wwood-bioruby 1.2.11

data/lib/bio/db/rebase.rb

@@ -0,0 +1,456 @@
+#
+# bio/db/rebase.rb - Interface for EMBOSS formatted REBASE files
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
+#
+#  $Id:$
+#
+
+require 'yaml'
+require 'bio/reference'
+
+module Bio
+
+#
+# bio/db/rebase.rb - Interface for EMBOSS formatted REBASE files
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
+#
+#
+# = Description
+# 
+# Bio::REBASE provides utilties for interacting with REBASE data in EMBOSS
+# format.  REBASE is the Restriction Enzyme Database, more information
+# can be found here:
+# 
+# * http://rebase.neb.com
+# 
+# EMBOSS formatted files located at:
+# 
+# * http://rebase.neb.com/rebase/rebase.f37.html
+# 
+# These files are the same as the "emboss_?.???" files located at:
+# 
+# * ftp://ftp.neb.com/pub/rebase/
+# 
+# To easily get started with the data you can simply type this command
+# at your shell prompt:
+# 
+#   % wget ftp://ftp.neb.com/pub/rebase/emboss*
+# 
+# 
+# = Usage
+# 
+#   require 'bio'
+#   require 'pp'
+# 
+#   enz = File.read('emboss_e')
+#   ref = File.read('emboss_r')
+#   sup = File.read('emboss_s')
+# 
+#   # When creating a new instance of Bio::REBASE
+#   # the contents of the enzyme file must be passed.
+#   # The references and suppiers file contents
+#   # may also be passed.
+#   rebase = Bio::REBASE.new( enz )
+#   rebase = Bio::REBASE.new( enz, ref )
+#   rebase = Bio::REBASE.new( enz, ref, sup )
+# 
+#   # The 'read' class method allows you to read in files
+#   # that are REBASE EMBOSS formatted
+#   rebase = Bio::REBASE.read( 'emboss_e' )
+#   rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r' )
+#   rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r', 'emboss_s' )
+# 
+#   # The data loaded may be saved in YAML format
+#   rebase.save_yaml( 'enz.yaml' )
+#   rebase.save_yaml( 'enz.yaml', 'ref.yaml' )
+#   rebase.save_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' )
+# 
+#   # YAML formatted files can also be read with the
+#   # class method 'load_yaml'
+#   rebase = Bio::REBASE.load_yaml( 'enz.yaml' )
+#   rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml' )
+#   rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' )
+# 
+#   pp rebase.enzymes[0..4]                     # ["AarI", "AasI", "AatI", "AatII", "Acc16I"]
+#   pp rebase.enzyme_name?('aasi')              # true
+#   pp rebase['AarI'].pattern                   # "CACCTGC"
+#   pp rebase['AarI'].blunt?                    # false
+#   pp rebase['AarI'].organism                  # "Arthrobacter aurescens SS2-322"
+#   pp rebase['AarI'].source                    # "A. Janulaitis"
+#   pp rebase['AarI'].primary_strand_cut1       # 11
+#   pp rebase['AarI'].primary_strand_cut2       # 0
+#   pp rebase['AarI'].complementary_strand_cut1 # 15
+#   pp rebase['AarI'].complementary_strand_cut2 # 0
+#   pp rebase['AarI'].suppliers                 # ["F"]
+#   pp rebase['AarI'].supplier_names            # ["Fermentas International Inc."]
+# 
+#   pp rebase['AarI'].isoschizomers             # Currently none stored in the references file
+#   pp rebase['AarI'].methylation               # ""
+# 
+#   pp rebase['EcoRII'].methylation             # "2(5)"
+#   pp rebase['EcoRII'].suppliers               # ["F", "J", "M", "O", "S"]
+#   pp rebase['EcoRII'].supplier_names  # ["Fermentas International Inc.", "Nippon Gene Co., Ltd.",
+#                                       # "Roche Applied Science", "Toyobo Biochemicals",
+#                                       # "Sigma Chemical Corporation"]
+# 
+#   # Number of enzymes in the database
+#   pp rebase.size                              # 673
+#   pp rebase.enzymes.size                      # 673
+# 
+#   rebase.each do |name, info|
+#     pp "#{name}:  #{info.methylation}" unless info.methylation.empty?
+#   end
+#
+
+class REBASE
+
+  class DynamicMethod_Hash < Hash #:nodoc:
+    # Define a writer or reader
+    # * Allows hash[:kay]= to be accessed like hash.key=
+    # * Allows hash[:key] to be accessed like hash.key
+    def method_missing(method_id, *args)
+      k = self.class
+      if method_id.to_s[-1].chr == '='
+        k.class_eval do
+          define_method(method_id) { |s| self[ method_id.to_s[0..-2].to_sym ] = s }
+        end
+        k.instance_method(method_id).bind(self).call(args[0])
+      else
+        k.class_eval do
+          define_method(method_id) { self[method_id] }
+        end
+        k.instance_method(method_id).bind(self).call
+      end
+    end
+  end
+
+  class EnzymeEntry < DynamicMethod_Hash #:nodoc:
+    @@supplier_data = {}
+    def self.supplier_data=(d); @@supplier_data = d; end
+
+    def supplier_names
+      ret = []
+      self.suppliers.each { |s| ret << @@supplier_data[s] }
+      ret
+    end
+  end
+
+  # Calls _block_ once for each element in <tt>@data</tt> hash, passing that element as a parameter.
+  #
+  # ---
+  # *Arguments*
+  # * Accepts a block
+  # *Returns*:: results of _block_ operations
+  def each
+    @data.each { |item| yield item }
+  end
+
+  # Make the instantiated class act like a Hash on @data
+  # Does the equivalent and more of this:
+  #  def []( key ); @data[ key ]; end
+  #  def size; @data.size; end
+  def method_missing(method_id, *args) #:nodoc:
+    self.class.class_eval do
+      define_method(method_id) { |a| Hash.instance_method(method_id).bind(@data).call(a) }
+    end
+    Hash.instance_method(method_id).bind(@data).call(*args)
+  end
+
+  # Constructor
+  #
+  # ---
+  # *Arguments*
+  # * +enzyme_lines+: (_required_) contents of EMBOSS formatted enzymes file 
+  # * +reference_lines+: (_optional_) contents of EMBOSS formatted references file 
+  # * +supplier_lines+: (_optional_) contents of EMBOSS formatted suppliers files 
+  # * +yaml+: (_optional_, _default_ +false+) enzyme_lines, reference_lines, and supplier_lines are read as YAML if set to true 
+  # *Returns*:: Bio::REBASE
+  def initialize( enzyme_lines, reference_lines = nil, supplier_lines = nil, yaml = false )
+    # All your REBASE are belong to us.
+
+    if yaml
+      @enzyme_data = enzyme_lines
+      @reference_data = reference_lines
+      @supplier_data = supplier_lines
+    else
+      @enzyme_data = parse_enzymes(enzyme_lines)
+      @reference_data = parse_references(reference_lines)
+      @supplier_data = parse_suppliers(supplier_lines)
+    end
+
+    EnzymeEntry.supplier_data = @supplier_data
+    setup_enzyme_data
+  end
+
+  # List the enzymes available
+  #
+  # ---
+  # *Arguments*
+  # * _none_
+  # *Returns*:: +Array+ sorted enzyme names
+  def enzymes
+    @data.keys.sort
+  end
+  
+  # Check if supplied name is the name of an available enzyme
+  #
+  # ---
+  # *Arguments*
+  # * +name+: Enzyme name
+  # *Returns*:: +true/false+
+  def enzyme_name?(name)
+    enzymes.each do |e|
+      return true if e.downcase == name.downcase
+    end
+    return false
+  end
+
+  # Save the current data
+  #  rebase.save_yaml( 'enz.yaml' )
+  #  rebase.save_yaml( 'enz.yaml', 'ref.yaml' )
+  #  rebase.save_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' )
+  #
+  # ---
+  # *Arguments*
+  # * +f_enzyme+: (_required_) Filename to save YAML formatted output of enzyme data
+  # * +f_reference+: (_optional_) Filename to save YAML formatted output of reference data
+  # * +f_supplier+: (_optional_) Filename to save YAML formatted output of supplier data  
+  # *Returns*:: nothing
+  def save_yaml( f_enzyme, f_reference=nil, f_supplier=nil )
+    File.open(f_enzyme, 'w') { |f| f.puts YAML.dump(@enzyme_data) }
+    File.open(f_reference, 'w') { |f| f.puts YAML.dump(@reference_data) } if f_reference
+    File.open(f_supplier, 'w') { |f| f.puts YAML.dump(@supplier_data) } if f_supplier
+    return
+  end
+
+  # Read REBASE EMBOSS-formatted files
+  #  rebase = Bio::REBASE.read( 'emboss_e' )
+  #  rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r' )
+  #  rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r', 'emboss_s' )
+  #
+  # ---
+  # *Arguments*
+  # * +f_enzyme+: (_required_) Filename to read enzyme data
+  # * +f_reference+: (_optional_) Filename to read reference data
+  # * +f_supplier+: (_optional_) Filename to read supplier data  
+  # *Returns*:: Bio::REBASE object
+  def self.read( f_enzyme, f_reference=nil, f_supplier=nil )
+    e = IO.readlines(f_enzyme)
+    r = f_reference ? IO.readlines(f_reference) : nil
+    s = f_supplier ? IO.readlines(f_supplier) : nil
+    self.new(e,r,s)
+  end
+
+  # Read YAML formatted files
+  #  rebase = Bio::REBASE.load_yaml( 'enz.yaml' )
+  #  rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml' )
+  #  rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' )
+  #
+  # ---
+  # *Arguments*
+  # * +f_enzyme+: (_required_) Filename to read YAML-formatted enzyme data
+  # * +f_reference+: (_optional_) Filename to read YAML-formatted reference data
+  # * +f_supplier+: (_optional_) Filename to read YAML-formatted supplier data  
+  # *Returns*:: Bio::REBASE object
+  def self.load_yaml( f_enzyme, f_reference=nil, f_supplier=nil )
+    e = YAML.load_file(f_enzyme)
+    r = f_reference ? YAML.load_file(f_reference) : nil
+    s = f_supplier ? YAML.load_file(f_supplier) : nil
+    self.new(e,r,s,true)
+  end
+
+  #########
+  protected
+  #########
+
+  def setup_enzyme_data
+    @data = {}
+    
+    @enzyme_data.each do |name, hash|
+      @data[name] = EnzymeEntry.new
+      d = @data[name]
+      d.pattern                   = hash[:pattern]
+      # d.blunt?= is a syntax error
+      d[:blunt?] = (hash[:blunt].to_i == 1 ? true : false)
+      d.primary_strand_cut1       = hash[:c1].to_i
+      d.complementary_strand_cut1 = hash[:c2].to_i
+      d.primary_strand_cut2       = hash[:c3].to_i
+      d.complementary_strand_cut2 = hash[:c4].to_i
+
+      # Set up keys just in case there's no reference data supplied
+      [:organism, :isoschizomers, 
+      :methylation, :source].each { |k| d[k] = '' }
+      d.suppliers = []
+      d.references = []
+    end
+
+    setup_enzyme_and_reference_association
+  end
+
+  def setup_enzyme_and_reference_association
+    return unless @reference_data
+    @reference_data.each do |name, hash|
+      d = @data[name]
+      [:organism, :isoschizomers, 
+      :methylation, :source].each { |k| d[k] = hash[k] }
+      d.suppliers = hash[:suppliers].split('')
+      d.references = []
+      hash[:references].each { |k| d.references << raw_to_reference(k) }
+    end
+  end
+
+  # data is a hash indexed by the :name of each entry which is also a hash
+  # * data[enzyme_name] has the following keys:
+  #   :name, :pattern, :len, :ncuts, :blunt, :c1, :c2, :c3, :c4
+  #   :c1 => First 5' cut
+  #   :c2 => First 3' cut
+  #   :c3 => Second 5' cut
+  #   :c4 => Seocnd 3' cut
+  def parse_enzymes( lines )
+    data = {}
+    return data if lines == nil
+    lines.each_line do |line|
+      next if line[0].chr == '#'
+      line.chomp!
+      
+      a = line.split("\s")
+      
+      data[ a[0] ] = {
+        :name => a[0],
+        :pattern => a[1],
+        :len => a[2],
+        :ncuts => a[3],
+        :blunt => a[4],
+        :c1 => a[5],
+        :c2 => a[6],
+        :c3 => a[7],
+        :c4 => a[8]
+      }
+    end  # lines.each
+    data
+  end
+
+  # data is a hash indexed by the :name of each entry which is also a hash
+  # * data[enzyme_name] has the following keys:
+  #   :organism, :isoschizomers, :references, :source, :methylation, :suppliers, :name, :number_of_references
+  def parse_references( lines )
+    data = {}
+    return data if lines == nil
+    index = 1
+    h = {}
+    references_left = 0
+
+    lines.each_line do |line|
+      next if line[0].chr == '#'  # Comment
+      next if line[0..1] == '//'  # End of entry marker
+      line.chomp!
+
+      if (1..7).include?( index )
+        h[index] = line
+        references_left = h[index].to_i if index == 7
+        index += 1
+        next
+      end
+
+      if index == 8
+        h[index] ||= []
+        h[index] << line
+        references_left -= 1
+      end
+
+      if references_left == 0
+        data[ h[1] ] = {
+          :name => h[1],
+          :organism => h[2],
+          :isoschizomers => h[3],
+          :methylation => h[4],
+          :source => h[5],
+          :suppliers => h[6],
+          :number_of_references => h[7],
+          :references => h[8]
+        }
+        index = 1
+        h = {}
+      end
+    end  # lines.each
+    data
+  end
+
+  # data is a hash indexed by the supplier code
+  #   data[supplier_code]
+  #   returns the suppliers name
+  def parse_suppliers( lines )
+    data = {}
+    return data if lines == nil
+    lines.each_line do |line|
+      next if line[0].chr == '#'
+      data[$1] = $2 if line =~ %r{(.+?)\s(.+)}
+    end
+    data
+  end
+
+  # Takes a string in one of the three formats listed below and returns a
+  # Bio::Reference object
+  # * Possible input styles:
+  #   a = 'Inagaki, K., Hikita, T., Yanagidani, S., Nomura, Y., Kishimoto, N., Tano, T., Tanaka, H., (1993) Biosci. Biotechnol. Biochem., vol. 57, pp. 1716-1721.'
+  #   b = 'Nekrasiene, D., Lapcinskaja, S., Kiuduliene, L., Vitkute, J., Janulaitis, A., Unpublished observations.'
+  #   c = "Grigaite, R., Maneliene, Z., Janulaitis, A., (2002) Nucleic Acids Res., vol. 30."
+  def raw_to_reference( line )
+    a = line.split(', ')
+
+    if a[-1] == 'Unpublished observations.'
+      title = a.pop.chop
+      pages = volume = year = journal = ''
+    else
+      title = ''
+
+      pages_or_volume = a.pop.chop
+      if pages_or_volume =~ %r{pp\.\s}
+        pages = pages_or_volume
+        pages.gsub!('pp. ', '')
+        volume = a.pop
+      else
+        pages = ''
+        volume = pages_or_volume
+      end
+
+      volume.gsub!('vol. ', '')
+
+      year_and_journal = a.pop
+      year_and_journal =~ %r{\((\d+)\)\s(.+)}
+      year = $1
+      journal = $2
+    end
+
+    authors = []
+
+    last_name = nil
+    a.each do |e|
+      if last_name
+        authors << "#{last_name}, #{e}"
+        last_name = nil
+      else
+        last_name = e
+      end
+    end
+
+    ref = {
+      'title' => title,
+      'pages' => pages,
+      'volume' => volume,
+      'year' => year,
+      'journal' => journal,
+      'authors' => authors,
+    }
+
+    Bio::Reference.new(ref)
+  end
+
+end # REBASE
+end # Bio