bioinform 0.0.1 → 0.1.0

data/spec/support/same_by_spec.rb

@@ -0,0 +1,36 @@
+require 'spec_helper'
+require 'bioinform/support/same_by'
+
+describe Enumerable do
+  describe '#same_by?' do
+    it 'should be work with both hashes and arrays' do
+      ['a','b','c'].same_by?{|k| k.length}
+      {'a'=>13,'b'=>12,'c'=>14}.same_by?{|k,v| v < 20}
+    end
+    it 'should be true for empty collections' do
+      [].same_by?(&:length).should be_true
+      [].same_by?.should be_true
+    end
+    context 'without block' do
+      it 'should compare if all elements of collection are the same' do
+        %w{cat cat cat}.same_by?.should be_true
+        %w{cat dog rat}.same_by?.should be_false
+      end
+    end
+    context 'with a block' do
+      it 'should compare enumerables by a value of block' do
+        %w{cat dog rat}.same_by?(&:length).should be_true
+        %w{cat dog rabbit}.same_by?(&:length).should be_false
+      end
+      it 'should be true if all elements are true' do
+        [4,8,2,2].same_by?(&:even?).should be_true
+      end
+      it 'should be true if all elements are false' do
+        [1,3,9,7].same_by?(&:even?).should be_true
+      end
+      it 'should be false if some elements are true and some are false' do
+        [1,8,3,2].same_by?(&:even?).should be_false
+      end
+    end
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bioinform
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.1.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-30 00:00:00.000000000 Z
+date: 2012-06-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: active_support
@@ -58,26 +58,53 @@ files:
 - bioinform.gemspec
 - lib/bioinform.rb
 - lib/bioinform/data_models.rb
-- lib/bioinform/data_models/iupac.rb
-- lib/bioinform/data_models/iupac_word.rb
-- lib/bioinform/data_models/positional_count_matrix.rb
-- lib/bioinform/data_models/positional_matrix.rb
-- lib/bioinform/data_models/positional_probability_matrix.rb
-- lib/bioinform/data_models/positional_weight_matrix.rb
+- lib/bioinform/data_models/collection.rb
+- lib/bioinform/data_models/old_style_models_TO_BE_REMOVED/iupac.rb
+- lib/bioinform/data_models/old_style_models_TO_BE_REMOVED/iupac_word.rb
+- lib/bioinform/data_models/old_style_models_TO_BE_REMOVED/positional_count_matrix.rb
+- lib/bioinform/data_models/old_style_models_TO_BE_REMOVED/positional_matrix.rb
+- lib/bioinform/data_models/old_style_models_TO_BE_REMOVED/positional_probability_matrix.rb
+- lib/bioinform/data_models/old_style_models_TO_BE_REMOVED/positional_weight_matrix.rb
+- lib/bioinform/data_models/parser.rb
+- lib/bioinform/data_models/parsers.rb
+- lib/bioinform/data_models/parsers/array_parser.rb
+- lib/bioinform/data_models/parsers/hash_parser.rb
+- lib/bioinform/data_models/parsers/string_fantom_parser.rb
+- lib/bioinform/data_models/parsers/string_parser.rb
+- lib/bioinform/data_models/pcm.rb
+- lib/bioinform/data_models/pm.rb
+- lib/bioinform/data_models/ppm.rb
+- lib/bioinform/data_models/pwm.rb
 - lib/bioinform/support.rb
 - lib/bioinform/support/callable_symbol.rb
+- lib/bioinform/support/collect_hash.rb
 - lib/bioinform/support/curry_except_self.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/pmap.rb
-- lib/bioinform/support/ptap.rb
-- lib/bioinform/support/same.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/callable_symbol_spec.rb
-- spec/pmap_test.rb
-- spec/positional_matrix_spec.rb
-- spec/ptap_spec.rb
-- spec/same_spec.rb
+- spec/data_models/parser_spec.rb
+- spec/data_models/parsers/array_parser_spec.rb
+- spec/data_models/parsers/hash_parser_spec.rb
+- spec/data_models/parsers/string_fantom_parser_spec.rb
+- spec/data_models/parsers/string_parser_spec.rb
+- spec/data_models/pm_spec.rb
+- spec/data_models/pwm_spec.rb
+- spec/spec_helper.rb
+- spec/support/callable_symbol_spec.rb
+- spec/support/collect_hash_spec.rb
+- spec/support/curry_except_self_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
+- spec/support/same_by_spec.rb
 homepage: ''
 licenses: []
 post_install_message: 
@@ -106,8 +133,20 @@ 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/callable_symbol_spec.rb
-- spec/pmap_test.rb
-- spec/positional_matrix_spec.rb
-- spec/ptap_spec.rb
-- spec/same_spec.rb
+- spec/data_models/parser_spec.rb
+- spec/data_models/parsers/array_parser_spec.rb
+- spec/data_models/parsers/hash_parser_spec.rb
+- spec/data_models/parsers/string_fantom_parser_spec.rb
+- spec/data_models/parsers/string_parser_spec.rb
+- spec/data_models/pm_spec.rb
+- spec/data_models/pwm_spec.rb
+- spec/spec_helper.rb
+- spec/support/callable_symbol_spec.rb
+- spec/support/collect_hash_spec.rb
+- spec/support/curry_except_self_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
+- spec/support/same_by_spec.rb

data/lib/bioinform/support/pmap.rb

@@ -1,10 +0,0 @@
-require 'bioinform/support/curry_except_self'
-
-module Enumerable
-  def pmap!(*args,&block)
-    map! &block.curry_except_self(*args)
-  end
-  def pmap(*args,&block)
-    dup.pmap!(*args, &block)
-  end
-end

data/lib/bioinform/support/ptap.rb

@@ -1,7 +0,0 @@
-require 'bioinform/support/curry_except_self'
-class Object
-  def ptap(*args,&block)
-    tap &block.curry_except_self(*args)
-  end
-end
-

data/spec/callable_symbol_spec.rb

@@ -1,37 +0,0 @@
-require 'test/unit'
-require 'bioinform/support/callable_symbol'
-
-class TestEnumerablePmap < Test::Unit::TestCase
-  def test_with_tap
-    assert_equal ['abc','def','ghi'], ['abc','','','def','ghi'].tap(&:delete.(''))
-    
-    x = ['abc','','','def','ghi']
-    assert_equal false, ['abc','def','ghi'].equal?(x.tap(&:delete.('')))
-    
-    x = ['abc','','','def','ghi']
-    assert_equal true, x.equal?(x.tap(&:delete.('')))
-    
-    x = ['abc','','','def','ghi']
-    assert_equal ['abc','','','def','ghi'], ['abc','','','def','ghi'].tap(&:to_s)
-  end
-  
-  def test_pmap_bang_without_parameters
-    x = [1,2,3]
-    assert_equal x.map!(&:to_s), ['1', '2', '3']
-    assert_equal x, ['1', '2', '3']
-  end
-  def test_with_map_bang_with_parameters
-    y = [1,2,3]
-    assert_equal y.map!(&:to_s.(2)), ['1', '10', '11']
-    assert_equal y, ['1', '10', '11']
-  end
-  def test_with_map_without_bang
-    x = [1,2,3]
-    assert_equal x.map(&:to_s.(2)), ['1', '10', '11']
-    assert_equal x, [1, 2, 3]
-  end
-  def test_one_more_with_map
-    assert_equal [[1,2,3],[4,5,6]].map(&:join.(' ')).join("\n"), "1 2 3\n4 5 6"
-    assert_equal [1,2,3,4,5].map(&:to_s.(2)), ['1', '10', '11', '100', '101']
-  end
-end

data/spec/pmap_test.rb

@@ -1,24 +0,0 @@
-require 'test/unit'
-require 'bioinform/support/pmap'
-
-class TestEnumerablePmap < Test::Unit::TestCase
-  def test_pmap_bang_without_parameters
-    x = [1,2,3]
-    assert_equal x.pmap!(&:to_s), ['1', '2', '3']
-    assert_equal x, ['1', '2', '3']
-  end
-  def test_pmap_bang_with_parameters
-    y = [1,2,3]
-    assert_equal y.pmap!(2, &:to_s), ['1', '10', '11']
-    assert_equal y, ['1', '10', '11']
-  end
-  def test_pmap_without_bang
-    x = [1,2,3]
-    assert_equal x.pmap(2, &:to_s), ['1', '10', '11']
-    assert_equal x, [1, 2, 3]
-  end
-  def test_one_more_pmap
-    assert_equal [[1,2,3],[4,5,6]].pmap(' ',&:join).join("\n"), "1 2 3\n4 5 6"
-    assert_equal [1,2,3,4,5].pmap(2,&:to_s), ['1', '10', '11', '100', '101']
-  end
-end

data/spec/positional_matrix_spec.rb

@@ -1,169 +0,0 @@
-require 'test/unit'
-require 'bioinform/data_models/positional_matrix'
-
-class PositionalMatrixTest < Test::Unit::TestCase
-  def test_input_has_name
-    m = PositionalMatrix.new <<-EOF
-      > Testmatrix_1
-      1.23 4.56 1.2  1.0
-      1.45 1.23 1.48 1.9
-      -5.6 7  4.56 10.1
-      4.13 -15.6  8.7 0.0
-      2.2 3.3 4.4 5.5
-    EOF
-    assert_equal m.matrix, [[1.23, 4.56, 1.2,  1.0], [1.45, 1.23, 1.48, 1.9], [-5.6, 7, 4.56, 10.1], [4.13, -15.6, 8.7, 0.0],[2.2, 3.3, 4.4, 5.5]]
-    assert_equal m.name, 'Testmatrix_1'
-  end
-  
-  def test_input_has_tabs_and_multiple_spaces_and_carriage_returns_at_eol
-    m = PositionalMatrix.new <<-EOF
-      1.23\t4.56 1.2  1.0\r
-      1.45 1.23   1.48 1.9\r
-      -5.6 7.8  4.56 10.1
-      4.13 -15.6\t\t8.7 0.0
-      2.2 3.3 4.4 5.5
-    EOF
-    assert_equal m.matrix, [[1.23, 4.56, 1.2,  1.0], [1.45, 1.23, 1.48, 1.9], [-5.6, 7.8, 4.56, 10.1], [4.13, -15.6, 8.7, 0.0],[2.2, 3.3, 4.4, 5.5]]
-  end
-
-  def test_input_has_finishing_and_leading_newlines
-    m = PositionalMatrix.new <<-EOF
-      
-      > Testmatrix_1
-      1.23 4.56 1.2  1.0
-      1.45 1.23 1.48 1.9
-      -5.6 7  4.56 10.1
-      4.13 -15.6  8.7 0.0
-      2.2 3.3 4.4 5.5
-      
-    EOF
-    assert_equal m.matrix, [[1.23, 4.56, 1.2,  1.0], [1.45, 1.23, 1.48, 1.9], [-5.6, 7.0, 4.56, 10.1], [4.13, -15.6, 8.7, 0.0],[2.2, 3.3, 4.4, 5.5]]
-  end
-  
-  def test_input_has_no_name
-    m = PositionalMatrix.new <<-EOF
-      1.23 4.56 1.2  1.0
-      1.45 1.23 1.48 1.9
-      -5.6 7  4.56 10.1
-      4.13 -15.6  8.7 0.0
-      2.2 3.3 4.4 5.5
-    EOF
-    assert_equal m.matrix, [[1.23, 4.56, 1.2,  1.0], [1.45, 1.23, 1.48, 1.9], [-5.6, 7.0, 4.56, 10.1], [4.13, -15.6, 8.7, 0.0],[2.2, 3.3, 4.4, 5.5]]
-    assert_equal m.name, nil
-  end
-  
-  def test_input_positions_as_rows
-  m = PositionalMatrix.new <<-EOF
-      Testmatrix-2
-      1.23 4.56 1.2  1.0 78 12.3
-      1.45 1.23 1.48 1.9 10.1 12.0
-      -5.6 7  4.56 10.1 4 12
-      4.13 -15.6  8.7 0.0 1.1 5
-    EOF
-    assert_equal m.matrix, [[1.23, 1.45, -5.6,  4.13], [4.56, 1.23, 7.0, -15.6], [1.2, 1.48, 4.56, 8.7], [1.0, 1.9, 10.1, 0.0],[78, 10.1, 4.0, 1.1], [12.3, 12.0, 12.0, 5.0]]
-    assert_equal m.name, 'Testmatrix-2'
-  end
-  
-  def test_fails_on_nonnumeric_data
-    assert_raise ArgumentError do
-      m = PositionalMatrix.new <<-EOF
-        1.23ss 4.56ww 1.2  1.0
-        1.45zz 1.23 1.48 1.9
-        -5.6 7  4.56 10.1
-        4.13 -15.6  8.7 0.0
-        2.2 3.3 4.4 5.5
-      EOF
-    end
-  end
-  
-  def test_fails_on_different_row_size
-    assert_raise ArgumentError do
-      m = PositionalMatrix.new <<-EOF
-        > Testmatrix_1
-        1.23 4.56 1.2  1.0
-        1.45 1.23 1.48
-        -5.6 7  4.56 10.1
-        4.13 -15.6  8.7 0.0
-        2.2 3.3 4.4 5.5
-      EOF
-    end
-  end
-  
-  def test_fails_if_either_row_nor_col_has_size_4
-    assert_raise ArgumentError do
-    m = PositionalMatrix.new <<-EOF
-      1 2 3 4 5 
-      2 2 -2 2 2
-      3 3 3 3 3
-      4 -4 4 -4 -4 
-      5 5 -5 -5 5
-    EOF
-    end
-  end  
-  
-  def test_to_s
-    m = PositionalMatrix.new <<-EOF
-      > Testmatrix_1
-      1.23 4.56  1.2  1.0
-      1.45 1.23  1.48 1.9
-      -5.6 7  4.56 10.1
-      4.13 -15.6   8.7 0.0
-      2.2 3.3 4.4 5.5
-    EOF
-    assert_equal m.to_s, "Testmatrix_1\n1.23\t4.56\t1.2\t1.0\n1.45\t1.23\t1.48\t1.9\n-5.6\t7.0\t4.56\t10.1\n4.13\t-15.6\t8.7\t0.0\n2.2\t3.3\t4.4\t5.5"
-    assert_equal m.to_s(false), "1.23\t4.56\t1.2\t1.0\n1.45\t1.23\t1.48\t1.9\n-5.6\t7.0\t4.56\t10.1\n4.13\t-15.6\t8.7\t0.0\n2.2\t3.3\t4.4\t5.5"
-  end
-  
-  def test_pretty_string
-    m = PositionalMatrix.new <<-EOF
-      > Testmatrix_1
-      1.23 4.56  1.2  1.0
-      1.45 1.23  1.48 1.9
-      -5.6 7  4.56 10.1
-      4.13 -15.6   8.7 0.0
-      2.2 3.3 4.4 5.5
-    EOF
-    assert_equal m.pretty_string, "Testmatrix_1\n   A      C      G      T   \n  1.23   4.56    1.2    1.0\n  1.45   1.23   1.48    1.9\n  -5.6    7.0   4.56   10.1\n  4.13  -15.6    8.7    0.0\n   2.2    3.3    4.4    5.5"
-    assert_equal m.pretty_string(false), "   A      C      G      T   \n  1.23   4.56    1.2    1.0\n  1.45   1.23   1.48    1.9\n  -5.6    7.0   4.56   10.1\n  4.13  -15.6    8.7    0.0\n   2.2    3.3    4.4    5.5"
-  end
-  
-  def test_to_hash
-    m = PositionalMatrix.new <<-EOF
-      > Testmatrix_1
-      1.23 4.56  1.2  1.0
-      1.45 1.23  1.48 1.9
-      -5.6 7  4.56 10.1
-      4.13 -15.6   8.7 0.0
-      2.2 3.3 4.4 5.5
-    EOF
-    assert_equal m.to_hash, {A: [1.23, 1.45, -5.6, 4.13, 2.2], C:[4.56, 1.23, 7.0, -15.6, 3.3], G:[1.2, 1.48, 4.56, 8.7, 4.4], T:[1.0, 1.9, 10.1, 0.0, 5.5]}.with_indifferent_access
-  end
-  
-  def test_hash_input
-    m = PositionalMatrix.new(A: [1.23, 1.45, -5.6, 4.13, 2.2], C:[4.56, 1.23, 7, -15.6, 3.3],'G' => [1.2, 1.48, 4.56, 8.7, 4.4], 'T'=>[1.0, 1.9, 10.1, 0.0, 5.5])
-    assert_equal m.matrix, [[1.23, 4.56, 1.2,  1.0], [1.45, 1.23, 1.48, 1.9], [-5.6, 7.0, 4.56, 10.1], [4.13, -15.6, 8.7, 0.0],[2.2, 3.3, 4.4, 5.5]]
-  end
-  
-  def test_size
-    m = PositionalMatrix.new(A: [1.23, 1.45, -5.6, 4.13, 2.2], C:[4.56, 1.23, 7, -15.6, 3.3],'G' => [1.2, 1.48, 4.56, 8.7, 4.4], 'T'=>[1.0, 1.9, 10.1, 0.0, 5.5])
-    assert_equal m.size, 5
-    assert_equal m.length, m.size
-  end
-  
-  def test_fantom_parser
-    input = <<-EOS
-      NA  motif_CTNCAG					
-      P0	A	C	G	T	
-      P1	0	1878368	0	0	
-      P2	0	0	0	1878368	
-      P3	469592	469592	469592	469592	
-      P4	0	1878368	0	0	
-      P5	1878368	0	0	0	
-      P6	0	0	1878368	0	
-    EOS
-    m = PositionalMatrix.new input, PositionalMatrix::FantomParser
-    assert_equal 'motif_CTNCAG', m.name
-    assert_equal [[0,1878368,0,0],[0,0,0,1878368],[469592,469592,469592,469592],[0,1878368,0,0],[1878368,0,0,0],[0,0,1878368,0]], m.matrix
-  end
-  
-end

data/spec/ptap_spec.rb

@@ -1,17 +0,0 @@
-require 'test/unit'
-require 'bioinform/support/ptap'
-
-class TestEnumerablePmap < Test::Unit::TestCase
-  def test_ptap
-    assert_equal ['abc','def','ghi'], ['abc','','','def','ghi'].ptap('',&:delete)
-    
-    x = ['abc','','','def','ghi']
-    assert_equal false, ['abc','def','ghi'].equal?(x.ptap('',&:delete))
-    
-    x = ['abc','','','def','ghi']
-    assert_equal true, x.equal?(x.ptap('',&:delete))
-    
-    x = ['abc','','','def','ghi']
-    assert_equal ['abc','','','def','ghi'], ['abc','','','def','ghi'].ptap(&:to_s)
-  end
-end

data/spec/same_spec.rb

@@ -1,19 +0,0 @@
-require 'test/unit'
-require 'bioinform/support/same'
-
-class TestEnumerableSame < Test::Unit::TestCase
-  def test_same
-    assert_equal(true, [1,3,9,7].same?(&:even?))
-    assert_equal(true, [4,8,2,2].same?(&:even?))
-    assert_equal(false, [1,8,3,2].same?(&:even?))
-    
-    assert_equal(true, %w{cat dog rat}.same?(&:length))
-    assert_equal(false, %w{cat dog rabbit}.same?(&:length))
-    
-    assert_equal(true, %w{cat cat cat}.same?)
-    assert_equal(false, %w{cat dog rat}.same?)
-    
-    assert_equal(true, [].same?(&:length))
-    assert_equal(true, [].same?)
-  end
-end