test/scan_collection_test.rb in macroape-3.3.7 vs test/scan_collection_test.rb in macroape-3.3.8

@@ -1,36 +1,48 @@
 require_relative 'test_helper'
 
 class TestScanCollection < Test::Unit::TestCase
+  def setup
+    @start_dir = Dir.pwd
+    Dir.chdir File.join(File.dirname(__FILE__), 'data')
+  end
+  def teardown
+    Dir.chdir(@start_dir)
+  end
+
   def test_scan_pcm
-    assert_equal File.read('test/data/KLF4_f2_scan_results_default_cutoff.txt').gsub("\r\n", "\n"),
-                 Helpers.scan_collection_output('test/data/KLF4_f2.pcm test/data/test_collection.yaml --silent --pcm').gsub("\r\n","\n")
+    assert_equal File.read('KLF4_f2_scan_results_default_cutoff.txt').gsub("\r\n", "\n"),
+                 Helpers.scan_collection_output('KLF4_f2.pcm test_collection.yaml --silent --pcm --boundary lower').gsub("\r\n","\n")
   end
   def test_scan_default_cutoff
-    assert_equal File.read('test/data/KLF4_f2_scan_results_default_cutoff.txt').gsub("\r\n", "\n"),
-                 Helpers.scan_collection_output('test/data/KLF4_f2.pat test/data/test_collection.yaml --silent').gsub("\r\n","\n")
+    assert_equal File.read('KLF4_f2_scan_results_default_cutoff.txt').gsub("\r\n", "\n"),
+                 Helpers.scan_collection_output('KLF4_f2.pwm test_collection.yaml --silent --boundary lower').gsub("\r\n","\n")
   end
+  def test_scan_weak_threshold
+    assert_equal File.read('KLF4_f2_scan_results_weak_threshold.txt').gsub("\r\n", "\n"),
+                 Helpers.scan_collection_output('KLF4_f2.pwm test_collection_weak.yaml --silent').gsub("\r\n","\n")
+  end
   def test_scan_and_output_all_results
-    assert_equal File.read('test/data/KLF4_f2_scan_results_all.txt').gsub("\r\n", "\n"),
-                 Helpers.scan_collection_output('test/data/KLF4_f2.pat test/data/test_collection.yaml --all --silent').gsub("\r\n","\n")
-      
+    assert_equal File.read('KLF4_f2_scan_results_all.txt').gsub("\r\n", "\n"),
+                 Helpers.scan_collection_output('KLF4_f2.pwm test_collection.yaml --all --silent --boundary lower').gsub("\r\n","\n")
+
   end
   def test_scan_precise_mode
-    assert_equal File.read('test/data/KLF4_f2_scan_results_precise_mode.txt').gsub("\r\n","\n"),
-                 Helpers.scan_collection_output('test/data/KLF4_f2.pat test/data/test_collection.yaml --precise --all --silent').gsub("\r\n", "\n")
+    assert_equal File.read('KLF4_f2_scan_results_precise_mode.txt').gsub("\r\n","\n"),
+                 Helpers.scan_collection_output('KLF4_f2.pwm test_collection.yaml --precise --all --silent --boundary lower').gsub("\r\n", "\n")
   end
   def test_process_query_pwm_from_stdin
-    assert_equal Helpers.scan_collection_output('test/data/KLF4_f2.pat test/data/test_collection.yaml --silent'),
-                Helpers.provide_stdin(File.read('test/data/KLF4_f2.pat')) {
-                  Helpers.scan_collection_output('.stdin test/data/test_collection.yaml --silent')
+    assert_equal Helpers.scan_collection_output('KLF4_f2.pwm test_collection.yaml --silent --boundary lower'),
+                Helpers.provide_stdin(File.read('KLF4_f2.pwm')) {
+                  Helpers.scan_collection_output('.stdin test_collection.yaml --silent --boundary lower')
                 }
   end
 
   def test_scan_medium_length_motif
     assert_match /Query motif medium_motif_name gives 0 recognized words for a given P-value of 0\.0005 with the rough discretization level of 1. Forcing precise discretization level of 10/,
-                 Helpers.scan_collection_stderr('test/data/medium_motif.pat test/data/test_collection.yaml --precise --all --silent').gsub("\r\n", "\n")
+                 Helpers.scan_collection_stderr('medium_motif.pwm test_collection.yaml --precise --all --silent --boundary lower').gsub("\r\n", "\n")
   end
   def test_scan_short_length_motif
     assert_match /Query motif short_motif_name gives 0 recognized words for a given P-value of 0\.0005 with the precise discretization level of 10\. It.s impossible to scan collection for this motif/,
-                 Helpers.scan_collection_stderr('test/data/short_motif.pat test/data/test_collection.yaml --precise --all --silent').gsub("\r\n", "\n")
+                 Helpers.scan_collection_stderr('short_motif.pwm test_collection.yaml --precise --all --silent --boundary lower').gsub("\r\n", "\n")
   end
 end