bio 1.0.0 → 1.1.0

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

@@ -1,214 +1,203 @@
 #
-# bio/db/kegg/genome.rb - KEGG/GENOME database class
+# = bio/db/kegg/genome.rb - KEGG/GENOME database class
 #
-#   Copyright (C) 2001, 2002 KATAYAMA Toshiaki <k@bioruby.org>
+# Copyright::  Copyright (C) 2001, 2002, 2007 Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
 #
-#  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: genome.rb,v 0.14 2005/09/08 01:22:11 k Exp $
+# $Id: genome.rb,v 0.18 2007/06/28 11:27:24 k Exp $
 #
 
 require 'bio/db'
 
 module Bio
+class KEGG
 
-  class KEGG
+# == Description
+#
+# Parser for the KEGG GENOME database
+#
+# == References
+#
+# * ftp://ftp.genome.jp/pub/kegg/genomes/genome
+#
+class GENOME < KEGGDB
 
-    class GENOME < KEGGDB
+  DELIMITER	= RS = "\n///\n"
+  TAGSIZE	= 12
 
-      DELIMITER	= RS = "\n///\n"
-      TAGSIZE	= 12
+  def initialize(entry)
+    super(entry, TAGSIZE)
+  end
 
-      def initialize(entry)
-        super(entry, TAGSIZE)
-      end
 
+  # ENTRY -- Returns contents of the ENTRY record as a String.
+  def entry_id
+    field_fetch('ENTRY')[/\S+/]
+  end
+  
+  # NAME -- Returns contents of the NAME record as a String.
+  def name
+    field_fetch('NAME')
+  end
 
-      # ENTRY
-      def entry_id
-        field_fetch('ENTRY')
-      end
-      
-      # NAME
-      def name
-        field_fetch('NAME')
-      end
+  # DEFINITION -- Returns contents of the DEFINITION record as a String.
+  def definition
+    field_fetch('DEFINITION')
+  end
+  alias organism definition
+
+  # TAXONOMY -- Returns contents of the TAXONOMY record as a Hash.
+  def taxonomy
+    unless @data['TAXONOMY']
+      taxid, lineage = subtag2array(get('TAXONOMY'))
+      taxid   = taxid   ? truncate(tag_cut(taxid))   : ''
+      lineage = lineage ? truncate(tag_cut(lineage)) : ''
+      @data['TAXONOMY'] = {
+        'taxid'	=> taxid,
+        'lineage'	=> lineage,
+      }
+      @data['TAXONOMY'].default = ''
+    end
+    @data['TAXONOMY']
+  end
 
-      # DEFINITION
-      def definition
-        field_fetch('DEFINITION')
-      end
-      alias organism definition
-
-      # TAXONOMY
-      def taxonomy
-        unless @data['TAXONOMY']
-          taxid, lineage = subtag2array(get('TAXONOMY'))
-          taxid   = taxid   ? truncate(tag_cut(taxid))   : ''
-          lineage = lineage ? truncate(tag_cut(lineage)) : ''
-          @data['TAXONOMY'] = {
-            'taxid'	=> taxid,
-            'lineage'	=> lineage,
-          }
-          @data['TAXONOMY'].default = ''
-        end
-        @data['TAXONOMY']
-      end
+  # Returns NCBI taxonomy ID from the TAXONOMY record as a String.
+  def taxid
+    taxonomy['taxid']
+  end
 
-      def taxid
-        taxonomy['taxid']
-      end
+  # Returns contents of the TAXONOMY/LINEAGE record as a String.
+  def lineage
+    taxonomy['lineage']
+  end
 
-      def lineage
-        taxonomy['lineage']
-      end
+  # DATA_SOURCE -- Returns contents of the DATA_SOURCE record as a String.
+  def data_source
+    field_fetch('DATA_SOURCE')
+  end
 
-      # COMMENT
-      def comment
-        field_fetch('COMMENT')
-      end
-      
-      # REFERENCE
-      def references
-        unless @data['REFERENCE']
-          ary = []
-          toptag2array(get('REFERENCE')).each do |ref|
-            hash = Hash.new('')
-            subtag2array(ref).each do |field|
-              case tag_get(field)
-              when /AUTHORS/
-                authors = truncate(tag_cut(field))
-                authors = authors.split(', ')
-                authors[-1] = authors[-1].split(/\s+and\s+/)
-                authors = authors.flatten.map { |a| a.sub(',', ', ') }
-                hash['authors']	= authors
-              when /TITLE/
-                hash['title']	= truncate(tag_cut(field))
-              when /JOURNAL/
-                journal = truncate(tag_cut(field))
-                if journal =~ /(.*) (\d+):(\d+)-(\d+) \((\d+)\) \[UI:(\d+)\]$/
-                  hash['journal']	= $1
-                  hash['volume']	= $2
-                  hash['pages']		= $3
-                  hash['year']		= $5
-                  hash['medline']	= $6
-                else
-                  hash['journal'] = journal
-                end
-              end
-            end
-            ary.push(Reference.new(hash))
-          end
-          @data['REFERENCE'] = References.new(ary)
-        end
-        @data['REFERENCE']
-      end
+  # ORIGINAL_DB -- Returns contents of the ORIGINAL_DB record as a String.
+  def original_db
+    field_fetch('ORIGINAL_DB')
+  end
 
-      # CHROMOSOME
-      def chromosomes
-        unless @data['CHROMOSOME']
-          @data['CHROMOSOME'] = []
-          toptag2array(get('CHROMOSOME')).each do |chr|
-            hash = Hash.new('')
-            subtag2array(chr).each do |field|
-              hash[tag_get(field)] = truncate(tag_cut(field))
-            end
-            @data['CHROMOSOME'].push(hash)
-          end
-        end
-        @data['CHROMOSOME']
-      end
+  # DISEASE -- Returns contents of the COMMENT record as a String.
+  def disease
+    field_fetch('DISEASE')
+  end
 
-      # PLASMID
-      def plasmids
-        unless @data['PLASMID']
-          @data['PLASMID'] = []
-          toptag2array(get('PLASMID')).each do |chr|
-            hash = Hash.new('')
-            subtag2array(chr).each do |field|
-              hash[tag_get(field)] = truncate(tag_cut(field))
+  # COMMENT -- Returns contents of the COMMENT record as a String.
+  def comment
+    field_fetch('COMMENT')
+  end
+  
+  # REFERENCE -- Returns contents of the REFERENCE records as an Array of
+  # Bio::Reference objects.
+  def references
+    unless @data['REFERENCE']
+      ary = []
+      toptag2array(get('REFERENCE')).each do |ref|
+        hash = Hash.new('')
+        subtag2array(ref).each do |field|
+          case tag_get(field)
+          when /AUTHORS/
+            authors = truncate(tag_cut(field))
+            authors = authors.split(', ')
+            authors[-1] = authors[-1].split(/\s+and\s+/)
+            authors = authors.flatten.map { |a| a.sub(',', ', ') }
+            hash['authors']	= authors
+          when /TITLE/
+            hash['title']	= truncate(tag_cut(field))
+          when /JOURNAL/
+            journal = truncate(tag_cut(field))
+            if journal =~ /(.*) (\d+):(\d+)-(\d+) \((\d+)\) \[UI:(\d+)\]$/
+              hash['journal']	= $1
+              hash['volume']	= $2
+              hash['pages']	= $3
+              hash['year']	= $5
+              hash['medline']	= $6
+            else
+              hash['journal'] = journal
             end
-            @data['PLASMID'].push(hash)
           end
         end
-        @data['PLASMID']
+        ary.push(Reference.new(hash))
       end
+      @data['REFERENCE'] = References.new(ary)
+    end
+    @data['REFERENCE']
+  end
 
-      # SCAFFOLD
-      def scaffolds
-        unless @data['SCAFFOLD']
-          @data['SCAFFOLD'] = []
-          toptag2array(get('SCAFFOLD')).each do |chr|
-            hash = Hash.new('')
-            subtag2array(chr).each do |field|
-              hash[tag_get(field)] = truncate(tag_cut(field))
-            end
-            @data['SCAFFOLD'].push(hash)
-          end
+  # CHROMOSOME -- Returns contents of the CHROMOSOME records as an Array
+  # of Hash.
+  def chromosomes
+    unless @data['CHROMOSOME']
+      @data['CHROMOSOME'] = []
+      toptag2array(get('CHROMOSOME')).each do |chr|
+        hash = Hash.new('')
+        subtag2array(chr).each do |field|
+          hash[tag_get(field)] = truncate(tag_cut(field))
         end
-        @data['SCAFFOLD']
+        @data['CHROMOSOME'].push(hash)
       end
+    end
+    @data['CHROMOSOME']
+  end
 
-      # STATISTICS
-      def statistics
-        unless @data['STATISTICS']
-          hash = Hash.new(0.0)
-          get('STATISTICS').each_line do |line|
-            case line
-            when /nucleotides:\s+(\d+)/
-              hash['nalen'] = $1.to_i
-            when /protein genes:\s+(\d+)/
-              hash['num_gene'] = $1.to_i
-            when /RNA genes:\s+(\d+)/
-              hash['num_rna'] = $1.to_i
-            when /G\+C content:\s+(\d+.\d+)/
-              hash['gc'] = $1.to_f
-            end
-          end
-          @data['STATISTICS'] = hash
+  # PLASMID -- Returns contents of the PLASMID records as an Array of Hash.
+  def plasmids
+    unless @data['PLASMID']
+      @data['PLASMID'] = []
+      toptag2array(get('PLASMID')).each do |chr|
+        hash = Hash.new('')
+        subtag2array(chr).each do |field|
+          hash[tag_get(field)] = truncate(tag_cut(field))
         end
-        @data['STATISTICS']
-      end
-
-      def nalen
-        statistics['nalen']
-      end
-      alias length nalen
-
-      def num_gene
-        statistics['num_gene']
+        @data['PLASMID'].push(hash)
       end
+    end
+    @data['PLASMID']
+  end
 
-      def num_rna
-        statistics['num_rna']
+  # STATISTICS -- Returns contents of the STATISTICS record as a Hash.
+  def statistics
+    unless @data['STATISTICS']
+      hash = Hash.new(0.0)
+      get('STATISTICS').each_line do |line|
+        case line
+        when /nucleotides:\s+(\d+)/
+          hash['num_nuc'] = $1.to_i
+        when /protein genes:\s+(\d+)/
+          hash['num_gene'] = $1.to_i
+        when /RNA genes:\s+(\d+)/
+          hash['num_rna'] = $1.to_i
+        end
       end
+      @data['STATISTICS'] = hash
+    end
+    @data['STATISTICS']
+  end
 
-      def gc
-        statistics['gc']
-      end
+  # Returns number of nucleotides from the STATISTICS record as a Fixnum.
+  def nalen
+    statistics['num_nuc']
+  end
+  alias length nalen
 
-      # GENOMEMAP
-      def genomemap
-        field_fetch('GENOMEMAP')
-      end
+  # Returns number of protein genes from the STATISTICS record as a Fixnum.
+  def num_gene
+    statistics['num_gene']
+  end
 
-    end
-    
+  # Returns number of rna from the STATISTICS record as a Fixnum.
+  def num_rna
+    statistics['num_rna']
   end
 
-end
+end # GENOME
+    
+end # KEGG
+end # Bio
 
 
 
@@ -237,9 +226,7 @@ if __FILE__ == $0
       %w( REFERENCE references ),
       %w( CHROMOSOME chromosomes ),
       %w( PLASMID plasmids ),
-      %w( SCAFFOLD plasmids ),
-      %w( STATISTICS statistics nalen num_gene num_rna gc ),
-      %w( GENOMEMAP genomemap ),
+      %w( STATISTICS statistics nalen num_gene num_rna ),
     ].each do |x|
       puts "### " + x.shift
       x.each do |m|
@@ -252,111 +239,3 @@ if __FILE__ == $0
 end
 
 
-=begin
-
-= Bio::KEGG::GENOME
-
-=== Initialize
-
---- Bio::KEGG::GENOME.new(entry)
-
-=== ENTRY
-
---- Bio::KEGG::GENOME#entry_id -> String
-
-      Returns contents of the ENTRY record as a String.
-
-=== NAME
-
---- Bio::KEGG::GENOME#name -> String
-
-      Returns contents of the NAME record as a String.
-
-=== DEFINITION
-
---- Bio::KEGG::GENOME#definition -> String
-
-      Returns contents of the DEFINITION record as a String.
-
---- Bio::KEGG::GENOME#organism -> String
-
-      Alias for the 'definition' method.
-
-=== TAXONOMY
-
---- Bio::KEGG::GENOME#taxonomy -> Hash
-
-      Returns contents of the TAXONOMY record as a Hash.
-
---- Bio::KEGG::GENOME#taxid -> String
-
-      Returns NCBI taxonomy ID from the TAXONOMY record as a String.
-
---- Bio::KEGG::GENOME#lineage -> String
-
-      Returns contents of the TAXONOMY/LINEAGE record as a String.
-
-=== COMMENT
-
---- Bio::KEGG::GENOME#comment -> String
-
-      Returns contents of the COMMENT record as a String.
-
-=== REFERENCE
-
---- Bio::GenBank#references -> Array
-
-      Returns contents of the REFERENCE records as an Array of Bio::Reference
-      objects.
-
-=== CHROMOSOME
-
---- Bio::KEGG::GENOME#chromosomes -> Array
-
-      Returns contents of the CHROMOSOME records as an Array of Hash.
-
-=== PLASMID
-
---- Bio::KEGG::GENOME#plasmids -> Array
-
-      Returns contents of the PLASMID records as an Array of Hash.
-
-=== SCAFFOLD
-
---- Bio::KEGG::GENOME#scaffolds -> Array
-
-      Returns contents of the SCAFFOLD records as an Array of Hash.
-
-=== STATISTICS
-
---- Bio::KEGG::GENOME#statistics -> Hash
-
-      Returns contents of the STATISTICS record as a Hash.
-
---- Bio::KEGG::GENOME#nalen -> Fixnum
-
-      Returns number of nucleotides from the STATISTICS record as a Fixnum.
-
---- Bio::KEGG::GENOME#num_gene -> Fixnum
-
-      Returns number of protein genes from the STATISTICS record as a Fixnum.
-
---- Bio::KEGG::GENOME#num_rna -> Fixnum
-
-      Returns number of rna from the STATISTICS record as a Fixnum.
-
---- Bio::KEGG::GENOME#gc -> Float
-
-      Returns G+C content from the STATISTICS record as a Float.
-
-=== GENOMEMAP
-
---- Bio::KEGG::GENOME#genomemap -> String
-
-      Returns contents of the GENOMEMAP record as a String.
-
-== SEE ALSO
-
-  ftp://ftp.genome.jp/pub/kegg/genomes/genome
-
-=end