bio 0.7.0

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

@@ -0,0 +1,299 @@
+#
+# = bio/db/kegg/kgml.rb - KEGG KGML parser class
+#
+# Copyright::	Copyright (C) 2005
+# 		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: kgml.rb,v 1.2 2005/11/05 08:29:53 k Exp $
+#
+# == KGML (KEGG XML) parser
+#
+# See http://www.genome.jp/kegg/xml/ for more details on KGML.
+#
+# === Examples
+#
+#  file = ARGF.read
+#  kgml = Bio::KEGG::KGML.new(file)
+#
+#  # <pathway> attributes
+#  puts kgml.name
+#  puts kgml.org
+#  puts kgml.number
+#  puts kgml.title
+#  puts kgml.image
+#  puts kgml.link
+#
+#  kgml.entries.each do |entry|
+#    # <entry> attributes
+#    puts entry.id
+#    puts entry.name
+#    puts entry.names
+#    puts entry.type
+#    puts entry.link
+#    puts entry.reaction
+#    puts entry.map
+#    # <graphics> attributes
+#    puts entry.label	# This is an accessor for <graphics name="">
+#    puts entry.x
+#    puts entry.y
+#    puts entry.type
+#    puts entry.width
+#    puts entry.height
+#    puts entry.fgcolor
+#    puts entry.bgcolor
+#  end
+#
+#  kgml.relations.each do |relation|
+#    # <relation> attributes
+#    puts relation.entry1
+#    puts relation.entry2
+#    puts relation.type
+#    # <subtype> attributes
+#    puts relation.name
+#    puts relation.value
+#    # or
+#    relation.subtype.each do |value, name|
+#      puts value, name
+#    end
+#  end
+#
+#  kgml.reactions.each do |reaction|
+#    # <reaction> attributes
+#    puts reaction.name
+#    puts reaction.type
+#    # <substrate> attributes
+#    reaction.substrates.each do |name|
+#      puts name
+#      # <alt> attributes
+#      altnames = reaction.alt[name]
+#      altnames.each do |altname|
+#        puts altname
+#      end
+#    end
+#    # <product> attributes
+#    reaction.products.each do |name|
+#      puts name
+#      # <alt> attributes
+#      altnames = reaction.alt[name]
+#      altnames.each do |altname|
+#        puts altname
+#      end
+#    end
+#  end
+#
+#--
+#
+#  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 'rexml/document'
+
+module Bio
+class KEGG
+
+class KGML
+
+  def initialize(xml)
+    @dom = REXML::Document.new(xml)
+    parse_root
+    parse_entry
+    parse_relation
+    parse_reaction
+  end
+  attr_reader :name, :org, :number, :title, :image, :link
+  attr_reader :entries, :relations, :reactions		# Array
+
+  class Entry
+    attr_accessor :id, :name, :names, :type, :link, :reaction, :map
+    attr_accessor :label, :x, :y, :type, :width, :height, :fgcolor, :bgcolor
+  end
+
+  class Relation
+    attr_accessor :entry1, :entry2, :type
+    attr_accessor :name, :value
+    attr_accessor :subtype      			# Hash
+  end
+
+  class Reaction
+    attr_accessor :name, :type
+    attr_accessor :substrates, :products		# Array
+    attr_accessor :alt					# Hash
+  end
+
+  def parse_root
+    root    = @dom.root.attributes
+    @name   = root["name"]
+    @org    = root["org"]
+    @number = root["number"]
+    @title  = root["title"]
+    @image  = root["image"]
+    @link   = root["link"]
+  end
+
+  def parse_entry
+    @entries = Array.new
+
+    @dom.elements.each("/pathway/entry") { |node|
+      attr = node.attributes
+      entry = Entry.new
+      entry.id        = attr["id"].to_i
+      entry.map       = attr["map"]
+      entry.name      = attr["name"]
+      entry.names     = entry.name.split(/\s+/)
+      entry.type      = attr["type"]
+      entry.link      = attr["link"]
+      entry.reaction  = attr["reaction"]
+
+      node.elements.each("graphics") { |graphics|
+        attr = graphics.attributes
+        entry.x       = attr["x"].to_i
+        entry.y       = attr["y"].to_i
+        entry.type    = attr["type"]
+        entry.label   = attr["label"]	# name
+        entry.width   = attr["width"].to_i
+        entry.height  = attr["height"].to_i
+        entry.fgcolor = attr["fgcolor"]
+        entry.bgcolor = attr["bgcolor"]
+      }
+      @entries << entry
+    }
+  end
+
+  def parse_relation
+    @relations = Array.new
+
+    @dom.elements.each("/pathway/relation") { |node|
+      attr = node.attributes
+      relation = Relation.new
+      relation.entry1 = attr["entry1"].to_i
+      relation.entry2 = attr["entry2"].to_i
+      relation.type   = attr["type"]
+
+      hash = Hash.new
+      node.elements.each("subtype") { |subtype|
+        attr = subtype.attributes
+        relation.name  = name  = attr["name"]
+        relation.value = value = attr["value"].to_i
+        hash[value] = name
+      }
+      relation.subtype = hash
+      @relations << relation
+    }
+  end
+
+  def parse_reaction
+    @reactions = Array.new
+
+    @dom.elements.each("/pathway/reaction") { |node|
+      attr = node.attributes
+      reaction = Reaction.new
+      reaction.name = attr["name"]
+      reaction.type = attr["type"]
+
+      substrates = Array.new
+      products   = Array.new
+      hash       = Hash.new
+
+      node.elements.each("substrate") { |substrate|
+        name = substrate.attributes["name"]
+        substrates << name
+        substrate.elements.each("alt") { |alt|
+          hash[name] ||= Array.new
+          hash[name] << alt.attributes["name"]
+        }
+      }
+      node.elements.each("product") { |product|
+        name = product.attributes["name"]
+        products << name
+        product.elements.each("alt") { |alt|
+          hash[name] ||= Array.new
+          hash[name] << alt.attributes["name"]
+        }
+      }
+
+      reaction.substrates = substrates
+      reaction.products   = products
+      reaction.alt        = hash
+
+      @reactions << reaction
+    }
+  end
+
+end # KGML
+end # KEGG
+end # Bio
+
+
+if __FILE__ == $0
+  require 'pp'
+  xml = ARGF.read
+  pp Bio::KEGG::KGML.new(xml)
+end
+
+
+=begin
+
+# This is a test implementation which reflects original KGML data structure.
+
+class KGML
+
+  class Pathway
+    attr_accessor :name, :org, :number, :title, :image, :link
+    attr_accessor :entries, :relations, :reactions
+
+    class Entry
+      attr_accessor :id, :name, :type, :link, :reaction, :map
+      attr_accessor :components, :graphics
+
+      class Component
+        attr_accessor :id
+      end
+
+      class Graphics
+        attr_accessor :name, :x, :y, :type, :width, :height, :fgcolor, :bgcolor
+      end
+    end
+
+    class Relation
+      attr_accessor :entry1, :entry2, :type
+      attr_accessor :
+
+      class Subtype
+        attr_accessor :name, :value
+      end
+    end
+
+    class Reaction
+      attr_accessor :name, :type
+
+      class Substrate
+        attr_accessor :name
+      end
+
+      class Product
+        attr_accessor :name
+      end
+
+      class Alt
+        attr_accessor :name
+      end
+    end
+  end
+
+end
+=end

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

@@ -0,0 +1,178 @@
+#
+# bio/db/kegg/ko.rb - KO (KEGG Orthology) database class
+#
+#   Copyright (C) 2003 KATAYAMA Toshiaki <k@bioruby.org>
+#   Copyright (C) 2003 Masumi Itoh <m@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: ko.rb,v 1.5 2005/09/08 01:22:11 k Exp $
+#
+
+require 'bio/db'
+
+module Bio
+
+  class KEGG
+    
+    class KO < KEGGDB
+      
+      DELIMITER	= RS = "\n///\n"
+      TAGSIZE	= 12
+
+      def initialize(entry)
+        super(entry, TAGSIZE)
+      end
+      
+      
+      def entry_id
+        field_fetch('ENTRY')[/\S+/]
+      end
+      
+      def name
+        field_fetch('NAME')
+      end
+      
+      def names
+        name.split(', ')
+      end
+      
+      def definition
+        field_fetch('DEFINITION')
+      end
+      
+      def keggclass
+        field_fetch('CLASS')
+      end
+
+      def keggclasses
+        keggclass.gsub(/ \[[^\]]+/, '').split(/\] ?/)
+      end
+      
+      def pathways
+        keggclass.scan(/\[PATH:(.*?)\]/).flatten
+      end
+      
+      def dblinks
+        unless @data['DBLINKS']
+          hash = {}
+          get('DBLINKS').scan(/(\S+):\s*(.*)\n/).each do |k, v|
+            hash[k] = v.split(/\s+/)
+          end
+          @data['DBLINKS'] = hash
+        end
+        @data['DBLINKS']		# Hash of DB:ID in DBLINKS
+      end
+      
+      def genes
+        unless @data['GENES']
+          hash = {}
+          k = ''
+          get('GENES').each_line do |line|
+            line.chomp!
+            line[0, @tagsize] = '' 
+            if line =~ /(\S+):/
+              k = $1
+              hash[k] = []
+            end
+            line[0, 5] = ''
+            line.gsub(/\(\S+/, '').each(' ') do |u|
+              hash[k] << u.strip
+            end
+          end
+          @data['GENES'] = hash
+        end
+        @data['GENES']		# Hash of DB:ID in DBLINKS
+      end
+      
+    end
+    
+  end
+  
+end
+
+
+
+if __FILE__ == $0
+
+  require 'bio/io/fetch'
+
+  flat = Bio::Fetch.query('ko', 'K00001')
+  entry = Bio::KEGG::KO.new(flat)
+
+  p entry.entry_id
+  p entry.name
+  p entry.names
+  p entry.definition
+  p entry.keggclass
+  p entry.keggclasses
+  p entry.pathways
+  p entry.dblinks
+  p entry.genes
+
+end
+
+
+=begin
+
+= Bio::KEGG::KO
+
+KO (KEGG Orthology) entry parser.
+
+* ((<URL:http://www.genome.jp/dbget-bin/get_htext?KO>))
+* ((<URL:ftp://ftp.genome.jp/pub/kegg/tarfiles/ko>))
+
+--- Bio::KEGG::KO.new(entry)
+
+Reads a flat file format entry of the KO database.
+
+--- Bio::KEGG::KO#entry_id -> String
+
+Returns ID of the entry.
+
+--- Bio::KEGG::KO#name -> String
+
+Returns NAME field of the entry.
+
+--- Bio::KEGG::KO#names -> Array
+
+Returns an Array of names in NAME field.
+
+--- Bio::KEGG::KO#definition -> String
+
+Returns DEFINITION field of the entry.
+
+--- Bio::KEGG::KO#keggclass
+
+Returns CLASS field of the entry.
+
+--- Bio::KEGG::KO#keggclasses
+
+Returns an Array of biological classes in CLASS field.
+
+--- Bio::KEGG::KO#pathways
+
+Returns an Array of KEGG/PATHWAY ID in CLASS field.
+
+--- Bio::KEGG::KO#dblinks
+
+Returns a Hash of Array of the database name and entry IDs in DBLINKS field.
+
+--- Bio::KEGG::KO#genes
+
+Returns a Hash of Array of the organism ID and entry IDs in GENES field.
+
+=end
+