preprocess_collection_test.rb in macroape-3.3.8

- old
+ new
@@ -1,70 +1,65 @@
 require_relative 'test_helper'
 require 'yaml'
 
-# Don't use YAML.load_file() instead of YAML.load(File.read()) because in ruby before v1.93 p194
+# Don't use YAML.load_file() instead of YAML.load(File.read()) because in ruby before v1.9.3 p194
 # it doesn't immediately release file descriptor (if I understood error right way) so File.delete fails
 
 class TestPreprocessCollection < Test::Unit::TestCase
   def setup
     @start_dir = Dir.pwd
     Dir.chdir File.join(File.dirname(__FILE__), 'data')
   end
   def teardown
     File.delete('test_collection.yaml.tmp')  if File.exist? 'test_collection.yaml.tmp'
+    File.delete('my_collection.yaml')  if File.exist? 'my_collection.yaml'
     Dir.chdir(@start_dir)
   end
 
+  def test_weak_thresholds
+    Helpers.run_preprocess_collection('test_collection test_collection.yaml.tmp -p 0.0005,0.0001,0.00005 --silent')
+    assert_equal YAML.load(File.read('test_collection_weak.yaml')), YAML.load(File.read('test_collection.yaml.tmp'))
+  end
+
   def test_multipvalue_preprocessing
-    Helpers.run_preprocess_collection('test_collection -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent')
+    Helpers.run_preprocess_collection('test_collection test_collection.yaml.tmp -p 0.0005,0.0001,0.00005 --silent --boundary lower')
     assert_equal YAML.load(File.read('test_collection.yaml')), YAML.load(File.read('test_collection.yaml.tmp'))
   end
 
   def test_preprocessing_collection_from_a_single_file
-    Helpers.run_preprocess_collection('test_collection_single_file.txt -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent')
+    Helpers.run_preprocess_collection('test_collection_single_file.txt test_collection.yaml.tmp -p 0.0005,0.0001,0.00005 --silent --boundary lower')
     assert_equal YAML.load(File.read('test_collection.yaml')), YAML.load(File.read('test_collection.yaml.tmp'))
   end
 
   def test_preprocessing_collection_from_stdin
-    Helpers.provide_stdin('test_collection/GABPA_f1.pat  test_collection/KLF4_f2.pat  test_collection/SP1_f1.pat'){
-      Helpers.run_preprocess_collection('.stdin -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent')
+    Helpers.provide_stdin('test_collection/GABPA_f1.pwm  test_collection/KLF4_f2.pwm  test_collection/SP1_f1.pwm'){
+      Helpers.run_preprocess_collection('.stdin test_collection.yaml.tmp -p 0.0005,0.0001,0.00005 --silent --boundary lower')
     }
     assert_equal YAML.load(File.read('test_collection.yaml')), YAML.load(File.read('test_collection.yaml.tmp'))
   end
 
   def test_preprocessing_folder_pcm
-    Helpers.run_preprocess_collection('test_collection_pcm -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent --pcm')
+    Helpers.run_preprocess_collection('test_collection_pcm test_collection.yaml.tmp -p 0.0005,0.0001,0.00005 --silent --pcm --boundary lower')
     assert_equal YAML.load(File.read('test_collection.yaml')), YAML.load(File.read('test_collection.yaml.tmp'))
   end
 
   def test_preprocessing_collection_from_a_single_file_pcm
-    Helpers.run_preprocess_collection('test_collection_single_file_pcm.txt -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent --pcm')
+    Helpers.run_preprocess_collection('test_collection_single_file_pcm.txt test_collection.yaml.tmp -p 0.0005,0.0001,0.00005 --silent --pcm --boundary lower')
     assert_equal YAML.load(File.read('test_collection.yaml')), YAML.load(File.read('test_collection.yaml.tmp'))
   end
 
   def test_preprocessing_collection_from_a_collection
-    Helpers.run_preprocess_collection('collection_without_thresholds.yaml -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent')
+    Helpers.run_preprocess_collection('collection_without_thresholds.yaml test_collection.yaml.tmp -p 0.0005,0.0001,0.00005 --silent --boundary lower')
     assert_equal YAML.load(File.read('test_collection.yaml')), YAML.load(File.read('test_collection.yaml.tmp'))
   end
   def test_preprocessing_collection_from_a_pcm_collection
-    Helpers.run_preprocess_collection('collection_pcm_without_thresholds.yaml -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent --pcm')
+    Helpers.run_preprocess_collection('collection_pcm_without_thresholds.yaml test_collection.yaml.tmp -p 0.0005,0.0001,0.00005 --silent --pcm --boundary lower')
     assert_equal YAML.load(File.read('test_collection.yaml')), YAML.load(File.read('test_collection.yaml.tmp'))
   end
 
   def test_preprocessing_collection_from_stdin_pcm
     Helpers.provide_stdin('test_collection_pcm/GABPA_f1.pcm  test_collection_pcm/KLF4_f2.pcm  test_collection_pcm/SP1_f1.pcm'){
-      Helpers.run_preprocess_collection('.stdin -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent --pcm')
+      Helpers.run_preprocess_collection('.stdin test_collection.yaml.tmp -p 0.0005,0.0001,0.00005 --silent --pcm --boundary lower')
     }
     assert_equal YAML.load(File.read('test_collection.yaml')), YAML.load(File.read('test_collection.yaml.tmp'))
-  end
-
-  def test_with_name_specified
-    Helpers.run_preprocess_collection('test_collection -n my_collection -p 0.0005 0.0001 0.00005 --silent')
-    assert_equal YAML.load(File.read('test_collection.yaml')).set_parameters(name:'my_collection'), YAML.load(File.read('my_collection.yaml'))
-    File.delete('my_collection.yaml')
-  end
-
-  def test_with_name_and_output_specified
-    Helpers.run_preprocess_collection('test_collection -n my_collection -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent')
-    assert_equal YAML.load(File.read('test_collection.yaml')).set_parameters(name:'my_collection'), YAML.load(File.read('test_collection.yaml.tmp'))
   end
 end
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