bioinform 0.1.5 → 0.1.6

data/.gitignore

@@ -14,5 +14,4 @@ rdoc
 spec/reports
 test/tmp
 test/version_tmp
-tmp
-TODO.txt
+tmp

data/TODO.txt

@@ -0,0 +1,18 @@
+Create Collection class. Rewrite MACRO-APE to use this class.
+
+Create CLI-apps:
+-- to merge many files(or whole folder) to a Collection
+
+Make Parsers to be switcheable in runtime so that one could parse string composed of two motifs in different formats.
+
+Decide:
+-- Whether PPM should have `words_count`/`weight`?
+   PPM format such that parser got both matrix and count (if PPM have `word_count`)
+-- can_parse?
+-- Whether to cache suffices:  cache :best_suffix, obsolete: [:discrete!, :background!, ...]
+
+Specs
+-- PM#==  (!)
+-- PWM#probabilities, #score_variance, #gauss_estimation
+-- pcm2pwm
+-- split_motifs

data/bin/pcm2pwm

@@ -0,0 +1,4 @@
+#!/usr/bin/env ruby
+
+require 'bioinform/cli/pcm2pwm'
+Bioinform::CLI::PCM2PWM.main(ARGV)

data/bin/split_motifs

@@ -0,0 +1,4 @@
+#!/usr/bin/env ruby
+
+require 'bioinform/cli/split_motifs'
+Bioinform::CLI::SplitMotifs.main(ARGV)

data/lib/bioinform/cli/pcm2pwm.rb

@@ -0,0 +1,47 @@
+require 'bioinform'
+require 'docopt'
+require 'shellwords'
+
+module Bioinform
+  module CLI
+    module PCM2PWM
+      def self.main(argv)
+        doc = <<-DOCOPT
+PCM to PWM converter.
+It transforms files with PCMs into files with PWMs. Folder for resulting files to save files can be specified. Resulting PWM files have the same name as original file but have another extension (.pwm by default).
+When filelist is empty, it's obtained from STDIN. One can use it: `ls -b pcm_folder/*.pcm | pcm2pwm` (ls -b option escape spaces in filenames)
+
+Usage:
+  #{__FILE__} [options] [<pcm-files>...]
+  
+Options:
+  -h --help           Show this screen.
+  -e --extension EXT  Extension of output files [default: pwm]
+  -f --folder FOLDER  Where to save output files [default: .]
+        DOCOPT
+
+        options = Docopt::docopt(doc, argv: argv)
+        
+        if options['<pcm-files>'].empty?
+          filelist = $stdin.read.shellsplit
+        else
+          filelist = options['<pcm-files>']
+        end
+        
+        folder = options['--folder']
+        Dir.mkdir(folder)  unless Dir.exist?(folder)
+        
+        filelist.each do |pcm_filename|
+          pwm = Bioinform::PCM.new( File.read(pcm_filename) ).to_pwm
+          File.open(Bioinform::CLI.output_filename(pcm_filename, options['--extension'], folder), 'w') do |f|
+            f.puts pwm
+          end
+        end
+        
+      rescue Docopt::Exit => e
+        puts e.message
+      end
+      
+    end
+  end
+end

data/lib/bioinform/cli/split_motifs.rb

@@ -0,0 +1,46 @@
+require 'bioinform'
+require 'docopt'
+
+module Bioinform
+  module CLI
+    module SplitMotifs
+      
+      def self.main(argv)
+        doc = <<-DOCOPT
+Motif splitter.
+It get a file with a set of motifs and splits it into motifs according to their names.
+
+Usage:
+  #{__FILE__} [options] <collection-file>
+  
+Options:
+  -h --help                Show this screen.
+  -m --data-model MODEL    Data model: PM, PCM, PPM or PWM [default: PM]
+  -e --extension EXT       Extension of output files (by default it's based on data model)
+  -f --folder FOLDER       Where to save output files [default: .]
+        DOCOPT
+
+        options = Docopt::docopt(doc, argv: argv)
+        
+        folder = options['--folder']
+        Dir.mkdir(folder)  unless Dir.exist?(folder)
+        
+        data_model = Bioinform.const_get(options['--data-model'].upcase)
+        extension = options['--extension'] || options['--data-model'].downcase
+        
+        collection_filename = options['<collection-file>']
+        raise "File #{collection_filename} not exist"  unless File.exist? collection_filename
+        input = File.read(collection_filename)
+        
+        data_model.choose_parser(input).split_on_motifs(input, data_model).each do |motif|
+          File.open(File.join(folder, "#{motif.name}.#{extension}"), 'w') do |f|
+            f.puts motif
+          end
+        end
+      rescue Docopt::Exit => e
+        puts e.message
+      end
+      
+    end
+  end
+end

data/lib/bioinform/cli.rb

@@ -0,0 +1,7 @@
+module Bioinform
+  module CLI
+    def self.output_filename(input_filename, extension, folder)
+      File.join(folder, File.basename(input_filename, File.extname(input_filename)) + ".#{extension}")
+    end
+  end
+end

data/lib/bioinform/data_models/pcm.rb

@@ -1,7 +1,6 @@
 require 'bioinform/support'
-require 'bioinform/data_models/pm'
-require 'bioinform/data_models/ppm'
-require 'bioinform/data_models/pwm'
+require 'bioinform/data_models'
+
 module Bioinform
   class PCM < PM
     def count

data/lib/bioinform/data_models/pm.rb

@@ -32,9 +32,9 @@ module Bioinform
     def self.valid_matrix?(matrix)
       matrix.is_a?(Array) &&
       ! matrix.empty? &&
-      matrix.all?(&:is_a?.(Array)) &&
+      matrix.all?{|pos| pos.is_a?(Array)} &&
       matrix.all?{|pos| pos.size == 4} &&
-      matrix.all?(&:all?.(&:is_a?.(Numeric)))
+      matrix.all?{|pos| pos.all?{|el| el.is_a?(Numeric)}}
     rescue 
       false
     end
@@ -56,22 +56,37 @@ module Bioinform
     end
     alias_method :size, :length
     
-    def to_s(with_name = true)
-      matrix_str = each_position.map(&:join.("\t")).join("\n")
-      if with_name && @name 
+    def to_s(options = {})
+      default_options = {with_name: true, letters_as_rows: false}
+      options = default_options.merge(options)
+      if options[:letters_as_rows]
+        hsh = to_hash
+        matrix_str = [:A,:C,:G,:T].collect{|letter| "#{letter}|" + hsh[letter].join("\t")}.join("\n")
+      else
+        matrix_str = each_position.map{|pos| pos.join("\t")}.join("\n")
+      end
+      
+      if options[:with_name] && @name 
         @name + "\n" + matrix_str
       else 
         matrix_str
       end
     end
     
-    def pretty_string(with_name = true)
+    def pretty_string(options = {})
+      default_options = {with_name: true, letters_as_rows: false}
+      
+      return to_s(options)  if options[:letters_as_rows]
+      
+      options = default_options.merge(options)
       header = %w{A C G T}.map{|el| el.rjust(4).ljust(7)}.join + "\n"
       matrix_rows = each_position.map do |position|
         position.map{|el| el.round(3).to_s.rjust(6)}.join(' ')
       end
+      
       matrix_str = matrix_rows.join("\n")
-      if with_name && @name
+      
+      if options[:with_name] && @name
         @name + "\n" + header + matrix_str
       else
         header + matrix_str
@@ -80,7 +95,7 @@ module Bioinform
     
     def to_hash
       hsh = %w{A C G T}.each_with_index.collect_hash do |letter, letter_index| 
-        [ letter, @matrix.map(&:at.(letter_index)) ]
+        [ letter, @matrix.map{|pos| pos[letter_index]} ]
       end
       hsh.with_indifferent_access
     end

data/lib/bioinform/data_models/ppm.rb

@@ -1,5 +1,5 @@
 require 'bioinform/support'
-require 'bioinform/data_models/pm'
+require 'bioinform/data_models'
 
 module Bioinform
   class PPM < PM

data/lib/bioinform/data_models/pwm.rb

@@ -1,5 +1,5 @@
 require 'bioinform/support'
-require 'bioinform/data_models/pm'
+require 'bioinform/data_models'
 module Bioinform
   class PWM < PM
     def score_mean

data/lib/bioinform/data_models.rb

@@ -2,7 +2,8 @@ require 'bioinform/parsers'
 
 require 'bioinform/data_models/pm'
 require 'bioinform/data_models/pcm'
-require 'bioinform/data_models/pwm'
 require 'bioinform/data_models/ppm'
+require 'bioinform/data_models/pwm'
+
 #require 'bioinform/data_models/iupac_word'
 #require 'bioinform/data_models/iupac_wordset'

data/lib/bioinform/parsers/parser.rb

@@ -27,6 +27,10 @@ module Bioinform
       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

data/lib/bioinform/parsers/string_parser.rb

@@ -4,7 +4,7 @@ require 'bioinform/parsers/parser'
 
 module Bioinform  
   class StringParser < Parser
-    attr_reader :scanner
+    attr_reader :scanner, :row_acgt_markers
     def initialize(input)
       raise ArgumentError  unless input.is_a?(String)
       super
@@ -20,7 +20,7 @@ module Bioinform
     end
     
     def row_pat 
-      /(?<row>(#{number_pat} )*#{number_pat})\n?/
+      /([ACGT]\s*[:|]?\s*)?(?<row>(#{number_pat} )*#{number_pat})\n?/
     end
     
     def scan_row
@@ -43,16 +43,23 @@ module Bioinform
     
     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).merge(name: name)
     end
     
@@ -80,6 +87,5 @@ module Bioinform
     def self.split_on_motifs(input, pm_klass = PM)
       split(input).map{|el| pm_klass.new(el)}
     end
-
   end
 end

data/lib/bioinform/support.rb

@@ -1,13 +1,10 @@
 require 'active_support/core_ext/string/filters'
 require 'active_support/core_ext/hash/indifferent_access'
 
-require 'bioinform/support/callable_symbol'
 require 'bioinform/support/collect_hash'
 require 'bioinform/support/delete_many'
-require 'bioinform/support/has_keys'
 require 'bioinform/support/multiline_squish'
 require 'bioinform/support/same_by'
-require 'bioinform/support/yaml_dump_file'
 require 'bioinform/support/inverf'
 require 'bioinform/support/deep_dup'
 

data/lib/bioinform/version.rb

@@ -1,3 +1,3 @@
 module Bioinform
-  VERSION = "0.1.5"
+  VERSION = "0.1.6"
 end

data/lib/bioinform.rb

@@ -1,6 +1,8 @@
 require 'bioinform/version'
 require 'bioinform/support'
+require 'bioinform/parsers'
 require 'bioinform/data_models'
+require 'bioinform/cli'
 
 module Bioinform
   # Your code goes here...

data/spec/cli/cli_spec.rb

@@ -0,0 +1,13 @@
+require 'spec_helper'
+require 'bioinform/cli'
+
+describe Bioinform::CLI do
+  describe '::output_filename' do
+    it 'should change extension and folder' do
+      Bioinform::CLI.output_filename('test.pcm', 'pwm', '.').should == './test.pwm'
+      Bioinform::CLI.output_filename('test.pcm', 'pat', 'pwm_folder').should == 'pwm_folder/test.pat'
+      Bioinform::CLI.output_filename('pcm/test.pcm', 'pat', 'pwm_folder').should == 'pwm_folder/test.pat'
+      Bioinform::CLI.output_filename('test.pcm', 'pat', '../pwm_folder').should == '../pwm_folder/test.pat'
+    end
+  end
+end

data/spec/cli/pcm2pwm_spec.rb

@@ -0,0 +1,6 @@
+require 'spec_helper'
+require 'bioinform/cli/pcm2pwm'
+
+describe Bioinform::CLI::PCM2PWM do
+
+end

data/spec/cli/split_motifs_spec.rb

@@ -0,0 +1,6 @@
+require 'spec_helper'
+require 'bioinform/cli/split_motifs'
+
+describe Bioinform::CLI::SplitMotifs do
+
+end

data/spec/data_models/pm_spec.rb

@@ -34,7 +34,12 @@ module Bioinform
           @pm.to_s.should == "Stub name\n1\t2\t3\t4\n1\t4\t5\t6.5"
         end
         it 'should not return a name if argument is set to false' do
-          @pm.to_s(false).should == "1\t2\t3\t4\n1\t4\t5\t6.5"
+          @pm.to_s(with_name: false).should == "1\t2\t3\t4\n1\t4\t5\t6.5"
+        end
+      end
+      context 'in letters_as_rows mode' do
+        it 'should print matrix with row-markers' do
+          @pm.to_s(letters_as_rows: true).should == "A|1\t1\nC|2\t4\nG|3\t5\nT|4\t6.5"
         end
       end
     end
@@ -62,7 +67,7 @@ module Bioinform
           @pm.pretty_string.should match(/MyName\n/)
         end
         it 'should not contain name if parameter `with_name` is false' do
-          @pm.pretty_string(false).should_not match(/MyName\n/)
+          @pm.pretty_string(with_name: false).should_not match(/MyName\n/)
         end
       end
       context 'without name specified' do
@@ -71,7 +76,13 @@ module Bioinform
         end
         it 'should not contain name whether parameter `with_name` is or isn\'t false' do
           @pm.pretty_string.should_not match(/MyName\n/)
-          @pm.pretty_string(false).should_not match(/MyName\n/)
+          @pm.pretty_string(with_name: false).should_not match(/MyName\n/)
+        end
+      end
+      context 'in letters_as_rows mode' do
+        it 'should print matrix with row-markers as to_s do' do
+          @pm = PM.new( [[1.1,2.22,3.333,4.4444],[5.5,6.66,7.777,8.8888]] )
+          @pm.pretty_string(letters_as_rows: true).should == @pm.to_s(letters_as_rows: true)
         end
       end
     end

data/spec/parsers/parser_spec.rb

@@ -28,6 +28,19 @@ module Bioinform
       end
     end
     
+    context '::choose' do
+      it 'should create parser of appropriate type' do
+        Parser.choose([[1,2,3,4],[5,6,7,8]]).should be_kind_of(Parser)
+        Parser.choose([[1,2,3,4],[5,6,7,8]]).input.should == [[1,2,3,4],[5,6,7,8]]
+        Parser.choose(matrix: [[1,2,3,4],[5,6,7,8]], name: 'Name').should be_kind_of(TrivialParser)
+        Parser.choose(matrix: [[1,2,3,4],[5,6,7,8]], name: 'Name').input.should == {matrix: [[1,2,3,4],[5,6,7,8]], name: 'Name'}
+        Parser.choose("1 2 3 4\n5 6 7 8").should be_kind_of(StringParser)
+        Parser.choose("1 2 3 4\n5 6 7 8").input.should == "1 2 3 4\n5 6 7 8"
+      end
+      
+    end
+
+    
     context '::normalize_hash_keys' do
       it 'should convert both symbolic and string keys, in both upcase and downcase to symbolic upcases' do
         Parser.normalize_hash_keys( {a: 1, C: 2, 'g' => 3, 'T' => 4} ).should == {A: 1, C: 2, G: 3, T: 4}

data/spec/parsers/string_parser_spec.rb

@@ -79,7 +79,25 @@ module Bioinform
                       matrix: [[1,2,3,4],[5,6,7,8]] },
       
       'string with windows crlf' => {input: "1 2 3 4\r\n5 6 7 8",
-                      matrix: [[1,2,3,4],[5,6,7,8]] }      
+                      matrix: [[1,2,3,4],[5,6,7,8]] },
+                      
+      'Nx4 string with acgt-header' => {input: "A C G T\n1 2 3 4\n5 6 7 8", 
+                      matrix: [[1,2,3,4],[5,6,7,8]] },
+                      
+      'Nx4 string with name and acgt-header' => {input: "Name\nA C G T\n1 2 3 4\n5 6 7 8", 
+                      matrix: [[1,2,3,4],[5,6,7,8]], name: 'Name'},
+      
+      'Nx4 string with acgt-row-markers' => {input: "A 1 5\nC : 2 6\nG3 7\nT |4 8", 
+                      matrix: [[1,2,3,4],[5,6,7,8]] },
+      
+      '4x4 string with acgt-header' => {input: "A C G T\n1 2 3 4\n5 6 7 8\n0 0 0 0\n2 2 2 2", 
+                      matrix: [[1,2,3,4],[5,6,7,8],[0,0,0,0],[2,2,2,2]] },
+      
+      '4x4 string with acgt-row-markers' => {input: "A|1 2 3 4\nC|5 6 7 8\nG|0 0 0 0\nT|2 2 2 2", 
+                      matrix: [[1,5,0,2],[2,6,0,2],[3,7,0,2],[4,8,0,2]] },
+                      
+      '4x4 string with name and acgt-row-markers' => {input: "Name\nA:1 2 3 4\nC:5 6 7 8\nG:0 0 0 0\nT:2 2 2 2", 
+                      matrix: [[1,5,0,2],[2,6,0,2],[3,7,0,2],[4,8,0,2]], name: 'Name' }
     }
     
     bad_cases = {

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bioinform
 version: !ruby/object:Gem::Version
-  version: 0.1.5
+  version: 0.1.6
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-09-01 00:00:00.000000000 Z
+date: 2012-09-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport
@@ -46,7 +46,9 @@ dependencies:
 description: A bunch of useful classes for bioinformatics
 email:
 - prijutme4ty@gmail.com
-executables: []
+executables:
+- pcm2pwm
+- split_motifs
 extensions: []
 extra_rdoc_files: []
 files:
@@ -55,8 +57,14 @@ files:
 - LICENSE
 - README.md
 - Rakefile
+- TODO.txt
+- bin/pcm2pwm
+- bin/split_motifs
 - bioinform.gemspec
 - lib/bioinform.rb
+- lib/bioinform/cli.rb
+- lib/bioinform/cli/pcm2pwm.rb
+- lib/bioinform/cli/split_motifs.rb
 - lib/bioinform/data_models.rb
 - lib/bioinform/data_models/collection.rb
 - lib/bioinform/data_models/pcm.rb
@@ -72,17 +80,17 @@ files:
 - lib/bioinform/support/advanced_scan.rb
 - lib/bioinform/support/array_product.rb
 - lib/bioinform/support/array_zip.rb
-- lib/bioinform/support/callable_symbol.rb
 - lib/bioinform/support/collect_hash.rb
 - lib/bioinform/support/deep_dup.rb
 - lib/bioinform/support/delete_many.rb
-- lib/bioinform/support/has_keys.rb
 - lib/bioinform/support/inverf.rb
 - lib/bioinform/support/multiline_squish.rb
 - lib/bioinform/support/partial_sums.rb
 - lib/bioinform/support/same_by.rb
-- lib/bioinform/support/yaml_dump_file.rb
 - lib/bioinform/version.rb
+- spec/cli/cli_spec.rb
+- spec/cli/pcm2pwm_spec.rb
+- spec/cli/split_motifs_spec.rb
 - spec/data_models/pcm_spec.rb
 - spec/data_models/pm_spec.rb
 - spec/data_models/ppm_spec.rb
@@ -95,10 +103,8 @@ files:
 - spec/support/advanced_scan_spec.rb
 - spec/support/array_product_spec.rb
 - spec/support/array_zip_spec.rb
-- spec/support/callable_symbol_spec.rb
 - spec/support/collect_hash_spec.rb
 - spec/support/delete_many_spec.rb
-- spec/support/has_keys_spec.rb
 - spec/support/inverf_spec.rb
 - spec/support/multiline_squish_spec.rb
 - spec/support/partial_sums_spec.rb
@@ -131,6 +137,9 @@ summary: Classes for work with different input formats of positional matrices an
   several useful extensions for Enumerable module like parametric map and callable
   symbols
 test_files:
+- spec/cli/cli_spec.rb
+- spec/cli/pcm2pwm_spec.rb
+- spec/cli/split_motifs_spec.rb
 - spec/data_models/pcm_spec.rb
 - spec/data_models/pm_spec.rb
 - spec/data_models/ppm_spec.rb
@@ -143,10 +152,8 @@ test_files:
 - spec/support/advanced_scan_spec.rb
 - spec/support/array_product_spec.rb
 - spec/support/array_zip_spec.rb
-- spec/support/callable_symbol_spec.rb
 - spec/support/collect_hash_spec.rb
 - spec/support/delete_many_spec.rb
-- spec/support/has_keys_spec.rb
 - spec/support/inverf_spec.rb
 - spec/support/multiline_squish_spec.rb
 - spec/support/partial_sums_spec.rb

data/lib/bioinform/support/callable_symbol.rb

@@ -1,50 +0,0 @@
-# Useful extension for &:symbol - syntax to make it possible to pass arguments for method in block
-#   ['abc','','','def','ghi'].tap(&:delete.(''))             # ==> ['abc','def','ghi']
-#   [1,2,3].map(&:to_s.(2))                                  # ==> ['1','10','11']
-#   ['abc','cdef','xy','z','wwww'].select(&:size.() == 4)    # ==> ['cdef', 'wwww']
-#   ['abc','aaA','AaA','z'].count(&:upcase.().succ == 'AAB') # ==> 2
-#   [%w{1 2 3 4 5},%w{6 7 8 9}].map(&:join.().length)         # ==> [5,4]
-class Symbol
-  def call(*args, &block)
-    obj = BasicObject.new.instance_exec(self,args,block) do |meth,params,block| 
-      @postprocess_meth = [meth]
-      @postprocess_args = [params]
-      @postprocess_block = [block]
-      self
-    end
-    
-    def obj.to_proc
-      # proc/lambda are methods that cannot be used in BasicObject. It's possible to use ->(slf){...} syntax since ruby-1.9.3 p194 but it's too modern and not widely spreaded yet
-      ::Proc.new do |slf| 
-        @postprocess_meth.zip(@postprocess_args,@postprocess_block).inject(slf) do |result,(call_meth,call_args,call_block)| 
-          result.send(call_meth, *call_args,&call_block) 
-        end
-      end
-    end
-    
-    def obj.method_missing(meth,*args,&block)
-      @postprocess_meth << meth
-      @postprocess_args << args
-      @postprocess_block << block
-      self
-    end
-    
-    def obj.==(other)
-      method_missing(:==, other)
-    end
-    
-    obj
-  end
-end
-
-
-=begin
-# Much simplier but ['abc','cdef','xy','z','wwww'].select(&:size.() == 4) wouldn't work
-class Symbol
-  def call(*args, &block)
-    proc do |recv|
-      recv.__send__(self, *args, &block)
-    end
-  end
-end
-=end

data/lib/bioinform/support/has_keys.rb

@@ -1,14 +0,0 @@
-class Hash
-  def has_all_keys?(*keys)
-    keys.all?{|key| has_key? key}
-  end
-  def has_any_key?(*keys)
-    keys.any?{|key| has_key? key}
-  end
-  def has_none_key?(*keys)
-    keys.none?{|key| has_key? key}
-  end
-  def has_one_key?(*keys)
-    keys.one?{|key| has_key? key}
-  end
-end

data/lib/bioinform/support/yaml_dump_file.rb

@@ -1,5 +0,0 @@
-require 'yaml'
-
-def YAML.dump_file(obj,filename)
-  File.open(filename, 'w'){|f| YAML.dump(obj,f)}
-end

data/spec/support/callable_symbol_spec.rb

@@ -1,66 +0,0 @@
-require 'spec_helper'
-require 'bioinform/support/callable_symbol'
-
-# TODO: organize and write more correct descriptions
-describe Symbol do
-  describe '#call' do
-    context 'when symbol curries a block' do
-      it 'should pass a block to a corresponding proc' do
-        :map.(&:to_s).to_proc.call([1,2,3]).should == ['1','2','3']
-        [[1,2,3],[4,5,6]].map(&:map.(&:to_s)).should == [['1','2','3'],['4','5','6']]
-        [[1,2,3],[4,5,6]].map(&:map.(&:to_s.(2))).should == [['1','10','11'],['100','101','110']]
-        ['abc','cdef','xy','z','wwww'].select(&:size.() == 4).should == ['cdef', 'wwww']
-        
-        [%w{1 2 3 4 5},%w{6 7 8 9 10}].map(&:join.().length).should == [5,6]  # method chaining
-        ['abc','aaA','AaA','z'].count(&:upcase.().succ == 'AAB').should == 2 # method chaining with ==
-        [[1,2,3]].map(  &:map.(&:to_s.(2)).map(&:to_i)  ).should == [[1,10,11]]  # method chaining with block on initial symbol and on later symbols
-      end
-    end
-  
-    context 'returned object' do
-      
-      it 'should have to_proc method' do
-        expect { :to_s.() }.to respond_to :to_proc
-        expect { :to_s.(2) }.to respond_to :to_proc
-        expect { :to_s.(2) == '110' }.to respond_to :to_proc
-        expect { :to_s.(2).postprocess('arg1','arg2') }.to respond_to :to_proc
-      end
-      
-      context 'corresponding proc' do
-        it 'should call method, corresponding to symbol, on first argument' do
-          stub_obj = double('obj')
-          stub_obj.should_receive(:to_s).exactly(:twice)
-          prc_1 = :to_s.(2).to_proc
-          prc_2 = :to_s.(2).to_proc # When used with &, to_proc can be omitted: it's implicitly casted on call (see other examples)
-          prc_1.call(stub_obj) # These forms are almost equivalent, but second is much more concise
-          stub_obj.tap(&prc_2)
-        end
-        context 'when multiple arguments of call specified' do
-          it 'should call using given arguments' do
-            stub_obj = double('obj')
-            stub_obj.should_receive(:gsub).with('before','after')
-            prc = :gsub.('before','after')
-            stub_obj.tap(&prc)
-          end
-        end
-        context 'when the only argument of call specified' do
-          it 'should call using given argument' do
-            stub_obj = double('obj')
-            stub_obj.should_receive(:to_s).with(2)
-            prc = :to_s.(2)
-            stub_obj.tap(&prc)
-          end
-        end
-        context 'when no arguments given' do
-          it 'should call without any arguments' do
-            stub_obj = double('obj')
-            stub_obj.should_receive(:to_s).with()
-            prc = :to_s.()
-            stub_obj.tap(&prc)
-          end
-        end
-      end
-      
-    end
-  end
-end

data/spec/support/has_keys_spec.rb

@@ -1,48 +0,0 @@
-require 'spec_helper'
-require 'bioinform/support/has_keys'
-
-describe Hash do
-  describe '#has_all_keys?' do
-    it 'should be true if all given keys are at place' do
-      {a: 3, b: 6, c: 7, d: 13}.has_all_keys?(:a, :c).should be_true
-    end
-    
-    it 'should be false if any given of keys is missing' do
-      {a: 3, b: 6, c: 7, d: 13}.has_all_keys?(:a, :x).should be_false
-    end
-  end
-  
-  describe '#has_any_key?' do
-    it 'should be true if any of given keys is at place' do
-      {a: 3, b: 6, c: 7, d: 13}.has_any_key?(:a, :x).should be_true
-    end
-    
-    it 'should be false if no one of given is missing' do
-      {a: 3, b: 6, c: 7, d: 13}.has_any_key?(:x, :y).should be_false
-    end
-  end
-  
-  describe '#has_none_key?' do
-    it 'should be true if all given keys are missing' do
-      {a: 3, b: 6, c: 7, d: 13}.has_none_key?(:x, :y).should be_true
-    end
-    
-    it 'should be false if any of given keys is at place' do
-      {a: 3, b: 6, c: 7, d: 13}.has_none_key?(:a, :y).should be_false
-    end
-  end
-  
-  describe '#has_one_key?' do
-    it 'should be true if one of given keys is present' do
-      {a: 3, b: 6, c: 7, d: 13}.has_one_key?(:x, :a).should be_true
-    end
-    
-    it 'should be false if many of given keys are present' do
-      {a: 3, b: 6, c: 7, d: 13}.has_one_key?(:a, :c).should be_false
-    end
-    
-    it 'should be false if none of given keys is at place' do
-      {a: 3, b: 6, c: 7, d: 13}.has_one_key?(:x, :y).should be_false
-    end
-  end
-end