Merge pull request #32 from dvklopfenstein/master

Create test prior to modifying any code

tests/test_enrichment_fdr.py

@@ -2,17 +2,7 @@
 import os
 
 def test():
-  """Test to find this error below.
-
-       Traceback (most recent call last):
-         File "../scripts/find_enrichment.py", line 130, in <module>
-           study=study, methods=methods)
-         File "../scripts/../goatools/go_enrichment.py", line 93, in __init__
-           self.run_study(study)
-         File "../scripts/../goatools/go_enrichment.py", line 129, in run_study
-           p_val_distribution = calc_qval(study_count, study_n,
-       UnboundLocalError: local variable 'study_count' referenced before assignment
-  """
+  """Ensure that a study with only unknown GO Terms will run gracefully."""
   os.system("python {SCR} --alpha=0.05 {STUDY} {POP} {ASSN} --fdr --obo={OBO}".format(
     SCR="../scripts/find_enrichment.py",
     OBO="../go-basic.obo",

tests/test_get_paths.py

@@ -0,0 +1,23 @@
+
+from goatools.obo_parser import GODag
+import sys
+
+def chk_results(actual_paths, expected_paths):
+  for actual_path in actual_paths:
+    # GOTerm -> list of Strings
+    actual = [GO.id for GO in actual_path] 
+    if actual not in expected_paths:
+      raise Exception('ACTUAL {} NOT FOUND IN EXPECTED RESULTS\n'.format(actual))
+
+def test_paths_to_top():
+  dag = GODag("./data/mini_obo.obo")  
+  expected_paths = [
+    ['GO:0000001', 'GO:0000002', 'GO:0000005', 'GO:0000010'],
+    ['GO:0000001', 'GO:0000003', 'GO:0000005', 'GO:0000010'],
+    ['GO:0000001', 'GO:0000003', 'GO:0000006', 'GO:0000008', 'GO:0000010'] ]
+  actual_paths = dag.paths_to_top("GO:0000010")
+  chk_results(actual_paths, expected_paths)
+
+
+if __name__ == '__main__':
+  test_paths_to_top()