ngoto-bio 1.2.9.9001

data/lib/bio/data/na.rb

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+#
+# = bio/data/na.rb - Nucleic Acids
+#
+# Copyright::	Copyright (C) 2001, 2005
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	The Ruby License
+#
+# $Id: na.rb,v 0.23 2007/04/06 04:41:28 k Exp $
+#
+# == Synopsis
+#
+# Bio::NucleicAcid class contains data related to nucleic acids.
+#
+# == Usage
+#
+# Examples:
+#
+#   require 'bio'
+#
+#   puts "### na = Bio::NucleicAcid.new"
+#   na = Bio::NucleicAcid.new
+#
+#   puts "# na.to_re('yrwskmbdhvnatgc')"
+#   p na.to_re('yrwskmbdhvnatgc')
+#
+#   puts "# Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')"
+#   p Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')
+#
+#   puts "# na.weight('A')"
+#   p na.weight('A')
+#
+#   puts "# Bio::NucleicAcid.weight('A')"
+#   p Bio::NucleicAcid.weight('A')
+#
+#   puts "# na.weight('atgc')"
+#   p na.weight('atgc')
+#
+#   puts "# Bio::NucleicAcid.weight('atgc')"
+#   p Bio::NucleicAcid.weight('atgc')
+#
+
+module Bio
+
+class NucleicAcid
+
+  module Data
+
+    # IUPAC code
+    # * Faisst and Meyer (Nucleic Acids Res. 20:3-26, 1992)
+    # * http://www.ncbi.nlm.nih.gov/collab/FT/
+
+    NAMES = {
+
+      'y'	=> '[tc]',
+      'r'	=> '[ag]',
+      'w'	=> '[at]',
+      's'	=> '[gc]',
+      'k'	=> '[tg]',
+      'm'	=> '[ac]',
+
+      'b'	=> '[tgc]',
+      'd'	=> '[atg]',
+      'h'	=> '[atc]',
+      'v'	=> '[agc]',
+
+      'n'	=> '[atgc]',
+
+      'a'	=> 'a',
+      't'	=> 't',
+      'g'	=> 'g',
+      'c'	=> 'c',
+      'u'	=> 'u',
+
+      'A'	=> 'Adenine',
+      'T'	=> 'Thymine',
+      'G'	=> 'Guanine',
+      'C'	=> 'Cytosine',
+      'U'	=> 'Uracil',
+
+      'Y'	=> 'pYrimidine',
+      'R'	=> 'puRine',
+      'W'	=> 'Weak',
+      'S'	=> 'Strong',
+      'K'	=> 'Keto',
+      'M'	=> 'aroMatic',
+
+      'B'	=> 'not A',
+      'D'	=> 'not C',
+      'H'	=> 'not G',
+      'V'	=> 'not T',
+    }
+
+    WEIGHT = {
+
+      # Calculated by BioPerl's Bio::Tools::SeqStats.pm :-)
+
+      'a'	=> 135.15,
+      't'	=> 126.13,
+      'g'	=> 151.15,
+      'c'	=> 111.12,
+      'u'	=> 112.10,
+
+      :adenine	=> 135.15,
+      :thymine	=> 126.13,
+      :guanine	=> 151.15,
+      :cytosine	=> 111.12,
+      :uracil	=> 112.10,
+
+      :deoxyribose_phosphate	=> 196.11,
+      :ribose_phosphate		=> 212.11,
+
+      :hydrogen	=> 1.00794,
+      :water	=> 18.015,
+
+    }
+
+    def weight(x = nil, rna = nil)
+      if x
+        if x.length > 1
+          if rna
+            phosphate = WEIGHT[:ribose_phosphate]
+          else
+            phosphate = WEIGHT[:deoxyribose_phosphate]
+          end
+          hydrogen    = WEIGHT[:hydrogen]
+          water       = WEIGHT[:water]
+
+          total = 0.0
+          x.each_byte do |byte|
+            base = byte.chr.downcase
+            if WEIGHT[base]
+              total += WEIGHT[base] + phosphate - hydrogen * 2
+            else
+              raise "Error: invalid nucleic acid '#{base}'"
+            end
+          end
+          total -= water * (x.length - 1)
+        else
+          WEIGHT[x.to_s.downcase]
+        end
+      else
+        WEIGHT
+      end
+    end
+
+    def [](x)
+      NAMES[x]
+    end
+
+    # backward compatibility
+    def names
+      NAMES
+    end
+    alias na names
+
+    def name(x)
+      NAMES[x.to_s.upcase]
+    end
+
+    def to_re(seq, rna = false)
+      replace = {
+        'y' => '[tcy]',
+        'r' => '[agr]',
+        'w' => '[atw]',
+        's' => '[gcw]',
+        'k' => '[tgk]',
+        'm' => '[acm]',
+        'b' => '[tgcyskb]',
+        'd' => '[atgrwkd]',
+        'h' => '[atcwmyh]',
+        'v' => '[agcmrsv]',
+        'n' => '[atgcyrwskmbdhvn]'
+      }
+      replace.default = '.'
+
+      str = seq.to_s.downcase
+      str.gsub!(/[^atgcu]/) { |na|
+        replace[na]
+      }
+      if rna
+        str.tr!("t", "u")
+      end
+      Regexp.new(str)
+    end
+
+  end
+
+
+  # as instance methods
+  include Data
+
+  # as class methods
+  extend Data
+
+end
+
+end # module Bio
+
+
+if __FILE__ == $0
+
+  puts "### na = Bio::NucleicAcid.new"
+  na = Bio::NucleicAcid.new
+
+  puts "# na.to_re('yrwskmbdhvnatgc')"
+  p na.to_re('yrwskmbdhvnatgc')
+
+  puts "# Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')"
+  p Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')
+
+  puts "# na.weight('A')"
+  p na.weight('A')
+
+  puts "# Bio::NucleicAcid.weight('A')"
+  p Bio::NucleicAcid.weight('A')
+
+  puts "# na.weight('atgc')"
+  p na.weight('atgc')
+
+  puts "# Bio::NucleicAcid.weight('atgc')"
+  p Bio::NucleicAcid.weight('atgc')
+
+end

data/lib/bio/db/aaindex.rb

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+#
+# = bio/db/aaindex.rb - AAindex database class
+#
+# Copyright::  Copyright (C) 2001 
+#              KAWASHIMA Shuichi <s@bioruby.org>
+# Copyright::  Copyright (C) 2006
+#              Mitsuteru C. Nakao <n@bioruby.org>
+# License::    The Ruby License
+#
+# $Id: aaindex.rb,v 1.20 2007/04/05 23:35:40 trevor Exp $
+#
+# == Description
+#
+# Classes for Amino Acid Index Database (AAindex and AAindex2).
+# * AAindex Manual: http://www.genome.jp/dbget-bin/show_man?aaindex
+#
+# == Examples
+#
+#  aax1 = Bio::AAindex.auto("PRAM900102.aaindex1")
+#  aax2 = Bio::AAindex.auto("DAYM780301.aaindex2")
+#
+#  aax1 = Bio::AAindex1.new("PRAM900102.aaindex1")
+#  aax1.entry_id
+#  aax1.index
+#
+#  aax2 = Bio::AAindex2.new("DAYM780301.aaindex2")
+#  aax2.entry_id
+#  aax2.matrix
+#  aax2.matrix[2,2]
+#  aax2.matrix('R', 'A')
+#  aax2['R', 'A']
+#
+# == References
+#
+# * http://www.genome.jp/aaindex/
+#
+
+require "bio/db"
+require "matrix"
+
+module Bio
+
+  # Super class for AAindex1 and AAindex2
+  class AAindex < KEGGDB
+
+    # Delimiter
+    DELIMITER ="\n//\n"
+
+    # Delimiter
+    RS = DELIMITER
+
+    # Bio::DB API
+    TAGSIZE = 2
+
+    # Auto detecter for two AAindex formats.
+    # returns a Bio::AAindex1 object or a Bio::AAindex2 object.
+    def self.auto(str)
+      case str
+      when /^I /m 
+        Bio::AAindex1.new(str)
+      when /^M /m
+        Bio::AAindex2.new(str)
+      else
+        raise
+      end        
+    end
+
+    # 
+    def initialize(entry)
+      super(entry, TAGSIZE)
+    end
+
+    # Returns entry_id in the H line.
+    def entry_id
+      if @data['entry_id']
+        @data['entry_id']
+      else
+        @data['entry_id'] = field_fetch('H')
+      end
+    end
+
+    # Returns definition in the D line.
+    def definition
+      if @data['definition']
+        @data['definition']
+      else
+        @data['definition'] = field_fetch('D')
+      end
+    end
+
+    # Returns database links in the R line.
+    # cf.) ['LIT:123456', 'PMID:12345678']
+    def dblinks
+      if @data['ref']
+        @data['ref']
+      else
+        @data['ref'] = field_fetch('R').split(' ')
+      end
+    end
+
+    # Returns authors in the A line.
+    def author
+      if @data['author']
+        @data['author']
+      else
+        @data['author'] = field_fetch('A')
+      end
+    end
+
+    # Returns title in the T line.
+    def title
+      if @data['title']
+        @data['title']
+      else
+        @data['title'] = field_fetch('T')
+      end
+    end
+
+    # Returns journal name in the J line.
+    def journal
+      if @data['journal']
+        @data['journal']
+      else
+        @data['journal'] = field_fetch('J')
+      end
+    end
+
+    # Returns comment (if any).
+    def comment
+      if @data['comment']
+        @data['comment']
+      else
+        @data['comment'] = field_fetch('*')
+      end
+    end
+  end
+
+
+  # Class for AAindex1 format.
+  class AAindex1 < AAindex
+
+    def initialize(entry)
+      super(entry)
+    end
+
+    # Returns correlation_coefficient (Hash) in the C line.
+    #
+    # cf.) {'ABCD12010203' => 0.999, 'CDEF123456' => 0.543, ...}
+    def correlation_coefficient
+      if @data['correlation_coefficient']
+        @data['correlation_coefficient']
+      else
+        hash = {}
+        ary = field_fetch('C').split(' ')
+        ary.each do |x|
+          next unless x =~ /^[A-Z]/
+          hash[x] = ary[ary.index(x) + 1].to_f
+        end
+        @data['correlation_coefficient'] = hash
+      end
+    end
+
+    # Returns the index (Array) in the I line.
+    #
+    # an argument: :string, :float, :zscore or :integer
+    def index(type = :float)
+      aa = %w( A R N D C Q E G H I L K M F P S T W Y V )
+      values = field_fetch('I', 1).split(' ')
+
+      if values.size != 20
+        raise "Invalid format in #{entry_id} : #{values.inspect}"
+      end
+
+      if type == :zscore and values.size > 0
+        sum = 0.0
+        values.each do |a|
+          sum += a.to_f
+        end
+        mean = sum / values.size # / 20
+        var = 0.0
+        values.each do |a|
+          var += (a.to_f - mean) ** 2
+        end
+        sd = Math.sqrt(var)
+      end
+
+      if type == :integer
+        figure = 0
+        values.each do |a|
+          figure = [ figure, a[/\..*/].length - 1 ].max
+        end
+      end
+
+      hash = {}
+
+      aa.each_with_index do |a, i|
+        case type
+        when :string
+          hash[a] = values[i]
+        when :float
+          hash[a] = values[i].to_f
+        when :zscore
+          hash[a] = (values[i].to_f - mean) / sd
+        when :integer
+          hash[a] = (values[i].to_f * 10 ** figure).to_i
+        end
+      end
+      return hash
+    end
+
+  end
+
+
+  # Class for AAindex2 format.
+  class AAindex2 < AAindex
+
+    def initialize(entry)
+      super(entry)
+    end
+
+    # Returns row labels.
+    def rows
+      if @data['rows']
+        @data['rows']
+      else 
+        label_data
+        @rows
+      end
+    end
+
+    # Returns col labels.
+    def cols
+      if @data['cols']
+        @data['cols']
+      else 
+        label_data
+        @cols
+      end
+    end
+
+    # Returns the value of amino acids substitution (aa1 -> aa2).
+    def [](aa1 = nil, aa2 = nil)
+      matrix[cols.index(aa1), rows.index(aa2)]
+    end
+
+    # Returns amino acids matrix in Matrix.
+    def matrix(aa1 = nil, aa2 = nil)
+      return self[aa1, aa2] if aa1 and aa2
+
+      if @data['matrix'] 
+        @data['matrix'] 
+      else
+        ma = []
+        label_data.each_line do |line|
+          ma << line.strip.split(/\s+/).map {|x| x.to_f }
+        end
+        @data['matrix'] = Matrix[*ma]
+      end
+    end
+
+    # Returns amino acids matrix in Matrix  for the old format (<= ver 5.0).
+    def old_matrix # for AAindex <= ver 5.0
+      return @data['matrix'] if @data['matrix']
+
+      @aa = {} 
+      # used to determine row/column of the aa
+      attr_reader :aa
+      alias_method :aa, :rows
+      alias_method :aa, :cols
+
+      field = field_fetch('I')
+
+      case field
+      when / (ARNDCQEGHILKMFPSTWYV)\s+(.*)/ # 20x19/2 matrix
+        aalist = $1
+        values = $2.split(/\s+/)
+
+        0.upto(aalist.length - 1) do |i|
+          @aa[aalist[i].chr] = i
+        end
+
+        ma = Array.new
+        20.times do
+          ma.push(Array.new(20)) # 2D array of 20x(20)
+        end
+
+        for i in 0 .. 19 do
+          for j in i .. 19 do
+            ma[i][j] = values[i + j*(j+1)/2].to_f
+            ma[j][i] = ma[i][j]
+          end
+        end
+        @data['matrix'] = Matrix[*ma]
+      when / -ARNDCQEGHILKMFPSTWYV / # 21x20/2 matrix (with gap)
+        raise NotImplementedError
+      when / ACDEFGHIKLMNPQRSTVWYJ- / # 21x21 matrix (with gap)
+        raise NotImplementedError
+      end
+    end
+
+    private
+
+    def label_data
+      if @data['data'] 
+        @data['data'] 
+      else
+        label, data = get('M').split("\n", 2)
+        if /M rows = (\S+), cols = (\S+)/.match(label)
+          rows, cols = $1, $2
+          @rows = rows.split('')
+          @cols = cols.split('')
+        end
+        @data['data'] = data
+      end
+    end
+
+  end # class AAindex2
+
+end # module Bio
+
+
+if __FILE__ == $0
+  require 'bio/io/fetch'
+
+  puts "### AAindex1 (PRAM900102)"
+  aax1 = Bio::AAindex1.new(Bio::Fetch.query('aaindex', 'PRAM900102', 'raw'))
+  p aax1.entry_id
+  p aax1.definition
+  p aax1.dblinks
+  p aax1.author
+  p aax1.title
+  p aax1.journal
+  p aax1.comment
+  p aax1.correlation_coefficient
+  p aax1.index
+  p aax1
+  puts "### AAindex2 (DAYM780301)"
+  aax2 = Bio::AAindex2.new(Bio::Fetch.query('aaindex', 'DAYM780301', 'raw'))
+  p aax2.entry_id
+  p aax2.definition
+  p aax2.dblinks
+  p aax2.author
+  p aax2.title
+  p aax2.journal
+  p aax1.comment
+  p aax2.rows
+  p aax2.cols
+  p aax2.matrix
+  p aax2.matrix[2,2]
+  p aax2.matrix[2,3]
+  p aax2.matrix[4,3]
+  p aax2.matrix.determinant
+  p aax2.matrix.rank
+  p aax2.matrix.transpose
+  p aax2
+end
+

data/lib/bio/db/biosql/biosql_to_biosequence.rb

@@ -0,0 +1,67 @@
+#
+# = bio/db/biosql/biosql_to_biosequence.rb - Bio::SQL::Sequence to Bio::Sequence adapter module
+#
+# Copyright::   Copyright (C) 2008
+#               Naohisa Goto <ng@bioruby.org>,
+#               Raoul Jean Pierre Bonnal
+# License::     The Ruby License
+#
+# $Id:$
+#
+
+require 'bio/sequence'
+require 'bio/sequence/adapter'
+
+# Internal use only. Normal users should not use this module.
+#
+# Bio::SQL::Sequence to Bio::Sequence adapter module.
+# It is internally used in Bio::SQL::Sequence#to_biosequence.
+#
+module Bio::Sequence::Adapter::BioSQL
+
+  extend Bio::Sequence::Adapter
+
+  private
+
+  def_biosequence_adapter :seq 
+  
+  def_biosequence_adapter :entry_id
+
+  def_biosequence_adapter :primary_accession
+
+  def_biosequence_adapter :secondary_accessions
+
+  def_biosequence_adapter :molecule_type
+
+  #--
+  #TODO: identify where is stored data_class in biosql      
+  #++
+
+  def_biosequence_adapter :data_class
+
+  def_biosequence_adapter :definition, :description
+
+  def_biosequence_adapter :topology
+
+  def_biosequence_adapter :date_created
+
+  def_biosequence_adapter :date_modified
+
+  def_biosequence_adapter :division
+
+  def_biosequence_adapter :sequence_version
+
+  def_biosequence_adapter :keywords
+
+  def_biosequence_adapter :species
+
+  def_biosequence_adapter :classification, :taxonomy
+
+  def_biosequence_adapter :references
+
+  def_biosequence_adapter :features
+  
+  def_biosequence_adapter :comments
+
+end #module Bio::Sequence::Adapter::BioSQL
+