wwood-bioruby 1.2.11

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

@@ -0,0 +1,263 @@
+#
+# = bio/db/kegg/genes.rb - KEGG/GENES database class
+#
+# Copyright::   Copyright (C) 2001, 2002, 2006
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: genes.rb,v 0.26 2007/12/14 16:20:38 k Exp $
+#
+#
+# == KEGG GENES parser
+#
+# See http://www.genome.jp/kegg/genes.html
+#
+#
+# === Examples
+# 
+#  require 'bio/io/fetch'
+#  entry_string = Bio::Fetch.query('genes', 'b0002')
+# 
+#  entry = Bio::KEGG::GENES.new(entry_string)
+# 
+#  # ENTRY
+#  p entry.entry       # => Hash
+#
+#  p entry.entry_id    # => String
+#  p entry.division    # => String
+#  p entry.organism    # => String
+# 
+#  # NAME
+#  p entry.name        # => String
+#  p entry.genes       # => Array
+#  p entry.gene        # => String
+# 
+#  # DEFINITION
+#  p entry.definition  # => String
+#  p entry.eclinks     # => Array
+# 
+#  # PATHWAY
+#  p entry.pathway     # => String
+#  p entry.pathways    # => Array
+# 
+#  # POSITION
+#  p entry.position    # => String
+#  p entry.chromosome  # => String
+#  p entry.gbposition  # => String
+#  p entry.locations   # => Bio::Locations
+#
+#  # MOTIF
+#  p entry.motif       # => Hash of Array
+#
+#  # DBLINKS
+#  p entry.dblinks     # => Hash of Array
+# 
+#  # CODON_USAGE
+#  p entry.codon_usage # => Hash
+#  p entry.cu_list     # => Array
+# 
+#  # AASEQ
+#  p entry.aaseq       # => Bio::Sequence::AA
+#  p entry.aalen       # => Fixnum
+# 
+#  # NTSEQ
+#  p entry.ntseq       # => Bio::Sequence::NA
+#  p entry.naseq       # => Bio::Sequence::NA
+#  p entry.ntlen       # => Fixnum
+#  p entry.nalen       # => Fixnum
+# 
+
+module Bio
+
+  autoload :KEGGDB,    'bio/db'
+  autoload :Locations, 'bio/location'
+  autoload :Sequence,  'bio/sequence'
+
+class KEGG
+
+class GENES < KEGGDB
+
+  DELIMITER	= RS = "\n///\n"
+  TAGSIZE	= 12
+
+  def initialize(entry)
+    super(entry, TAGSIZE)
+  end
+
+
+  def entry
+    unless @data['ENTRY']
+      hash = Hash.new('')
+      if get('ENTRY').length > 30
+        e = get('ENTRY')
+        hash['id']       = e[12..29].strip
+        hash['division'] = e[30..39].strip
+        hash['organism'] = e[40..80].strip
+      end
+      @data['ENTRY'] = hash
+    end
+    @data['ENTRY']
+  end
+
+  def entry_id
+    entry['id']
+  end
+
+  def division
+    entry['division']			# CDS, tRNA etc.
+  end
+
+  def organism
+    entry['organism']			# H.sapiens etc.
+  end
+
+  def name
+    field_fetch('NAME')
+  end
+
+  def genes
+    name.split(', ')
+  end
+
+  def gene
+    genes.first
+  end
+
+  def definition
+    field_fetch('DEFINITION')
+  end
+
+  def eclinks
+    ec_list = definition.slice(/\[EC:(.*?)\]/, 1)
+    if ec_list
+      ec_list.strip.split(/\s+/)
+    else
+      []
+    end
+  end
+
+  def orthologs
+    lines_fetch('ORTHOLOGY')
+  end
+
+  def pathway
+    field_fetch('PATHWAY')
+  end
+
+  def pathways
+    pathway.scan(/\[PATH:(.*?)\]/).flatten
+  end
+
+  def position
+    unless @data['POSITION']
+      @data['POSITION'] = fetch('POSITION').gsub(/\s/, '')
+    end
+    @data['POSITION']
+  end
+
+  def chromosome
+    if position[/:/]
+      position.sub(/:.*/, '')
+    elsif ! position[/\.\./]
+      position
+    else
+      nil
+    end
+  end
+
+  def gbposition
+    position.sub(/.*?:/, '')
+  end
+
+  def locations
+    Bio::Locations.new(gbposition)
+  end
+
+  def motif
+    unless @data['MOTIF']
+      hash = {}
+      db = nil
+      lines_fetch('MOTIF').each do |line|
+        if line[/^\S+:/]
+          db, str = line.split(/:/)
+        else
+          str = line
+        end
+        hash[db] ||= []
+        hash[db] += str.strip.split(/\s+/)
+      end
+      @data['MOTIF'] = hash
+    end
+    @data['MOTIF']		# Hash of Array of IDs in MOTIF
+  end
+
+  def dblinks
+    unless @data['DBLINKS']
+      hash = {}
+      get('DBLINKS').scan(/(\S+):\s*(.*)\n?/).each do |db, str|
+        id_array = str.strip.split(/\s+/)
+        hash[db] = id_array
+      end
+      @data['DBLINKS'] = hash
+    end
+    @data['DBLINKS']		# Hash of Array of IDs in DBLINKS
+  end
+
+  def codon_usage(codon = nil)
+    unless @data['CODON_USAGE']
+      hash = Hash.new
+      list = cu_list
+      base = %w(t c a g)
+      base.each_with_index do |x, i|
+        base.each_with_index do |y, j|
+          base.each_with_index do |z, k|
+            hash["#{x}#{y}#{z}"] = list[i*16 + j*4 + k]
+          end
+        end
+      end
+      @data['CODON_USAGE'] = hash
+    end
+    @data['CODON_USAGE']
+  end
+
+  def cu_list
+    ary = []
+    get('CODON_USAGE').sub(/.*/,'').each_line do |line|	# cut 1st line
+      line.chomp.sub(/^.{11}/, '').scan(/..../) do |cu|
+        ary.push(cu.to_i)
+      end
+    end
+    return ary
+  end
+
+  def aaseq
+    unless @data['AASEQ']
+      @data['AASEQ'] = Bio::Sequence::AA.new(fetch('AASEQ').gsub(/\d+/, ''))
+    end
+    @data['AASEQ']
+  end
+
+  def aalen
+    fetch('AASEQ')[/\d+/].to_i
+  end
+
+  def ntseq
+    unless @data['NTSEQ']
+      @data['NTSEQ'] = Bio::Sequence::NA.new(fetch('NTSEQ').gsub(/\d+/, ''))
+    end
+    @data['NTSEQ']
+  end
+  alias naseq ntseq
+
+  def ntlen
+    fetch('NTSEQ')[/\d+/].to_i
+  end
+  alias nalen ntlen
+
+end
+
+end # KEGG
+end # Bio
+
+
+

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

@@ -0,0 +1,241 @@
+#
+# = bio/db/kegg/genome.rb - KEGG/GENOME database class
+#
+# Copyright::  Copyright (C) 2001, 2002, 2007 Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
+#
+# $Id: genome.rb,v 0.18 2007/06/28 11:27:24 k Exp $
+#
+
+require 'bio/db'
+
+module Bio
+class KEGG
+
+# == Description
+#
+# Parser for the KEGG GENOME database
+#
+# == References
+#
+# * ftp://ftp.genome.jp/pub/kegg/genomes/genome
+#
+class GENOME < KEGGDB
+
+  DELIMITER	= RS = "\n///\n"
+  TAGSIZE	= 12
+
+  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
+
+  # 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
+
+  # Returns NCBI taxonomy ID from the TAXONOMY record as a String.
+  def taxid
+    taxonomy['taxid']
+  end
+
+  # Returns contents of the TAXONOMY/LINEAGE record as a String.
+  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
+
+  # ORIGINAL_DB -- Returns contents of the ORIGINAL_DB record as a String.
+  def original_db
+    field_fetch('ORIGINAL_DB')
+  end
+
+  # DISEASE -- Returns contents of the COMMENT record as a String.
+  def disease
+    field_fetch('DISEASE')
+  end
+
+  # 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
+          end
+        end
+        ary.push(Reference.new(hash))
+      end
+      @data['REFERENCE'] = References.new(ary)
+    end
+    @data['REFERENCE']
+  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['CHROMOSOME'].push(hash)
+      end
+    end
+    @data['CHROMOSOME']
+  end
+
+  # 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['PLASMID'].push(hash)
+      end
+    end
+    @data['PLASMID']
+  end
+
+  # 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
+
+  # Returns number of nucleotides from the STATISTICS record as a Fixnum.
+  def nalen
+    statistics['num_nuc']
+  end
+  alias length nalen
+
+  # Returns number of protein genes from the STATISTICS record as a Fixnum.
+  def num_gene
+    statistics['num_gene']
+  end
+
+  # Returns number of rna from the STATISTICS record as a Fixnum.
+  def num_rna
+    statistics['num_rna']
+  end
+
+end # GENOME
+    
+end # KEGG
+end # Bio
+
+
+
+if __FILE__ == $0
+
+  begin
+    require 'pp'
+    def p(arg); pp(arg); end
+  rescue LoadError
+  end
+
+  require 'bio/io/flatfile'
+
+  ff = Bio::FlatFile.new(Bio::KEGG::GENOME, ARGF)
+
+  ff.each do |genome|
+
+    puts "### Tags"
+    p genome.tags
+
+    [
+      %w( ENTRY entry_id ),
+      %w( NAME name ),
+      %w( DEFINITION definition ),
+      %w( TAXONOMY taxonomy taxid lineage ),
+      %w( REFERENCE references ),
+      %w( CHROMOSOME chromosomes ),
+      %w( PLASMID plasmids ),
+      %w( STATISTICS statistics nalen num_gene num_rna ),
+    ].each do |x|
+      puts "### " + x.shift
+      x.each do |m|
+        p genome.send(m)
+      end
+    end
+
+  end
+
+end
+
+