bioinform 0.1.12 → 0.1.13

data/lib/bioinform/formatters/raw_formatter.rb

@@ -1,41 +1,41 @@
-class RawFormatter
-  attr_accessor :motif, :options
-  
-  def initialize(motif, options = {})
-    @motif = motif
-    
-    default_options = {with_name: true, letters_as_rows: false}
-    @options = default_options.merge(options)
-  end
-  
-  def name
-    motif.name
-  end
-  
-  def header
-    if options[:with_name] && name
-      name + "\n"
-    else
-      ''
-    end
-  end
-  
-  def matrix_string
-    if options[:letters_as_rows]
-      hsh = motif.to_hash
-      [:A,:C,:G,:T].collect{|letter| "#{letter}|" + hsh[letter].join("\t")}.join("\n")
-    else
-      motif.each_position.map{|pos| pos.join("\t")}.join("\n")
-    end
-  end
-  
-  def footer
-    # "\n"
-    ''
-  end
-  
-  
-  def to_s
-    header + matrix_string + footer
-  end
+class RawFormatter
+  attr_accessor :motif, :options
+  
+  def initialize(motif, options = {})
+    @motif = motif
+    
+    default_options = {with_name: true, letters_as_rows: false}
+    @options = default_options.merge(options)
+  end
+  
+  def name
+    motif.name
+  end
+  
+  def header
+    if options[:with_name] && name
+      name + "\n"
+    else
+      ''
+    end
+  end
+  
+  def matrix_string
+    if options[:letters_as_rows]
+      hsh = motif.to_hash
+      [:A,:C,:G,:T].collect{|letter| "#{letter}|" + hsh[letter].join("\t")}.join("\n")
+    else
+      motif.each_position.map{|pos| pos.join("\t")}.join("\n")
+    end
+  end
+  
+  def footer
+    # "\n"
+    ''
+  end
+  
+  
+  def to_s
+    header + matrix_string + footer
+  end
 end

data/lib/bioinform/formatters/transfac_formatter.rb

@@ -1,39 +1,39 @@
-class TransfacFormatter
-  attr_accessor :motif, :options
-  
-  def initialize(motif, options = {})
-    @motif = motif
-    
-    default_options = {with_name: true, letters_as_rows: false}
-    @options = default_options.merge(options)
-  end
-  
-  def name
-    motif.name
-  end
-  
-  def header
-    if options[:with_name] && name
-      "ID #{name}\nBF StubSpeciesName\nP0\tA\tC\tG\tT\n"
-    else
-      raise 'Transfac should have the name field'
-    end
-  end
-  
-  def matrix_string
-    motif.each_position.map.with_index{|pos,ind| 
-      line_number = ind.to_s
-      line_number = (line_number.size == 1) ? "0#{line_number}" : line_number
-      line_number + ' ' + pos.join("\t")
-    }.join("\n")
-  end
-  
-  def footer
-    #"XX\n//\n"
-    "\nXX\n//"
-  end
-  
-  def to_s
-    header + matrix_string + footer
-  end
+class TransfacFormatter
+  attr_accessor :motif, :options
+  
+  def initialize(motif, options = {})
+    @motif = motif
+    
+    default_options = {with_name: true, letters_as_rows: false}
+    @options = default_options.merge(options)
+  end
+  
+  def name
+    motif.name
+  end
+  
+  def header
+    if options[:with_name] && name
+      "ID #{name}\nBF StubSpeciesName\nP0\tA\tC\tG\tT\n"
+    else
+      raise 'Transfac should have the name field'
+    end
+  end
+  
+  def matrix_string
+    motif.each_position.map.with_index{|pos,ind| 
+      line_number = ind.to_s
+      line_number = (line_number.size == 1) ? "0#{line_number}" : line_number
+      line_number + ' ' + pos.join("\t")
+    }.join("\n")
+  end
+  
+  def footer
+    #"XX\n//\n"
+    "\nXX\n//"
+  end
+  
+  def to_s
+    header + matrix_string + footer
+  end
 end

data/lib/bioinform/formatters.rb

@@ -1,2 +1,2 @@
-require_relative 'formatters/raw_formatter'
+require_relative 'formatters/raw_formatter'
 require_relative 'formatters/transfac_formatter'

data/lib/bioinform/parsers/jaspar_parser.rb

@@ -1,35 +1,35 @@
-require_relative '../support'
-require_relative '../parsers/string_parser'
-
-module Bioinform
-  class JasparParser < StringParser
-    def header_pat
-      /(?<name>)/
-    end
-
-    def row_pat
-      /[ACGT]\s*\[\s*(?<row>(#{number_pat}\s+)*#{number_pat})\s*\]\n?/
-    end
-
-    def scan_splitter
-      scanner.scan(/(\/\/\n)+/)
-    end
-
-    def parse_matrix
-      matrix = []
-      while row_string = scan_row
-        matrix << split_row(row_string)
-      end
-      matrix.transpose
-    end
-
-    def parse!
-      scan_any_spaces
-      scan_splitter
-      name = parse_name
-      matrix = parse_matrix
-      Parser.parse!(matrix).tap{|result| result.name = name}
-    end
-
-  end
+require_relative '../support'
+require_relative '../parsers/string_parser'
+
+module Bioinform
+  class JasparParser < StringParser
+    def header_pat
+      /(?<name>)/
+    end
+
+    def row_pat
+      /[ACGT]\s*\[\s*(?<row>(#{number_pat}\s+)*#{number_pat})\s*\]\n?/
+    end
+
+    def scan_splitter
+      scanner.scan(/(\/\/\n)+/)
+    end
+
+    def parse_matrix
+      matrix = []
+      while row_string = scan_row
+        matrix << split_row(row_string)
+      end
+      matrix.transpose
+    end
+
+    def parse!
+      scan_any_spaces
+      scan_splitter
+      name = parse_name
+      matrix = parse_matrix
+      Parser.parse!(matrix).tap{|result| result.name = name}
+    end
+
+  end
 end

data/lib/bioinform/parsers/parser.rb

@@ -1,88 +1,88 @@
-require 'ostruct'
-require_relative '../support'
-require_relative '../data_models/pm'
-require_relative 'splittable_parser'
-
-module Bioinform
-  class Error < StandardError; end
-  class ParsingError < Error; end
-  class InvalidMatrix < Error; end
-  
-  class Parser
-    attr_reader :input
-
-    def initialize(*input)
-      if input.size == 1  # [ [1,2,3,4] ],  [  [[1,2,3,4],[5,6,7,8]] ]
-        if input.first.is_a?(Array) && input.first.all?{|el| el.is_a? Numeric}  # [ [1,2,3,4] ]
-          @input = input
-        else  # [  [[1,2,3,4],[5,6,7,8]] ]
-          @input = input.first
-        end
-      else #[ [1,2,3,4], [5,6,7,8] ], [   ]
-        @input = input
-      end
-    end
-
-    def parse!
-      matrix = self.class.transform_input(input)
-      raise InvalidMatrix unless self.class.valid_matrix?(matrix)
-      OpenStruct.new(matrix: matrix)
-    end
-
-    def parse
-      parse! rescue nil
-    end
-
-    def self.choose(input, data_model = PM)
-      data_model.choose_parser(input).new(input)
-    end
-
-    def self.parse!(*input)
-      self.new(*input).parse!
-    end
-    def self.parse(*input)
-      self.new(*input).parse
-    end
-
-    def self.valid_matrix?(matrix)
-      PM.valid_matrix?(matrix)
-    end
-
-    # {A: 1, C: 2, G: 3, T: 4}  -->  [1,2,3,4]
-    # {A: [1,2], C: [3,4], G: [5,6], T: [7,8]}  --> [[1,3,5,7],[2,4,6,8]] ( == [[1,2], [3,4], [5,6], [7,8]].transpose)
-    def self.array_from_acgt_hash(hsh)
-      hsh = normalize_hash_keys(hsh)
-      raise 'some of hash keys A,C,G,T are missing or hash has excess keys' unless hsh.keys.sort == [:A,:C,:G,:T]
-      result = [:A,:C,:G,:T].collect{|letter| hsh[letter] }
-      result.all?{|el| el.is_a?(Array)} ? result.transpose : result
-    end
-
-    # {a: 1, C: 2, 'g' => 3, 'T' => 4} --> {A: 1, C: 2, G: 3, T: 4}
-    def self.normalize_hash_keys(hsh)
-      hsh.collect_hash{|key,value| [key.to_s.upcase.to_sym, value] }
-    end
-
-    # [[1,2,3,4], [2,3,4,5]] --> [[1,2,3,4], [2,3,4,5]]
-    # [{A:1, C:2, G:3, T:4}, {A:2, C:3, G:4, T:5}] --> [{A:1, C:2, G:3, T:4}, {A:2, C:3, G:4, T:5}]
-    # {:A => [1,2,3], :c => [2,3,4], 'g' => [3,4,5], 'T' => [4,5,6]} --> [[1,2,3],[2,3,4],[3,4,5],[4,5,6]].transpose
-    def self.try_convert_to_array(input)
-      case input
-      when Array then input
-      when Hash then array_from_acgt_hash(input)
-      else raise TypeError, 'input of Bioinform::Parser::array_from_acgt_hash should be Array or Hash'
-      end
-    end
-
-    def self.transform_input(input)
-      result = try_convert_to_array(input).map{|el| try_convert_to_array(el)}
-      need_tranpose?(result) ? result.transpose : result
-    end
-
-    # point whether matrix input positions(need not be transposed -- false) or letters(need -- true) as first index
-    # [[1,3,5,7], [2,4,6,8]] --> false
-    # [[1,2],[3,4],[5,6],[7,8]] --> true
-    def self.need_tranpose?(input)
-      (input.size == 4) && input.any?{|x| x.size != 4}
-    end
-  end
+require 'ostruct'
+require_relative '../support'
+require_relative '../data_models/pm'
+require_relative 'splittable_parser'
+
+module Bioinform
+  class Error < StandardError; end
+  class ParsingError < Error; end
+  class InvalidMatrix < Error; end
+  
+  class Parser
+    attr_reader :input
+
+    def initialize(*input)
+      if input.size == 1  # [ [1,2,3,4] ],  [  [[1,2,3,4],[5,6,7,8]] ]
+        if input.first.is_a?(Array) && input.first.all?{|el| el.is_a? Numeric}  # [ [1,2,3,4] ]
+          @input = input
+        else  # [  [[1,2,3,4],[5,6,7,8]] ]
+          @input = input.first
+        end
+      else #[ [1,2,3,4], [5,6,7,8] ], [   ]
+        @input = input
+      end
+    end
+
+    def parse!
+      matrix = self.class.transform_input(input)
+      raise InvalidMatrix unless self.class.valid_matrix?(matrix)
+      OpenStruct.new(matrix: matrix)
+    end
+
+    def parse
+      parse! rescue nil
+    end
+
+    def self.choose(input, data_model = PM)
+      data_model.choose_parser(input).new(input)
+    end
+
+    def self.parse!(*input)
+      self.new(*input).parse!
+    end
+    def self.parse(*input)
+      self.new(*input).parse
+    end
+
+    def self.valid_matrix?(matrix)
+      PM.valid_matrix?(matrix)
+    end
+
+    # {A: 1, C: 2, G: 3, T: 4}  -->  [1,2,3,4]
+    # {A: [1,2], C: [3,4], G: [5,6], T: [7,8]}  --> [[1,3,5,7],[2,4,6,8]] ( == [[1,2], [3,4], [5,6], [7,8]].transpose)
+    def self.array_from_acgt_hash(hsh)
+      hsh = normalize_hash_keys(hsh)
+      raise 'some of hash keys A,C,G,T are missing or hash has excess keys' unless hsh.keys.sort == [:A,:C,:G,:T]
+      result = [:A,:C,:G,:T].collect{|letter| hsh[letter] }
+      result.all?{|el| el.is_a?(Array)} ? result.transpose : result
+    end
+
+    # {a: 1, C: 2, 'g' => 3, 'T' => 4} --> {A: 1, C: 2, G: 3, T: 4}
+    def self.normalize_hash_keys(hsh)
+      hsh.collect_hash{|key,value| [key.to_s.upcase.to_sym, value] }
+    end
+
+    # [[1,2,3,4], [2,3,4,5]] --> [[1,2,3,4], [2,3,4,5]]
+    # [{A:1, C:2, G:3, T:4}, {A:2, C:3, G:4, T:5}] --> [{A:1, C:2, G:3, T:4}, {A:2, C:3, G:4, T:5}]
+    # {:A => [1,2,3], :c => [2,3,4], 'g' => [3,4,5], 'T' => [4,5,6]} --> [[1,2,3],[2,3,4],[3,4,5],[4,5,6]].transpose
+    def self.try_convert_to_array(input)
+      case input
+      when Array then input
+      when Hash then array_from_acgt_hash(input)
+      else raise TypeError, 'input of Bioinform::Parser::array_from_acgt_hash should be Array or Hash'
+      end
+    end
+
+    def self.transform_input(input)
+      result = try_convert_to_array(input).map{|el| try_convert_to_array(el)}
+      need_tranpose?(result) ? result.transpose : result
+    end
+
+    # point whether matrix input positions(need not be transposed -- false) or letters(need -- true) as first index
+    # [[1,3,5,7], [2,4,6,8]] --> false
+    # [[1,2],[3,4],[5,6],[7,8]] --> true
+    def self.need_tranpose?(input)
+      (input.size == 4) && input.any?{|x| x.size != 4}
+    end
+  end
 end

data/lib/bioinform/parsers/splittable_parser.rb

@@ -1,57 +1,57 @@
-module Bioinform
-  class Parser
-    module SingleMotifParser
-      def self.included(base)
-        base.class_eval { extend ClassMethods }
-        include Enumerable
-        alias_method :split, :to_a
-      end
-      module ClassMethods
-        def split_on_motifs(input, pm_klass = PM)
-          [ input.is_a?(pm_klass) ? self : pm_klass.new(input, self) ]
-        end
-      end
-      def each
-        if block_given?
-          yield self
-        else
-          self.to_enum(:each)
-        end
-      end
-    end
-    include SingleMotifParser
-
-    module MultipleMotifsParser
-      def self.included(base)
-        base.class_eval { extend ClassMethods }
-        include Enumerable
-        alias_method :split, :to_a
-      end
-      module ClassMethods
-        def split_on_motifs(input, pm_klass = PM)
-          split(input).map{|el| el.is_a?(pm_klass) ? el : pm_klass.new(el)}
-        end
-        def split(input)
-          self.new(input).split
-        end
-        private :split
-      end
-
-      def scanner_reset
-      end
-
-      def each
-        if block_given?
-          scanner_reset
-          while result = parse
-            yield result
-          end
-        else
-          self.to_enum(:each)
-        end
-      end
-
-      private :scanner_reset
-    end
-  end
+module Bioinform
+  class Parser
+    module SingleMotifParser
+      def self.included(base)
+        base.class_eval { extend ClassMethods }
+        include Enumerable
+        alias_method :split, :to_a
+      end
+      module ClassMethods
+        def split_on_motifs(input, pm_klass = PM)
+          [ input.is_a?(pm_klass) ? self : pm_klass.new(input, self) ]
+        end
+      end
+      def each
+        if block_given?
+          yield self
+        else
+          self.to_enum(:each)
+        end
+      end
+    end
+    include SingleMotifParser
+
+    module MultipleMotifsParser
+      def self.included(base)
+        base.class_eval { extend ClassMethods }
+        include Enumerable
+        alias_method :split, :to_a
+      end
+      module ClassMethods
+        def split_on_motifs(input, pm_klass = PM)
+          split(input).map{|el| el.is_a?(pm_klass) ? el : pm_klass.new(el)}
+        end
+        def split(input)
+          self.new(input).split
+        end
+        private :split
+      end
+
+      def scanner_reset
+      end
+
+      def each
+        if block_given?
+          scanner_reset
+          while result = parse
+            yield result
+          end
+        else
+          self.to_enum(:each)
+        end
+      end
+
+      private :scanner_reset
+    end
+  end
 end

data/lib/bioinform/parsers/string_fantom_parser.rb

@@ -1,35 +1,35 @@
-require_relative '../support'
-require_relative '../parsers/string_parser'
-
-module Bioinform
-  class StringFantomParser < StringParser
-    def header_pat
-      /NA (?<name>[\w.+:-]+)\n[\w\d]+ A C G T.*\n/
-    end
-
-    def row_pat
-      /[\w\d]+ (?<row>(#{number_pat} )*#{number_pat})\n?/
-    end
-
-    def scan_splitter
-      scanner.scan(/(\/\/\n)+/)
-    end
-
-    def parse_matrix
-      matrix = []
-      while row_string = scan_row
-        matrix << split_row(row_string)[0,4]
-      end
-      matrix.transpose
-    end
-
-    def parse!
-      scan_any_spaces
-      scan_splitter
-      name = parse_name
-      matrix = parse_matrix
-      Parser.parse!(matrix).tap{|result| result.name = name}
-    end
-
-  end
+require_relative '../support'
+require_relative '../parsers/string_parser'
+
+module Bioinform
+  class StringFantomParser < StringParser
+    def header_pat
+      /NA (?<name>[\w.+:-]+)\n[\w\d]+ A C G T.*\n/
+    end
+
+    def row_pat
+      /[\w\d]+ (?<row>(#{number_pat} )*#{number_pat})\n?/
+    end
+
+    def scan_splitter
+      scanner.scan(/(\/\/\n)+/)
+    end
+
+    def parse_matrix
+      matrix = []
+      while row_string = scan_row
+        matrix << split_row(row_string)[0,4]
+      end
+      matrix.transpose
+    end
+
+    def parse!
+      scan_any_spaces
+      scan_splitter
+      name = parse_name
+      matrix = parse_matrix
+      Parser.parse!(matrix).tap{|result| result.name = name}
+    end
+
+  end
 end