aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorAlexanderlacuna2020-11-11 23:06:27 +0300
committerAlexanderlacuna2020-11-11 23:06:27 +0300
commit3396e1f008f3605439b38837f7a50407588d1f9b (patch)
tree3a25296868745c3e38a3f4ee8bba7fd928e2fb2c
parent424f44c0656da8f99dce0fa0a00bd5e6ba9bace3 (diff)
downloadgenenetwork2-3396e1f008f3605439b38837f7a50407588d1f9b.tar.gz
add tests for marker_regression/run_mapping.py
-rw-r--r--wqflask/tests/wqflask/marker_regression/test_run_mapping.py85
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)
+
+