bio 1.2.1 → 1.3.0

data/lib/bio/sequence/format_raw.rb

@@ -0,0 +1,23 @@
+#
+# = bio/sequence/format_raw.rb - Raw sequence formatter
+#
+# Copyright::  Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
+#
+# $Id: format_raw.rb,v 1.1.2.1 2008/03/04 11:28:46 ngoto Exp $
+#
+
+require 'bio/sequence/format'
+
+module Bio::Sequence::Format::Formatter
+
+  # Raw sequence output formatter class
+  class Raw < Bio::Sequence::Format::FormatterBase
+
+    # output raw sequence data
+    def output
+      "#{@sequence.seq}"
+    end
+  end #class Raw
+
+end #module Bio::Sequence::Format::Formatter

data/lib/bio/shell.rb

@@ -5,7 +5,7 @@
 #               Toshiaki Katayama <k@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: shell.rb,v 1.20 2007/07/09 11:17:09 k Exp $
+# $Id:$
 #
 
 require 'bio'
@@ -36,6 +36,8 @@ module Bio::Shell
   require 'bio/shell/plugin/emboss'
   require 'bio/shell/plugin/blast'
   require 'bio/shell/plugin/psort'
+  require 'bio/shell/plugin/ncbirest'
+  require 'bio/shell/plugin/togows'
 
   extend Ghost
 

data/lib/bio/shell/core.rb

@@ -5,7 +5,7 @@
 #               Toshiaki Katayama <k@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: core.rb,v 1.27 2007/06/28 11:21:40 k Exp $
+# $Id:$
 #
 
 module Bio::Shell::Core
@@ -556,7 +556,7 @@ module Bio::Shell::Ghost
     end
     STDERR.puts
     STDERR.puts
-    STDERR.print "  Version : BioRuby #{Bio::BIORUBY_VERSION.join(".")}"
+    STDERR.print "  Version : BioRuby #{Bio::BIORUBY_VERSION_ID}"
     STDERR.print " / Ruby #{RUBY_VERSION}"
     STDERR.puts
     STDERR.puts

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

@@ -5,7 +5,7 @@
 #               Toshiaki Katayama <k@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: entry.rb,v 1.10 2007/04/05 23:35:41 trevor Exp $
+# $Id:$
 #
 
 module Bio::Shell
@@ -86,10 +86,39 @@ module Bio::Shell
         puts "Retrieving entry from EMBOSS (#{arg})"
         entry = str
 
-      # KEGG API at http://www.genome.jp/kegg/soap/
+      # via Internet
       else
-        puts "Retrieving entry from KEGG API (#{arg})"
-        entry = bget(arg)
+        case db.to_s.downcase
+        when 'genbank', 'gb', 'nuccore', 'indsc'
+          # NCBI
+          puts "Retrieving entry from NCBI eUtils"
+          entry = efetch(entry_id)
+
+        when 'embl', 'emb', /\Aembl/, /\Auni/, 'sp', /\Aensembl/
+          # EBI
+          puts "Retrieving entry from EBI Dbfetch"
+          db = 'embl' if db == 'emb'
+          db = 'uniprotkb' if db == 'uniprot' or db == 'sp'
+          entry = biofetch(db, entry_id)
+
+        when 'ddbj', 'dbj', 'dad'
+          # TogoWS REST
+          puts "Retrieving entry from TogoWS"
+          db = 'ddbj' if db == 'dbj'
+          entry = togowsentry(db, entry_id)
+
+        else
+          togodblist = Bio::TogoWS::REST.entry_database_list rescue []
+          if togodblist.include?(db) then
+            # TogoWS REST
+            puts "Retrieving entry from TogoWS"
+            entry = togowsentry(db, entry_id)
+          else
+            # KEGG API at http://www.genome.jp/kegg/soap/
+            puts "Retrieving entry from KEGG API (#{arg})"
+            entry = bget(arg)
+          end
+        end
       end
     end
 

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

@@ -0,0 +1,64 @@
+#
+# = bio/shell/plugin/ncbirest.rb - plugin for NCBI eUtils
+#
+# Copyright::   Copyright (C) 2009
+#               Naohisa Goto <ng@bioruby.org>
+# License::     The Ruby License
+#
+# $Id:$
+#
+
+module Bio::Shell
+
+  private
+
+  # NCBI eUtils EFetch service.
+  #
+  # With 1 argument, it gets sequence(s) by using
+  # Bio::NCBI::REST::EFetch.sequence.
+  # Nucleotide or protein database is automatically selected for each id.
+  #
+  # Example:
+  #   efetch('AF237819')
+  # 
+  # With two or more arguments, and when the 2nd argument is Symbol,
+  # it calls the corresponding Bio::NCBI::REST::EFetch class method.
+  #
+  # Example:
+  #   efetch('13054692', :pubmed)
+  #   # the same as Bio::NCBI::REST::EFetch.pubmed('13054692')
+  #
+  # Otherwise, it acts the same as Bio::NCBI::REST.efetch.
+  def efetch(ids, *arg)
+    if arg.empty? then
+      Bio::NCBI::REST::EFetch.sequence(ids)
+    elsif arg[0].kind_of?(Symbol)
+      meth = arg[0]
+      case meth.to_s
+      when /\A(journal|omim|pmc|pubmed|sequence|taxonomy)\z/
+        Bio::NCBI::REST::EFetch.__send__(meth, ids, *(arg[1..-1]))
+      else
+        nil
+      end
+    else
+      Bio::NCBI::REST.efetch(ids, *arg)
+    end
+  end
+
+  # NCBI eUtils EInfo
+  def einfo
+    Bio::NCBI::REST.einfo
+  end
+
+  # NCBI eUtils ESearch
+  def esearch(str, *arg)
+    Bio::NCBI::REST.esearch(str, *arg)
+  end
+
+  # Same as Bio::NCBI::REST.esearch_count
+  def esearch_count(str, *arg)
+    Bio::NCBI::REST.esearch_count(str, *arg)
+  end
+
+end
+

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

@@ -0,0 +1,40 @@
+#
+# = bio/shell/plugin/togows.rb - plugin for TogoWS REST service
+#
+# Copyright::   Copyright (C) 2009
+#               Naohisa Goto <ng@bioruby.org>
+# License::     The Ruby License
+#
+# $Id:$
+#
+
+module Bio::Shell
+
+  private
+
+  # Shortcut method to fetch entry(entries) by using TogoWS REST "entry"
+  # service. Multiple databases may be used.
+  #
+  def togows(ids, *arg)
+    Bio::TogoWS::REST.retrieve(ids, *arg)
+  end
+
+  # Fetches entry(entries) by using TogoWS REST "entry" service.
+  # Same as Bio::TogoWS::REST.entry(database, ids, *arg).
+  def togowsentry(database, ids, *arg)
+    Bio::TogoWS::REST.entry(database, ids, *arg)
+  end
+
+  # Database search by using TogoWS REST "search" service.
+  # Same as Bio::TogoWS::REST.search(database, term, *arg).
+  def togowssearch(database, term, *arg)
+    Bio::TogoWS::REST.search(database, term, *arg)
+  end
+
+  # Data format conversion by using TogoWS REST "convert" service.
+  # Same as Bio::TogoWS::REST.convert(data, format_from, format_to).
+  def togowsconvert(data, format_from, format_to)
+    Bio::TogoWS::REST.convert(data, format_from, format_to)
+  end
+
+end

data/lib/bio/tree.rb

@@ -5,7 +5,7 @@
 #               Naohisa Goto <ng@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: tree.rb,v 1.8 2007/04/05 23:35:39 trevor Exp $
+# $Id:$
 #
 
 require 'matrix'
@@ -176,7 +176,9 @@ module Bio
         else
           str = sprintf('(Node:%x', (self.__id__ << 1) & 0xffffffff)
         end
-        str += " bootstrap=#{@bootstrap.inspect}" if @bootstrap
+        if defined?(@bootstrap) and @bootstrap then
+          str += " bootstrap=#{@bootstrap.inspect}"
+        end
         str += ")"
         str
       end

data/lib/bio/util/color_scheme.rb

@@ -5,10 +5,10 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: color_scheme.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
+#  $Id:$
 #
 
-module Bio #:nodoc:
+module Bio
 
 #
 # bio/util/color_scheme.rb - Popular color codings for nucleic and amino acids

data/lib/bio/util/contingency_table.rb

@@ -5,10 +5,10 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: contingency_table.rb,v 1.7 2007/04/05 23:35:41 trevor Exp $
+#  $Id:$
 #
 
-module Bio #:nodoc:
+module Bio
 
 #
 # bio/util/contingency_table.rb - Statistical contingency table analysis for aligned sequences

data/lib/bio/util/restriction_enzyme.rb

@@ -5,10 +5,10 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: restriction_enzyme.rb,v 1.16 2007/07/16 19:28:48 k Exp $
+#  $Id:$
 #
 
-module Bio #:nodoc:
+module Bio
 
   autoload :REBASE, 'bio/db/rebase'
 

data/lib/bio/util/restriction_enzyme/single_strand.rb

@@ -5,7 +5,7 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: single_strand.rb,v 1.7 2007/07/16 19:28:48 k Exp $
+#  $Id:$
 #
 
 require 'bio/util/restriction_enzyme'
@@ -133,7 +133,7 @@ class SingleStrand < Bio::Sequence::NA
 
     # Add one more 'n' if a cut is at the last position 
     right = ( (@cut_locations_in_enzyme_notation.max >= @stripped.length) ? ('n' * (@cut_locations_in_enzyme_notation.max - @stripped.length + 1)) : '')
-    [left, stripped, right].to_s
+    [left, stripped, right].join('')
   end
 
   # The sequence with 'n' pads, cut symbols, and spacing for alignment.
@@ -183,14 +183,15 @@ class SingleStrand < Bio::Sequence::NA
   def self.once(*ids)
     for id in ids
       module_eval <<-"end;"
-        alias_method :__#{id.to_i}__, :#{id.to_s}
-        private :__#{id.to_i}__
+        alias_method :__#{id.__id__}__, :#{id.to_s}
+        private :__#{id.__id__}__
         def #{id.to_s}(*args, &block)
-          (@__#{id.to_i}__ ||= [__#{id.to_i}__(*args, &block)])[0]
+          (@__#{id.__id__}__ ||= [__#{id.__id__}__(*args, &block)])[0]
         end
       end;
     end
   end
+  private_class_method :once
 
   once :pattern, :with_cut_symbols, :with_spaces, :to_re
 

data/lib/bio/version.rb

@@ -0,0 +1,25 @@
+#
+# = bio/version.rb - BioRuby version information
+#
+# Copyright::	Copyright (C) 2001-2009
+#		Toshiaki Katayama <k@bioruby.org>,
+#               Naohisa Goto <ng@bioruby.org>
+# License::	The Ruby License
+#
+
+module Bio
+
+  # BioRuby version (Array containing Integer)
+  BIORUBY_VERSION = [1, 3, 0].extend(Comparable).freeze
+
+  # Extra version specifier (String or nil).
+  # Existance of the value indicates pre-release version or modified version.
+  BIORUBY_EXTRA_VERSION = nil
+
+  # Version identifier, including extra version string (String)
+  # Unlike BIORUBY_VERSION, it is not comparable.
+  BIORUBY_VERSION_ID =
+    (BIORUBY_VERSION.join('.') + BIORUBY_EXTRA_VERSION.to_s).freeze
+
+end #module Bio
+

data/rdoc.zsh

@@ -0,0 +1,8 @@
+#!/usr/bin/env zsh
+
+#DIAGRAM='--diagram'
+WEBCVS='http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi'
+
+rdoc ${DIAGRAM} --op rdoc --inline-source \
+  --webcvs "${WEBCVS}/bioruby/\%s?cvsroot=bioruby" \
+  bin/*(.) lib/**/*.rb [A-Z]*(.) doc/*rd etc/bioinformatics/*(.)

data/sample/demo_sequence.rb

@@ -0,0 +1,158 @@
+#
+# = sample/demo_sequence.rb - demonstration of sequence manipulation
+#
+# Copyright::   Copyright (C) 2000-2006
+#               Toshiaki Katayama <k@bioruby.org>,
+#               Mitsuteru C. Nakao <n@bioruby.org>
+# License::     The Ruby License
+#
+# $Id:$
+#
+# == Description
+#
+# Demonstration of biological sequence manipulation.
+#
+# == Usage
+#
+# Simply run this script.
+#
+#  $ ruby demo_sequence.rb
+#
+# == Development information
+#
+# The code was moved from lib/bio/sequence.rb.
+#
+
+require 'bio'
+
+#if __FILE__ == $0
+
+  puts "== Test Bio::Sequence::NA.new"
+  p Bio::Sequence::NA.new('')
+  p na = Bio::Sequence::NA.new('atgcatgcATGCATGCAAAA')
+  p rna = Bio::Sequence::NA.new('augcaugcaugcaugcaaaa')
+
+  puts "\n== Test Bio::Sequence::AA.new"
+  p Bio::Sequence::AA.new('')
+  p aa = Bio::Sequence::AA.new('ACDEFGHIKLMNPQRSTVWYU')
+
+  puts "\n== Test Bio::Sequence#to_s"
+  p na.to_s
+  p aa.to_s
+
+  puts "\n== Test Bio::Sequence#subseq(2,6)"
+  p na
+  p na.subseq(2,6)
+
+  puts "\n== Test Bio::Sequence#[2,6]"
+  p na
+  p na[2,6]
+
+  puts "\n== Test Bio::Sequence#to_fasta('hoge', 8)"
+  puts na.to_fasta('hoge', 8)
+
+  puts "\n== Test Bio::Sequence#window_search(15)"
+  p na
+  na.window_search(15) {|x| p x}
+
+  puts "\n== Test Bio::Sequence#total({'a'=>0.1,'t'=>0.2,'g'=>0.3,'c'=>0.4})"
+  p na.total({'a'=>0.1,'t'=>0.2,'g'=>0.3,'c'=>0.4})
+
+  puts "\n== Test Bio::Sequence#composition"
+  p na
+  p na.composition
+  p rna
+  p rna.composition
+
+  puts "\n== Test Bio::Sequence::NA#splicing('complement(join(1..5,16..20))')"
+  p na
+  p na.splicing("complement(join(1..5,16..20))")
+  p rna
+  p rna.splicing("complement(join(1..5,16..20))")
+
+  puts "\n== Test Bio::Sequence::NA#complement"
+  p na.complement
+  p rna.complement
+  p Bio::Sequence::NA.new('tacgyrkmhdbvswn').complement
+  p Bio::Sequence::NA.new('uacgyrkmhdbvswn').complement
+
+  puts "\n== Test Bio::Sequence::NA#translate"
+  p na
+  p na.translate
+  p rna
+  p rna.translate
+
+  puts "\n== Test Bio::Sequence::NA#gc_percent"
+  p na.gc_percent
+  p rna.gc_percent
+
+  puts "\n== Test Bio::Sequence::NA#illegal_bases"
+  p na.illegal_bases
+  p Bio::Sequence::NA.new('tacgyrkmhdbvswn').illegal_bases
+  p Bio::Sequence::NA.new('abcdefghijklmnopqrstuvwxyz-!%#$@').illegal_bases
+
+  puts "\n== Test Bio::Sequence::NA#molecular_weight"
+  p na
+  p na.molecular_weight
+  p rna
+  p rna.molecular_weight
+
+  puts "\n== Test Bio::Sequence::NA#to_re"
+  p Bio::Sequence::NA.new('atgcrymkdhvbswn')
+  p Bio::Sequence::NA.new('atgcrymkdhvbswn').to_re
+  p Bio::Sequence::NA.new('augcrymkdhvbswn')
+  p Bio::Sequence::NA.new('augcrymkdhvbswn').to_re
+
+  puts "\n== Test Bio::Sequence::NA#names"
+  p na.names
+
+  puts "\n== Test Bio::Sequence::NA#pikachu"
+  p na.pikachu
+
+  puts "\n== Test Bio::Sequence::NA#randomize"
+  print "Orig  : "; p na
+  print "Rand  : "; p na.randomize
+  print "Rand  : "; p na.randomize
+  print "Rand  : "; p na.randomize.randomize
+  print "Block : "; na.randomize do |x| print x end; puts
+
+  print "Orig  : "; p rna
+  print "Rand  : "; p rna.randomize
+  print "Rand  : "; p rna.randomize
+  print "Rand  : "; p rna.randomize.randomize
+  print "Block : "; rna.randomize do |x| print x end; puts
+
+  puts "\n== Test Bio::Sequence::NA.randomize(counts)"
+  print "Count : "; p counts = {'a'=>10,'c'=>20,'g'=>30,'t'=>40}
+  print "Rand  : "; p Bio::Sequence::NA.randomize(counts)
+  print "Count : "; p counts = {'a'=>10,'c'=>20,'g'=>30,'u'=>40}
+  print "Rand  : "; p Bio::Sequence::NA.randomize(counts)
+  print "Block : "; Bio::Sequence::NA.randomize(counts) {|x| print x}; puts
+
+  puts "\n== Test Bio::Sequence::AA#codes"
+  p aa
+  p aa.codes
+
+  puts "\n== Test Bio::Sequence::AA#names"
+  p aa
+  p aa.names
+
+  puts "\n== Test Bio::Sequence::AA#molecular_weight"
+  p aa.subseq(1,20)
+  p aa.subseq(1,20).molecular_weight
+
+  puts "\n== Test Bio::Sequence::AA#randomize"
+  aaseq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA'
+  s = Bio::Sequence::AA.new(aaseq)
+  print "Orig  : "; p s
+  print "Rand  : "; p s.randomize
+  print "Rand  : "; p s.randomize
+  print "Rand  : "; p s.randomize.randomize
+  print "Block : "; s.randomize {|x| print x}; puts
+
+  puts "\n== Test Bio::Sequence::AA.randomize(counts)"
+  print "Count : "; p counts = s.composition
+  print "Rand  : "; puts Bio::Sequence::AA.randomize(counts)
+  print "Block : "; Bio::Sequence::AA.randomize(counts) {|x| print x}; puts
+
+#end