add tests for marker_regression/run_mapping.py

1 files changed, 85 insertions, 0 deletions

diff --git a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py
index 6521c41d..be6e6e48 100644
--- a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py
+++ b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py
@@ -7,6 +7,8 @@ from wqflask.marker_regression.run_mapping import geno_db_exists
 from wqflask.marker_regression.run_mapping import write_input_for_browser
 from wqflask.marker_regression.run_mapping import export_mapping_results
 from wqflask.marker_regression.run_mapping import trim_markers_for_figure
+from wqflask.marker_regression.run_mapping import get_perm_strata
+from wqflask.marker_regression.run_mapping import get_chr_lengths
 
 
 class AttributeSetter:
@@ -23,10 +25,27 @@ class MockDataSetGroup(AttributeSetter):
 
 class TestRunMapping(unittest.TestCase):
     def setUp(self):
+
         self.group = MockDataSetGroup(
             {"genofile": "~/genofiles/g1_file", "name": "GP1_", "species": "Human"})
+        chromosomes={
+    	 "3":AttributeSetter({
+    	 "name":"C1",
+    	 "length":"0.04"
+    	 }),
+    	  "4":AttributeSetter({
+    	 "name":"C2",
+    	 "length":"0.03"
+    	 }),
+    	  "5":AttributeSetter({
+    	 "name":"C4",
+    	 "length":"0.01"
+    	 })
+    	}
         self.dataset = AttributeSetter(
             {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"})
+
+        self.chromosomes=AttributeSetter({"chromosomes":chromosomes})
         self.trait = AttributeSetter(
             {"symbol": "IGFI", "chr": "X1", "mb": 123313})
 
@@ -196,3 +215,69 @@ class TestRunMapping(unittest.TestCase):
 
     		results=write_input_for_browser(this_dataset=self.dataset,gwas_results={},annotations={})
     		self.assertEqual(results,expected)
+
+
+    def test_get_perm_strata(self):
+    	categorical_vars=["C1","C2","W1"]
+    	used_samples=["S1","S2"]
+    	sample_list=AttributeSetter({"sample_attribute_values":{
+    		"S1":{
+    		 "C1":"c1_value",
+    		 "C2":"c2_value",
+    		 "W1":"w1_value"
+
+    		},
+    		"S2":{
+    		"W1":"w2_value",
+    		 "W2":"w2_value"
+
+    		},
+    		"S3":{
+
+    		"C1":"c1_value",
+    		"C2":"c2_value"
+
+    		},
+    		
+    		}})
+
+    	results=get_perm_strata(this_trait={},sample_list=sample_list,categorical_vars=categorical_vars,used_samples=used_samples)
+    	self.assertEqual(results,[2,1])
+
+
+    def test_get_chr_length(self):
+    	chromosomes=AttributeSetter({"chromosomes":self.chromosomes})
+    	dataset=AttributeSetter({"species":chromosomes})
+    	results=get_chr_lengths(mapping_scale="physic",mapping_method="reaper",dataset=dataset,qtl_results=[])
+    	chr_lengths=[]
+    	for key,chromo in self.chromosomes.chromosomes.items():
+    		chr_lengths.append({"chr":chromo.name,"size":chromo.length})
+
+    	self.assertEqual(chr_lengths,results)
+
+    	qtl_results=[{
+    	"chr":"16",
+    	"cM":"0.2"
+    	},
+    	{
+    	"chr":"12",
+    	"cM":"0.5"
+    	},
+    	{
+    	"chr":"18",
+    	"cM":"0.1"
+    	},
+    	{
+    	"chr":"22",
+    	"cM":"0.4"
+    	},
+    	]
+
+
+
+    	result_with_other_mapping_scale=get_chr_lengths(mapping_scale="other",mapping_method="reaper",dataset=dataset,qtl_results=qtl_results)
+    	expected_value= [{'chr': '1', 'size': '0'}, {'chr': '16', 'size': '500000.0'}, {'chr': '18', 'size': '400000.0'}]
+
+    	self.assertEqual(result_with_other_mapping_scale,expected_value)    	
+
+