bioinform 0.1.16 → 0.1.17

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 58c71a402e76e3edcd2105b21dd19a84b37b4c80
-  data.tar.gz: f300eba436a2b06c5b5feef4bb3fb95c0397b0a7
+  metadata.gz: 792006e928db4e7ce443f56f93b94e9f5cbc2e95
+  data.tar.gz: f7f4f25e156071fee5f242cc50ecdcd80741b596
 SHA512:
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-  data.tar.gz: f2162a51dec39a7c500474ac4739c40869c00be3b9f837224e35f21137436ea9a827b0d99d5e82d617f0aff30fa30da3dbfed3066d4684fe4cc629f96f3e8443
+  metadata.gz: 4d0c1b14cba03745ecdf19b14579533489619f22f584e3fda64a77b4d72ba0998930b8239ceb5212b0d09ca6aa88879abc29057354cd8b4650ae35dab5845a7e
+  data.tar.gz: 8e0a3b680e4e5ef765697abd6c0c449dc303ea75c1d886aef4c01a4a34f38a67008ac9bf2dc4f173ba0f7a3cd769cd22424670689fa727946bcc15767a5689ed

data/lib/bioinform/data_models/pm.rb

@@ -23,7 +23,7 @@ module Bioinform
 #    end
 
     def self.choose_parser(input)
-      [TrivialParser, YAMLParser, Parser, StringParser, StringFantomParser, JasparParser, TrivialCollectionParser, YAMLCollectionParser].find do |parser|
+      [TrivialParser, YAMLParser, Parser, StringParser, Bioinform::MatrixParser.new(has_name: false).wrapper, Bioinform::MatrixParser.new(has_name: true).wrapper, StringFantomParser, JasparParser, TrivialCollectionParser, YAMLCollectionParser].find do |parser|
         self.new(input, parser) rescue nil
       end
     end
@@ -40,6 +40,7 @@ module Bioinform
       raise 'No one parser can process input'  unless parser
       result = parser.new(input).parse
       @matrix = result.matrix
+      raise 'Non valid matrix' unless self.class.valid_matrix?(@matrix)
       self.name = result.name
 #      self.tags = result.tags || []
       self.background = result.background || [1, 1, 1, 1]

data/lib/bioinform/data_models/pwm.rb

@@ -1,5 +1,6 @@
 require_relative '../support'
 require_relative '../data_models'
+
 module Bioinform
   class PWM < PM
     def score_mean

data/lib/bioinform/parsers/matrix_parser.rb

@@ -1,3 +1,5 @@
+require 'ostruct'
+
 module Bioinform  
   class MatrixParser
     def initialize(options = {})
@@ -24,7 +26,7 @@ module Bioinform
 
       matrix = matrix.transpose  if @nucleotides_in == :rows
       # raise 'Matrix not valid' unless ! matrix.empty? && matrix.all?{|pos| pos.size == 4 }
-      {matrix: matrix, name: name}
+      OpenStruct.new(matrix: matrix, name: name)
     end
 
     def parse(input)
@@ -36,5 +38,28 @@ module Bioinform
     rescue
       false
     end
+
+    class TemporaryWrapper
+      attr_reader :input
+      include Bioinform::Parser::ClassMethods
+      include Bioinform::Parser::SingleMotifParser::ClassMethods
+      def initialize(parser)
+        @parser, input = parser, input
+      end
+      def parse
+        @parser.parse(@input)
+      end
+      def parse!
+        @parser.parse!(@input)
+      end
+      def new(input)
+        @input = input
+        self
+      end
+    end
+
+    def wrapper
+      TemporaryWrapper.new(self)
+    end
   end
 end

data/lib/bioinform/parsers/parser.rb

@@ -33,56 +33,60 @@ module Bioinform
       parse! rescue nil
     end
 
-    def self.choose(input, data_model = PM)
-      data_model.choose_parser(input).new(input)
-    end
+    module ClassMethods
+      def 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 parse!(*input)
+        new(*input).parse!
+      end
+      def parse(*input)
+        new(*input).parse
+      end
 
-    def self.valid_matrix?(matrix)
-      PM.valid_matrix?(matrix)
-    end
+      def 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}  -->  [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 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
+      # {a: 1, C: 2, 'g' => 3, 'T' => 4} --> {A: 1, C: 2, G: 3, T: 4}
+      def 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'
+      # [[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 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
-    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
+      def 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}
+      # 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 need_tranpose?(input)
+        (input.size == 4) && input.any?{|x| x.size != 4}
+      end
     end
+
+    extend ClassMethods
   end
 end

data/lib/bioinform/version.rb

@@ -1,3 +1,3 @@
 module Bioinform
-  VERSION = "0.1.16"
+  VERSION = "0.1.17"
 end

data/spec/data_models/pm_spec.rb

@@ -3,15 +3,15 @@ require_relative '../../lib/bioinform/data_models/pm'
 
 module Bioinform
   describe PM do
-    {:as_pcm => PCM, :as_pwm => PWM, :as_ppm => PPM}.each do |converter_method, result_klass|
+    {:as_pcm => [PCM, [[1,10,3,4],[5,6,7,0]]], :as_pwm => [PWM, [[1,2,3,4],[5,6,7,8]]], :as_ppm => [PPM, [[0.1,0.2,0.3,0.4],[0.5,0.1,0.3,0.1]]]}.each do |converter_method, (result_klass, matrix)|
       describe "##{converter_method}" do
         before :each do
           @collection = Collection.new(name: 'Collection 1')
-          @matrix = [[1,2,3,4],[5,6,7,8]]
+          @matrix = matrix
           @name = 'PM_motif'
           @background = [0.2,0.3,0.3,0.2]
           @tags = [@collection, 'Collection 2']
-          @pm = PM.new(matrix: @matrix, name: @name, background: @background, tags: @tags)
+          @pm = PM.new(matrix: matrix, name: @name, background: @background, tags: @tags)
           @conv_motif = @pm.send converter_method
         end
         it "should return an instance of #{result_klass}" do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bioinform
 version: !ruby/object:Gem::Version
-  version: 0.1.16
+  version: 0.1.17
 platform: ruby
 authors:
 - Ilya Vorontsov
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-26 00:00:00.000000000 Z
+date: 2014-05-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: docopt