nimbus 0.10 → 1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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,
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+ :silent
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  )
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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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  # 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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  user_config_params = {}
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+ dirname = Dir.pwd
98
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  if File.exists?(File.expand_path(config_file, Dir.pwd))
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105
  begin
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- 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
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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
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  else
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  @training_file = File.expand_path(DEFAULTS[:training_file], Dir.pwd) if File.exists? File.expand_path(DEFAULTS[:training_file], Dir.pwd)
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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
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  # It could include errors on the configuration input data, training related info and/or testing related info.
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  def log_configuration
201
+ return if @silent
193
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  if !@do_training && !@do_testing
194
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  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
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  #
97
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  # 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
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  @importances = {}
102
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  @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
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+ 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
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