bio 0.7.0

data/lib/bio/db/kegg/brite.rb

@@ -0,0 +1,51 @@
+#
+# bio/db/kegg/brite.rb - KEGG/BRITE database class
+#
+#   Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
+#
+#  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: brite.rb,v 0.6 2005/09/08 01:22:11 k Exp $
+#
+
+require 'bio/db'
+
+module Bio
+
+  class KEGG
+
+    class BRITE < KEGGDB
+
+      DELIMITER	= RS = "\n///\n"
+      TAGSIZE	= 12
+
+      def initialize(entry)
+        super(entry, TAGSIZE)
+      end
+
+      # ENTRY
+      # DEFINITION
+      # RELATION
+      # FACTORS
+      # INTERACTION
+      # SOURCE
+      # REFERENCE
+
+    end
+
+  end
+
+end
+

data/lib/bio/db/kegg/cell.rb

@@ -0,0 +1,88 @@
+#
+# bio/db/kegg/cell.rb - KEGG/CELL database class
+#
+#   Copyright (C) 2001 KAWASHIMA Shuichi <s@bioruby.org>
+#
+#  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: cell.rb,v 1.7 2005/09/08 01:22:11 k Exp $
+#
+
+require "bio/db"
+
+module Bio
+
+  class KEGG
+
+    class CELL < KEGGDB
+
+      DELIMITER	= RS = "\n///\n"
+      TAGSIZE	= 12
+
+      def initialize(entry)
+        super(entry, TAGSIZE)
+      end
+
+      def entry_id
+        field_fetch('ENTRY')
+      end
+
+      def definition
+        field_fetch('DEFINITION')
+      end
+
+      def org
+        field_fetch('ORGANISM')
+      end
+      alias organism org
+
+      def mother
+        field_fetch('MOTHER')
+      end
+
+      def daughter
+        field_fetch('DAUGHTER').gsub(/ /, '').split(/,/)
+      end
+
+      def sister
+        field_fetch('SISTER')
+      end
+
+      def fate
+        field_fetch('CELL_FATE').gsub(/ /, '').split(/,/)
+      end
+
+      def contact
+        field_fetch('CONTACT').gsub(/ /, '').split(/,/)
+      end
+
+      def expression
+        field_fetch('EXPRESSION')
+      end
+
+      def fig
+        field_fetch('FIGURE')
+      end
+
+      def ref
+        field_fetch('REFERENCE')
+      end
+
+    end
+
+  end
+
+end
+

data/lib/bio/db/kegg/compound.rb

@@ -0,0 +1,130 @@
+#
+# bio/db/kegg/compound.rb - KEGG COMPOUND database class
+#
+#   Copyright (C) 2001, 2002, 2004 KATAYAMA Toshiaki <k@bioruby.org>
+#
+#  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: compound.rb,v 0.11 2005/09/08 01:22:11 k Exp $
+#
+
+require 'bio/db'
+
+module Bio
+
+  class KEGG
+
+    class COMPOUND < KEGGDB
+
+      DELIMITER	= RS = "\n///\n"
+      TAGSIZE	= 12
+
+      def initialize(entry)
+        super(entry, TAGSIZE)
+      end
+
+      # ENTRY
+      def entry_id
+        unless @data['ENTRY']
+          @data['ENTRY'] = fetch('ENTRY').split(/\s+/).first
+        end
+        @data['ENTRY']
+      end
+
+      # NAME
+      def names
+        lines_fetch('NAME') 
+      end
+      def name
+        names[0]
+      end
+
+      # FORMULA
+      def formula
+        field_fetch('FORMULA')
+      end
+
+      # MASS
+      def mass
+        field_fetch('MASS').to_f
+      end
+
+      # REACTION
+      def reactions
+        unless @data['REACTION']
+          @data['REACTION'] = fetch('REACTION').split(/\s+/)
+        end
+        @data['REACTION']
+      end
+
+      # RPAIR
+      def rpairs
+        unless @data['RPAIR']
+          @data['RPAIR'] = fetch('RPAIR').split(/\s+/)
+        end
+        @data['RPAIR']
+      end
+
+      # PATHWAY
+      def pathways
+        lines_fetch('PATHWAY') 
+      end
+
+      # ENZYME
+      def enzymes
+        unless @data['ENZYME']
+          field = fetch('ENZYME')
+          if /\(/.match(field)	# old version
+            @data['ENZYME'] = field.scan(/\S+ \(\S+\)/)
+          else
+            @data['ENZYME'] = field.scan(/\S+/)
+          end
+        end
+        @data['ENZYME']
+      end
+
+      # DBLINKS
+      def dblinks
+        lines_fetch('DBLINKS')
+      end
+
+      # ATOM, BOND
+      def kcf
+        return "#{get('ATOM')}#{get('BOND')}"
+      end
+
+    end
+
+  end
+
+end
+
+
+if __FILE__ == $0
+  entry = ARGF.read
+  cpd = Bio::KEGG::COMPOUND.new(entry)
+  p cpd.entry_id
+  p cpd.names
+  p cpd.name
+  p cpd.formula
+  p cpd.mass
+  p cpd.reactions
+  p cpd.rpairs
+  p cpd.pathways
+  p cpd.enzymes
+  p cpd.dblinks
+  p cpd.kcf
+end
+

data/lib/bio/db/kegg/enzyme.rb

@@ -0,0 +1,125 @@
+#
+# bio/db/kegg/enzyme.rb - KEGG/ENZYME database class
+#
+#   Copyright (C) 2001, 2002 KATAYAMA Toshiaki <k@bioruby.org>
+#
+#  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: enzyme.rb,v 0.8 2005/09/08 01:22:11 k Exp $
+#
+
+require 'bio/db'
+
+module Bio
+
+  class KEGG
+
+    class ENZYME < KEGGDB
+
+      DELIMITER	= RS = "\n///\n"
+      TAGSIZE	= 12
+
+      def initialize(entry)
+        super(entry, TAGSIZE)
+      end
+
+      # ENTRY
+      def entry_id
+        field_fetch('ENTRY')
+      end
+
+      # NAME
+      def names
+        lines_fetch('NAME')
+      end
+      def name
+        names[0]
+      end
+
+      # CLASS
+      def classes
+        lines_fetch('CLASS')
+      end
+
+      # SYSNAME
+      def sysname
+        field_fetch('SYSNAME')
+      end
+
+      # REACTION ';'
+      def reaction
+        field_fetch('REACTION')
+      end
+      
+      # SUBSTRATE
+      def substrates
+        lines_fetch('SUBSTRATE')
+      end
+
+      # PRODUCT
+      def products
+        lines_fetch('PRODUCT')
+      end
+
+      # COFACTOR
+      def cofactors
+        lines_fetch('COFACTOR')
+      end
+
+      # COMMENT
+      def comment
+        field_fetch('COMMENT')
+      end
+
+      # PATHWAY
+      def pathways
+        lines_fetch('PATHWAY')
+      end
+
+      # GENES
+      def genes
+        lines_fetch('GENES')
+      end
+
+      # DISEASE
+      def diseases
+        lines_fetch('DISEASE')
+      end
+
+      # MOTIF
+      def motifs
+        lines_fetch('MOTIF')
+      end
+
+      # STRUCTURES
+      def structures
+        unless @data['STRUCTURES']
+          @data['STRUCTURES'] =
+            fetch('STRUCTURES').sub(/(PDB: )*/,'').split(/\s+/)
+        end
+        @data['STRUCTURES']
+      end
+
+      # DBLINKS
+      def dblinks
+        lines_fetch('DBLINKS')
+      end
+
+    end
+
+  end
+
+end
+

data/lib/bio/db/kegg/expression.rb

@@ -0,0 +1,173 @@
+#
+# = bio/db/kegg/expression.rb - KEGG EXPRESSION database class
+#
+# Copyright::	Copyright (C) 2001-2003, 2005
+#		Shuichi Kawashima <shuichi@hgc.jp>,
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: expression.rb,v 1.9 2005/11/05 08:27:26 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
+#
+#++
+#
+
+require "bio/db"
+
+module Bio
+class KEGG
+
+class EXPRESSION
+
+  def initialize(entry)
+    @orf2val   = Hash.new('')
+    @orf2rgb   = Hash.new('')
+    @orf2ratio = Hash.new('')
+    @max_intensity = 10000
+    entry.split("\n").each do |line|
+      unless /^#/ =~ line
+        ary = line.split("\t")
+        orf = ary.shift
+        val = ary[2, 4].collect {|x| x.to_f}
+        @orf2val[orf] = val 
+      end
+    end
+  end
+  attr_reader :orf2val
+  attr_reader :orf2rgb
+  attr_reader :orf2ratio
+  attr_reader :max_intensity
+
+  def control_avg
+    sum = 0.0
+    @orf2val.values.each do |v|
+      sum += v[0] - v[1]
+    end
+    sum/orf2val.size
+  end
+
+  def target_avg
+    sum = 0.0
+    @orf2val.values.each do |v|
+      sum += v[2] - v[3]
+    end
+    sum/orf2val.size
+  end
+
+  def control_var
+    sum = 0.0
+    avg = self.control_avg
+    @orf2val.values.each do |v|
+      tmp = v[0] - v[1]
+      sum += (tmp - avg)*(tmp - avg)
+    end
+    sum/orf2val.size
+  end
+
+  def target_var
+    sum = 0.0
+    avg = self.target_avg
+    @orf2val.values.each do |v|
+      tmp = v[2] - v[3]
+      sum += (tmp - avg)*(tmp - avg)
+    end
+    sum/orf2val.size
+  end
+
+  def control_sd
+    var = self.control_var
+    Math.sqrt(var)
+  end
+
+  def target_sd
+    var = self.target_var
+    Math.sqrt(var)
+  end
+
+  def up_regulated(num=20, threshold=nil)
+    logy_minus_logx
+    ary = @orf2ratio.to_a.sort{|a, b| b[1] <=> a[1]}
+    if threshold != nil
+      i = 0
+      while ary[i][1] > threshold
+        i += 1
+      end
+      return ary[0..i]
+    else
+      return ary[0..num-1]
+    end
+  end
+
+  def down_regulated(num=20, threshold=nil)
+    logy_minus_logx
+    ary = @orf2ratio.to_a.sort{|a, b| a[1] <=> b[1]}
+    if threshold != nil
+      i = 0
+      while ary[i][1] < threshold
+        i += 1
+      end
+      return ary[0..i]
+    else
+      return ary[0..num-1]
+    end
+  end
+
+  def regulated(num=20, threshold=nil)
+    logy_minus_logx
+    ary = @orf2ratio.to_a.sort{|a, b| b[1].abs <=> a[1].abs}
+    if threshold != nil
+      i = 0
+      while ary[i][1].abs > threshold
+        i += 1
+      end
+      return ary[0..i]
+    else
+      return ary[0..num-1]
+    end
+  end
+
+  def logy_minus_logx
+    @orf2val.each do |k, v|
+      @orf2ratio[k] = (1.0/Math.log10(2))*(Math.log10(v[2]-v[3]) - Math.log10(v[0]-v[1]))
+    end
+  end
+
+  def val2rgb
+    col_unit = @max_intensity/255
+    @orf2val.each do |k, v|
+      tmp_val = ((v[0] - v[1])/col_unit).to_i
+      if tmp_val > 255
+        g = "ff" 
+      else
+        g = format("%02x", tmp_val)
+      end
+      tmp_val = ((v[2] - v[3])/col_unit).to_i
+      if tmp_val > 255
+        r = "ff" 
+      else
+        r = format("%02x", tmp_val)
+      end
+      @orf2rgb[k] = r + g + "00"
+    end
+  
+  end
+
+end # class EXPRESSION
+
+end # class KEGG
+end # module Bio