n"
-    if @config[:color]
-      splash_message_action
+    puts
+    if @config[:splash]
+      if @config[:color]
+        splash_message_action_color
+      else
+        splash_message_action
+      end
     end
     if @config[:color]
       print splash_message_color
     else
       print splash_message
     end
-    print "\n\n"
+    puts
+    puts
     print "  Version : BioRuby #{Bio::BIORUBY_VERSION.join(".")}"
-    print " / Ruby #{RUBY_VERSION}\n\n"
+    print " / Ruby #{RUBY_VERSION}"
+    puts
+    puts
   end
 
   def closing_splash
-    print "\n\n"
+    puts
+    puts
     if @config[:color]
       print splash_message_color
     else
       print splash_message
     end
-    print "\n\n"
+    puts
+    puts
   end
 
 end