nimbus 0.10 → 1.0

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Files changed (20) hide show
  1. data/lib/nimbus/application.rb +2 -1
  2. data/lib/nimbus/configuration.rb +15 -6
  3. data/lib/nimbus/tree.rb +1 -1
  4. data/spec/configuration_spec.rb +92 -0
  5. data/spec/fixtures/regression_config.yml +12 -0
  6. data/spec/fixtures/regression_random_forest.yml +1741 -0
  7. data/spec/fixtures/regression_snp_importances.txt +200 -0
  8. data/spec/fixtures/{testing_regression.data → regression_testing.data} +0 -0
  9. data/spec/fixtures/regression_testing_file_predictions.txt +200 -0
  10. data/spec/fixtures/{training_regression.data → regression_training.data} +0 -0
  11. data/spec/fixtures/regression_training_file_predictions.txt +758 -0
  12. data/spec/forest_spec.rb +57 -0
  13. data/spec/individual_spec.rb +13 -0
  14. data/spec/nimbus_spec.rb +17 -1
  15. data/spec/spec_helper.rb +7 -1
  16. data/spec/training_set_spec.rb +25 -0
  17. data/spec/tree_spec.rb +130 -0
  18. metadata +27 -10
  19. data/README.rdoc +0 -1
  20. data/spec/fixtures/config.yml +0 -11
data/lib/nimbus/application.rb CHANGED
@@ -11,7 +11,8 @@ module Nimbus
11
11
 
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  # Initialize a Nimbus::Application object.
13
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  # Check and load the configuration options.
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- def initialize
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+ def initialize(c = nil)
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+ @config = c unless c.nil?
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  nimbus_exception_handling do
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  config.load
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  @forest = nil
data/lib/nimbus/configuration.rb CHANGED
@@ -29,7 +29,8 @@ module Nimbus
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  :output_training_file,
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  :output_testing_file,
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  :output_tree_errors_file,
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- :output_snp_importances_file
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+ :output_snp_importances_file,
33
+ :silent
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34
  )
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  DEFAULTS = {
@@ -50,7 +51,9 @@ module Nimbus
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  :output_training_file => 'training_file_predictions.txt',
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  :output_testing_file => 'testing_file_predictions.txt',
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  :output_tree_errors_file => 'generalization_errors.txt',
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- :output_snp_importances_file => 'snp_importances.txt'
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+ :output_snp_importances_file => 'snp_importances.txt',
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+
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+ :silent => false
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  }
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58
 
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  # Initialize a Nimbus::Configuration object.
@@ -72,6 +75,8 @@ module Nimbus
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  @output_testing_file = File.expand_path(DEFAULTS[:output_testing_file], Dir.pwd)
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  @output_tree_errors_file = File.expand_path(DEFAULTS[:output_tree_errors_file], Dir.pwd)
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  @output_snp_importances_file = File.expand_path(DEFAULTS[:output_snp_importances_file], Dir.pwd)
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+
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+ @silent = ENV['nimbus_test'] == 'running_nimbus_tests' ? true : DEFAULTS[:silent]
75
80
  end
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81
 
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  # Accessor method for the tree-related subset of options.
@@ -95,18 +100,21 @@ module Nimbus
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  #
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  def load(config_file = DEFAULTS[:config_file])
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102
  user_config_params = {}
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+ dirname = Dir.pwd
98
104
  if File.exists?(File.expand_path(config_file, Dir.pwd))
99
105
  begin
100
- user_config_params = YAML.load(File.open(File.expand_path config_file, Dir.pwd))
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+ config_file_path = File.expand_path config_file, Dir.pwd
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+ user_config_params = YAML.load(File.open(config_file_path))
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+ dirname = File.dirname config_file_path
101
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  rescue ArgumentError => e
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  raise Nimbus::WrongFormatFileError, "It was not posible to parse the config file (#{config_file}): \r\n#{e.message} "
103
111
  end
104
112
  end
105
113
 
106
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  if user_config_params['input']
107
- @training_file = File.expand_path(user_config_params['input']['training'], Dir.pwd) if user_config_params['input']['training']
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- @testing_file = File.expand_path(user_config_params['input']['testing' ], Dir.pwd) if user_config_params['input']['testing']
109
- @forest_file = File.expand_path(user_config_params['input']['forest' ], Dir.pwd) if user_config_params['input']['forest']
115
+ @training_file = File.expand_path(user_config_params['input']['training'], dirname) if user_config_params['input']['training']
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+ @testing_file = File.expand_path(user_config_params['input']['testing' ], dirname) if user_config_params['input']['testing']
117
+ @forest_file = File.expand_path(user_config_params['input']['forest' ], dirname) if user_config_params['input']['forest']
110
118
  else
111
119
  @training_file = File.expand_path(DEFAULTS[:training_file], Dir.pwd) if File.exists? File.expand_path(DEFAULTS[:training_file], Dir.pwd)
112
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  @testing_file = File.expand_path(DEFAULTS[:testing_file ], Dir.pwd) if File.exists? File.expand_path(DEFAULTS[:testing_file ], Dir.pwd)
@@ -190,6 +198,7 @@ module Nimbus
190
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  #
191
199
  # It could include errors on the configuration input data, training related info and/or testing related info.
192
200
  def log_configuration
201
+ return if @silent
193
202
  if !@do_training && !@do_testing
194
203
  Nimbus.message "*" * 50
195
204
  Nimbus.message "* Nimbus could not find any input file: "
data/lib/nimbus/tree.rb CHANGED
@@ -96,7 +96,7 @@ module Nimbus
96
96
  #
97
97
  # This method computes importance estimations for every SNPs used in the tree (for any other SNP it would be 0).
98
98
  def estimate_importances(oob_ids)
99
- return nil if (@generalization_error.nil? && generalization_error_from_oob(oob_ids))
99
+ return nil if (@generalization_error.nil? && generalization_error_from_oob(oob_ids).nil?)
100
100
  oob_individuals_count = oob_ids.size
101
101
  @importances = {}
102
102
  @used_snps.uniq.each do |current_snp|
data/spec/configuration_spec.rb ADDED
@@ -0,0 +1,92 @@
1
+ # encoding: UTF-8
2
+ require File.dirname(__FILE__) + '/spec_helper'
3
+
4
+ describe Nimbus::Configuration do
5
+
6
+ it "loads configuration options from config file" do
7
+ config = Nimbus::Configuration.new
8
+ config.load fixture_file('regression_config.yml')
9
+
10
+ config.training_file.should == fixture_file('regression_training.data')
11
+ config.testing_file.should == fixture_file('regression_testing.data')
12
+ config.forest_file.should == fixture_file('regression_random_forest.yml')
13
+
14
+ config.forest_size.should == 3
15
+ config.tree_SNP_sample_size.should == 60
16
+ config.tree_SNP_total_count.should == 200
17
+ config.tree_node_min_size.should == 5
18
+ end
19
+
20
+ it 'tree method return tree-related subset of options' do
21
+ config = Nimbus::Configuration.new
22
+ tree_options = config.tree
23
+
24
+ tree_options[:snp_sample_size].should_not be_nil
25
+ tree_options[:snp_total_count].should_not be_nil
26
+ tree_options[:tree_node_min_size].should_not be_nil
27
+ end
28
+
29
+ it "creates a training set object from training data file" do
30
+ config = Nimbus::Configuration.new
31
+ config.load fixture_file('regression_config.yml')
32
+ config.training_set.should be_nil
33
+ config.load_training_data
34
+ config.training_set.should be_kind_of Nimbus::TrainingSet
35
+ config.training_set.all_ids.sort.should == (1..800).to_a
36
+
37
+ File.open(fixture_file('regression_training.data')) {|file|
38
+ feno1, id1, *snp_list_1 = file.readline.split
39
+ feno2, id2, *snp_list_2 = file.readline.split
40
+ feno3, id3, *snp_list_3 = file.readline.split
41
+
42
+ i1 = Nimbus::Individual.new(id1.to_i, feno1.to_f, snp_list_1.map{|snp| snp.to_i})
43
+ i2 = Nimbus::Individual.new(id2.to_i, feno2.to_f, snp_list_2.map{|snp| snp.to_i})
44
+ i3 = Nimbus::Individual.new(id3.to_i, feno3.to_f, snp_list_3.map{|snp| snp.to_i})
45
+
46
+ config.training_set.individuals[id1.to_i].id.should == i1.id
47
+ config.training_set.individuals[id2.to_i].fenotype.should == i2.fenotype
48
+ config.training_set.individuals[id3.to_i].snp_list.should == i3.snp_list
49
+
50
+ config.training_set.ids_fenotypes[id1.to_i] = feno1.to_f
51
+ config.training_set.ids_fenotypes[id2.to_i] = feno2.to_f
52
+ config.training_set.ids_fenotypes[id3.to_i] = feno3.to_f
53
+ }
54
+ end
55
+
56
+ it "reads testing data and yields one individual at a time" do
57
+ config = Nimbus::Configuration.new
58
+ config.load fixture_file('regression_config.yml')
59
+
60
+ test_individuals = []
61
+ File.open(fixture_file('regression_testing.data')) {|file|
62
+ file.each do |line|
63
+ data_id, *snp_list = line.strip.split
64
+ test_individuals << Nimbus::Individual.new(data_id.to_i, nil, snp_list.map{|snp| snp.to_i})
65
+ end
66
+ }
67
+ test_individuals.size.should == 200
68
+ config.read_testing_data{|individual|
69
+ test_individual = test_individuals.shift
70
+ individual.id.should_not be_nil
71
+ individual.id.should == test_individual.id
72
+ individual.snp_list.should_not be_empty
73
+ individual.snp_list.should == test_individual.snp_list
74
+ }
75
+ end
76
+
77
+ it "creates a forest object loading data from a yaml file" do
78
+ config = Nimbus::Configuration.new
79
+ config.load fixture_file('regression_config.yml')
80
+
81
+ trees = YAML.load(File.open fixture_file('regression_random_forest.yml'))
82
+ trees.first.keys.first.should == 189
83
+ trees.size.should == 3
84
+
85
+ forest = config.load_forest
86
+ forest.should be_kind_of Nimbus::Forest
87
+ forest.trees[0].should == trees.first
88
+ forest.trees[1].should == trees[1]
89
+ forest.trees.last.should == trees[2]
90
+ end
91
+
92
+ end
data/spec/fixtures/regression_config.yml ADDED
@@ -0,0 +1,12 @@
1
+ #Input files
2
+ input:
3
+ training: regression_training.data
4
+ testing: regression_testing.data
5
+ forest: regression_random_forest.yml
6
+
7
+ #Forest parameters
8
+ forest:
9
+ forest_size: 3 #how many trees
10
+ SNP_sample_size_mtry: 60 #mtry
11
+ SNP_total_count: 200
12
+ node_min_size: 5
data/spec/fixtures/regression_random_forest.yml ADDED
@@ -0,0 +1,1741 @@
1
+ ---
2
+ - 189:
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+ - 128:
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