bioinform 0.1.12 → 0.1.13

data/lib/bioinform/parsers/string_parser.rb

@@ -1,72 +1,72 @@
-require 'strscan'
-require_relative '../support'
-require_relative '../parsers/parser'
-
-module Bioinform
-  class StringParser < Parser
-    include MultipleMotifsParser
-    attr_reader :scanner, :row_acgt_markers
-
-    def initialize(input)
-      raise ArgumentError, 'StringParser should be initialized with a String'  unless input.is_a?(String)
-      super
-      @scanner = StringScanner.new(input.multiline_squish)
-    end
-
-    def number_pat
-      /[+-]?\d+(\.\d+)?([eE][+-]?\d{1,3})?/
-    end
-
-    def header_pat
-      />?\s*(?<name>\S+)\n/
-    end
-
-    def row_pat
-      /([ACGT]\s*[:|]?\s*)?(?<row>(#{number_pat} )*#{number_pat})\n?/
-    end
-
-    def scan_row
-      match = scanner.advanced_scan(row_pat)
-      match && match[:row]
-    end
-
-    def split_row(row_string)
-      row_string.split.map(&:to_f)
-    end
-
-    def scan_any_spaces
-      scanner.scan(/\s+/)
-    end
-
-    def parse_name
-      match = scanner.advanced_scan(header_pat)
-      match && match[:name]
-    end
-
-    def parse_matrix
-      matrix = []
-      @row_acgt_markers = true  if scanner.check(/A.*\nC.*\nG.*\nT.*\n?/)
-      while row_string = scan_row
-        matrix << split_row(row_string)
-      end
-      matrix
-    end
-
-    def parse_acgt_header
-      scanner.scan(/A\s*C\s*G\s*T\s*\n/i)
-    end
-
-    def parse!
-      scan_any_spaces
-      name = parse_name
-      parse_acgt_header
-      matrix = parse_matrix
-      matrix = matrix.transpose if row_acgt_markers
-      Parser.parse!(matrix).tap{|result| result.name = name}
-    end
-
-    def scanner_reset
-      scanner.reset
-    end
-  end
+require 'strscan'
+require_relative '../support'
+require_relative '../parsers/parser'
+
+module Bioinform
+  class StringParser < Parser
+    include MultipleMotifsParser
+    attr_reader :scanner, :row_acgt_markers
+
+    def initialize(input)
+      raise ArgumentError, 'StringParser should be initialized with a String'  unless input.is_a?(String)
+      super
+      @scanner = StringScanner.new(input.multiline_squish)
+    end
+
+    def number_pat
+      /[+-]?\d+(\.\d+)?([eE][+-]?\d{1,3})?/
+    end
+
+    def header_pat
+      />?\s*(?<name>\S+)\n/
+    end
+
+    def row_pat
+      /([ACGT]\s*[:|]?\s*)?(?<row>(#{number_pat} )*#{number_pat})\n?/
+    end
+
+    def scan_row
+      match = scanner.advanced_scan(row_pat)
+      match && match[:row]
+    end
+
+    def split_row(row_string)
+      row_string.split.map(&:to_f)
+    end
+
+    def scan_any_spaces
+      scanner.scan(/\s+/)
+    end
+
+    def parse_name
+      match = scanner.advanced_scan(header_pat)
+      match && match[:name]
+    end
+
+    def parse_matrix
+      matrix = []
+      @row_acgt_markers = true  if scanner.check(/A.*\nC.*\nG.*\nT.*\n?/)
+      while row_string = scan_row
+        matrix << split_row(row_string)
+      end
+      matrix
+    end
+
+    def parse_acgt_header
+      scanner.scan(/A\s*C\s*G\s*T\s*\n/i)
+    end
+
+    def parse!
+      scan_any_spaces
+      name = parse_name
+      parse_acgt_header
+      matrix = parse_matrix
+      matrix = matrix.transpose if row_acgt_markers
+      Parser.parse!(matrix).tap{|result| result.name = name}
+    end
+
+    def scanner_reset
+      scanner.reset
+    end
+  end
 end

data/lib/bioinform/parsers/trivial_parser.rb

@@ -1,34 +1,34 @@
-require_relative '../support'
-require_relative '../parsers/parser'
-require_relative '../data_models/collection'
-require 'yaml'
-
-module Bioinform
-  # TrivialParser can be used to parse hashes returned by #parse method of other parsers:
-  # PM.new({matrix:[[1,2,3,4],[5,6,7,8]], name: 'Name'}, TrivialParser)
-  # PM.new(StringParser.new("1 2 3 4\n5 6 7 8").parse)
-  # StringParser.new("First\n1 2 3 4\n5 6 7 8\nSecond\n0 0 0 0").map{|inp| PM.new(inp, TrivialParser)}
-  class TrivialParser < Parser
-    def initialize(input)
-      @input = input
-    end
-    def parse!
-      case input
-      when PM then input
-      when Motif then input.pm
-      when OpenStruct then input
-      when Hash then OpenStruct.new(input)
-      end
-    end
-  end
-
-  class TrivialCollectionParser < Parser
-    include MultipleMotifsParser
-    def initialize(input)
-      @input = input
-    end
-    def parse!
-      input.container.shift.pm
-    end
-  end
+require_relative '../support'
+require_relative '../parsers/parser'
+require_relative '../data_models/collection'
+require 'yaml'
+
+module Bioinform
+  # TrivialParser can be used to parse hashes returned by #parse method of other parsers:
+  # PM.new({matrix:[[1,2,3,4],[5,6,7,8]], name: 'Name'}, TrivialParser)
+  # PM.new(StringParser.new("1 2 3 4\n5 6 7 8").parse)
+  # StringParser.new("First\n1 2 3 4\n5 6 7 8\nSecond\n0 0 0 0").map{|inp| PM.new(inp, TrivialParser)}
+  class TrivialParser < Parser
+    def initialize(input)
+      @input = input
+    end
+    def parse!
+      case input
+      when PM then input
+      when Motif then input.pm
+      when OpenStruct then input
+      when Hash then OpenStruct.new(input)
+      end
+    end
+  end
+
+  class TrivialCollectionParser < Parser
+    include MultipleMotifsParser
+    def initialize(input)
+      @input = input
+    end
+    def parse!
+      input.container.shift.pm
+    end
+  end
 end

data/lib/bioinform/parsers/yaml_parser.rb

@@ -1,35 +1,35 @@
-require_relative '../support'
-require_relative 'parser'
-require_relative '../data_models/collection'
-require 'yaml'
-
-module Bioinform
-  # YAMLParser can be used to parse hashes returned by #parse method of other parsers:
-  # yaml_dump_of_pm = PM.new(...).to_yaml
-  # PM.new(yaml_dump_of_pm, YAMLParser)
-  class YAMLParser < Parser
-    def initialize(input)
-      @input = input
-    end
-    def parse!
-      YAML.load(input)
-    rescue Psych::SyntaxError
-      raise 'parsing error'
-    end
-  end
-
-  class YAMLCollectionParser < Parser
-    include MultipleMotifsParser
-    def initialize(input)
-      @input = input
-    end
-    def collection
-      @collection ||= YAML.load(input)
-    end
-    def parse!
-      collection.container.shift.pm
-    rescue Psych::SyntaxError
-      raise 'parsing error'
-    end
-  end
+require_relative '../support'
+require_relative 'parser'
+require_relative '../data_models/collection'
+require 'yaml'
+
+module Bioinform
+  # YAMLParser can be used to parse hashes returned by #parse method of other parsers:
+  # yaml_dump_of_pm = PM.new(...).to_yaml
+  # PM.new(yaml_dump_of_pm, YAMLParser)
+  class YAMLParser < Parser
+    def initialize(input)
+      @input = input
+    end
+    def parse!
+      YAML.load(input)
+    rescue Psych::SyntaxError
+      raise 'parsing error'
+    end
+  end
+
+  class YAMLCollectionParser < Parser
+    include MultipleMotifsParser
+    def initialize(input)
+      @input = input
+    end
+    def collection
+      @collection ||= YAML.load(input)
+    end
+    def parse!
+      collection.container.shift.pm
+    rescue Psych::SyntaxError
+      raise 'parsing error'
+    end
+  end
 end

data/lib/bioinform/parsers.rb

@@ -1,7 +1,7 @@
-require_relative 'parsers/parser'
-require_relative 'parsers/trivial_parser'
-require_relative 'parsers/yaml_parser'
-require_relative 'parsers/string_parser'
-require_relative 'parsers/string_fantom_parser'
-require_relative 'parsers/splittable_parser'
+require_relative 'parsers/parser'
+require_relative 'parsers/trivial_parser'
+require_relative 'parsers/yaml_parser'
+require_relative 'parsers/string_parser'
+require_relative 'parsers/string_fantom_parser'
+require_relative 'parsers/splittable_parser'
 require_relative 'parsers/jaspar_parser'

data/lib/bioinform/support/array_product.rb

@@ -1,6 +1,6 @@
-class Array
-  def self.product(*arrays)
-    return []  if arrays.empty?
-    arrays.first.product(*arrays[1..-1])
-  end
+class Array
+  def self.product(*arrays)
+    return []  if arrays.empty?
+    arrays.first.product(*arrays[1..-1])
+  end
 end

data/lib/bioinform/support/array_zip.rb

@@ -1,6 +1,6 @@
-class Array
-  def self.zip(*arrays)
-    return []  if arrays.empty?
-    arrays.first.zip(*arrays[1..-1])
-  end
+class Array
+  def self.zip(*arrays)
+    return []  if arrays.empty?
+    arrays.first.zip(*arrays[1..-1])
+  end
 end

data/lib/bioinform/support/collect_hash.rb

@@ -1,7 +1,7 @@
-module Enumerable
-  # %w{A C G T}.collect_hash{|k| [k*2, k*3] }
-  # # ==> {"AA" => "AAA", "CC" => "CCC", "GG" => "GGG", "TT" => "TTT"}
-  def collect_hash(&block)
-    block_given?  ?  Hash[ collect(&block) ]  :  Hash[ collect{|k,v| [k,v]} ]
-  end
+module Enumerable
+  # %w{A C G T}.collect_hash{|k| [k*2, k*3] }
+  # # ==> {"AA" => "AAA", "CC" => "CCC", "GG" => "GGG", "TT" => "TTT"}
+  def collect_hash(&block)
+    block_given?  ?  Hash[ collect(&block) ]  :  Hash[ collect{|k,v| [k,v]} ]
+  end
 end

data/lib/bioinform/support/deep_dup.rb

@@ -1,5 +1,5 @@
-class Object
-  def deep_dup
-    Marshal.load(Marshal.dump(self))
-  end
+class Object
+  def deep_dup
+    Marshal.load(Marshal.dump(self))
+  end
 end

data/lib/bioinform/support/delete_many.rb

@@ -1,14 +1,14 @@
-class Array
-  def delete_at_many(*indices)
-    indices.uniq.sort.reverse.each{|ind| delete_at ind}
-  end
-  def delete_many(*elements)
-    elements.each{|el| delete el}
-  end
-end
-
-class Hash
-  def delete_many(*keys)
-    keys.each{|el| delete el}
-  end
+class Array
+  def delete_at_many(*indices)
+    indices.uniq.sort.reverse.each{|ind| delete_at ind}
+  end
+  def delete_many(*elements)
+    elements.each{|el| delete el}
+  end
+end
+
+class Hash
+  def delete_many(*keys)
+    keys.each{|el| delete el}
+  end
 end

data/lib/bioinform/support/inverf.rb

@@ -1,13 +1,13 @@
-module Math
-  def self.inverf(x)
-    sign = x < 0 ? -1 : 1
-    x = x.abs
-    a = 8 / (3*Math::PI) * (Math::PI-3) / (4-Math::PI)
-    part0 = ( 2/(Math::PI*a) + (Math.log(1-x*x)) / 2 )**2
-    part = -2 / (Math::PI * a) - Math.log(1-x*x)/2 + Math.sqrt(-1/a * Math.log(1-x*x) + part0)
-    sign * Math.sqrt(part)
-  end
-  def inverf(x)
-    Math.inverf(x)
-  end
+module Math
+  def self.inverf(x)
+    sign = x < 0 ? -1 : 1
+    x = x.abs
+    a = 8 / (3*Math::PI) * (Math::PI-3) / (4-Math::PI)
+    part0 = ( 2/(Math::PI*a) + (Math.log(1-x*x)) / 2 )**2
+    part = -2 / (Math::PI * a) - Math.log(1-x*x)/2 + Math.sqrt(-1/a * Math.log(1-x*x) + part0)
+    sign * Math.sqrt(part)
+  end
+  def inverf(x)
+    Math.inverf(x)
+  end
 end

data/lib/bioinform/support/multiline_squish.rb

@@ -1,6 +1,6 @@
-require_relative 'third_part/active_support/core_ext/string/filters'
-class String
-  def multiline_squish
-    split("\n").map(&:squish).join("\n").gsub(/\A\n+/,'').gsub(/\n+\z/,'')
-  end
+require_relative 'third_part/active_support/core_ext/string/filters'
+class String
+  def multiline_squish
+    split("\n").map(&:squish).join("\n").gsub(/\A\n+/,'').gsub(/\n+\z/,'')
+  end
 end

data/lib/bioinform/support/parameters.rb

@@ -1,28 +1,28 @@
-require 'ostruct'
-module Bioinform
-  module Parameters
-    def self.included(base)
-      base.extend(ClassMethods)
-    end
-    module ClassMethods
-      def make_parameters(*params)
-        params.each do |param|
-          define_method(param){ parameters.send(param) }
-          define_method("#{param}="){|new_value| parameters.send("#{param}=", new_value) }
-        end
-      end
-    end
-    def parameters; @parameters ||= OpenStruct.new; end
-    def set_parameters(hsh)
-      hsh.each{|k,v| send("#{k}=", v) }
-      self
-    end
-    # return hash of parameters
-    def get_parameters
-      @parameters.marshal_dump
-    end
-    def parameter_defined?(param_name)
-      get_parameters.has_key?(param_name)
-    end
-  end
+require 'ostruct'
+module Bioinform
+  module Parameters
+    def self.included(base)
+      base.extend(ClassMethods)
+    end
+    module ClassMethods
+      def make_parameters(*params)
+        params.each do |param|
+          define_method(param){ parameters.send(param) }
+          define_method("#{param}="){|new_value| parameters.send("#{param}=", new_value) }
+        end
+      end
+    end
+    def parameters; @parameters ||= OpenStruct.new; end
+    def set_parameters(hsh)
+      hsh.each{|k,v| send("#{k}=", v) }
+      self
+    end
+    # return hash of parameters
+    def get_parameters
+      @parameters.marshal_dump
+    end
+    def parameter_defined?(param_name)
+      get_parameters.has_key?(param_name)
+    end
+  end
 end

data/lib/bioinform/support/partial_sums.rb

@@ -1,16 +1,16 @@
-require_relative 'collect_hash'
-
-class Array
-  def partial_sums(initial = 0.0)
-    sums = initial
-    map{|el| sums += el}
-  end
-end
-
-class Hash
-# {1 => 5, 4 => 3, 3 => 2}.partial_sums == {1=>5, 3=>7, 4=>10}
-  def partial_sums(initial = 0.0)
-    sums = initial
-    sort.collect_hash{|k,v| [k, sums += v]}
-  end
+require_relative 'collect_hash'
+
+class Array
+  def partial_sums(initial = 0.0)
+    sums = initial
+    map{|el| sums += el}
+  end
+end
+
+class Hash
+# {1 => 5, 4 => 3, 3 => 2}.partial_sums == {1=>5, 3=>7, 4=>10}
+  def partial_sums(initial = 0.0)
+    sums = initial
+    sort.collect_hash{|k,v| [k, sums += v]}
+  end
 end

data/lib/bioinform/support/same_by.rb

@@ -1,12 +1,12 @@
-module Enumerable
-  def same_by?(&block)
-    return true if empty?
-    if block_given?
-      first_result = yield(first)
-      all?{|el| first_result == yield(el)}
-    else
-      first_result = first
-      all?{|el| first_result == el}
-    end
-  end
-end
+module Enumerable
+  def same_by?(&block)
+    return true if empty?
+    if block_given?
+      first_result = yield(first)
+      all?{|el| first_result == yield(el)}
+    else
+      first_result = first
+      all?{|el| first_result == el}
+    end
+  end
+end

data/lib/bioinform/support/strip_doc.rb

@@ -1,9 +1,9 @@
-def strip_doc(doc)
-  doc.strip_doc
-end
-
-class String
-  def strip_doc
-    gsub(/^#{self[/\A +/]}/,'')
-  end
+def strip_doc(doc)
+  doc.strip_doc
+end
+
+class String
+  def strip_doc
+    gsub(/^#{self[/\A +/]}/,'')
+  end
 end

data/lib/bioinform/support/third_part/active_support/hash_with_indifferent_access.rb

@@ -3,6 +3,7 @@ require_relative 'core_ext/hash/keys'
 # This class has dubious semantics and we only have it so that
 # people can write <tt>params[:key]</tt> instead of <tt>params['key']</tt>
 # and they get the same value for both keys.
+unless defined? ActiveSupport::HashWithIndifferentAccess
 
 module ActiveSupport
   class HashWithIndifferentAccess < Hash
@@ -176,3 +177,5 @@ module ActiveSupport
 end
 
 HashWithIndifferentAccess = ActiveSupport::HashWithIndifferentAccess
+
+end

data/lib/bioinform/support.rb

@@ -1,18 +1,18 @@
-require_relative 'support/third_part/active_support/core_ext/string/filters'
-require_relative 'support/third_part/active_support/core_ext/hash/indifferent_access'
-
-require_relative 'support/collect_hash'
-require_relative 'support/delete_many'
-require_relative 'support/multiline_squish'
-require_relative 'support/same_by'
-require_relative 'support/inverf'
-require_relative 'support/deep_dup'
-
-require_relative 'support/partial_sums'
-
-require_relative 'support/array_zip'
-require_relative 'support/array_product'
-
-require_relative 'support/advanced_scan'
-require_relative 'support/parameters'
+require_relative 'support/third_part/active_support/core_ext/string/filters'
+require_relative 'support/third_part/active_support/core_ext/hash/indifferent_access'
+
+require_relative 'support/collect_hash'
+require_relative 'support/delete_many'
+require_relative 'support/multiline_squish'
+require_relative 'support/same_by'
+require_relative 'support/inverf'
+require_relative 'support/deep_dup'
+
+require_relative 'support/partial_sums'
+
+require_relative 'support/array_zip'
+require_relative 'support/array_product'
+
+require_relative 'support/advanced_scan'
+require_relative 'support/parameters'
 require_relative 'support/strip_doc'

data/lib/bioinform/version.rb

@@ -1,3 +1,3 @@
-module Bioinform
-  VERSION = "0.1.12"
-end
+module Bioinform
+  VERSION = "0.1.13"
+end

data/lib/bioinform.rb

@@ -1,10 +1,10 @@
-require_relative 'bioinform/version'
-require_relative 'bioinform/support'
-require_relative 'bioinform/parsers'
-require_relative 'bioinform/formatters'
-require_relative 'bioinform/data_models'
-require_relative 'bioinform/cli'
-
-module Bioinform
-  # Your code goes here...
-end
+require_relative 'bioinform/version'
+require_relative 'bioinform/support'
+require_relative 'bioinform/parsers'
+require_relative 'bioinform/formatters'
+require_relative 'bioinform/data_models'
+require_relative 'bioinform/cli'
+
+module Bioinform
+  # Your code goes here...
+end

data/spec/cli/cli_spec.rb

@@ -1,14 +1,14 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/cli'
-
-describe Bioinform::CLI do
-  describe '.change_folder_and_extension' do
-    it 'should change extension and folder' do
-      extend Bioinform::CLI::Helpers
-      change_folder_and_extension('test.pcm', 'pwm', '.').should == './test.pwm'
-      change_folder_and_extension('test.pcm', 'pat', 'pwm_folder').should == 'pwm_folder/test.pat'
-      change_folder_and_extension('pcm/test.pcm', 'pat', 'pwm_folder').should == 'pwm_folder/test.pat'
-      change_folder_and_extension('test.pcm', 'pat', '../pwm_folder').should == '../pwm_folder/test.pat'
-    end
-  end
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/cli'
+
+describe Bioinform::CLI do
+  describe '.change_folder_and_extension' do
+    it 'should change extension and folder' do
+      extend Bioinform::CLI::Helpers
+      change_folder_and_extension('test.pcm', 'pwm', '.').should == './test.pwm'
+      change_folder_and_extension('test.pcm', 'pat', 'pwm_folder').should == 'pwm_folder/test.pat'
+      change_folder_and_extension('pcm/test.pcm', 'pat', 'pwm_folder').should == 'pwm_folder/test.pat'
+      change_folder_and_extension('test.pcm', 'pat', '../pwm_folder').should == '../pwm_folder/test.pat'
+    end
+  end
 end