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authorAlexander Kabui2021-09-16 14:03:25 +0300
committerAlexander Kabui2021-09-16 14:03:25 +0300
commitce045ec96bf965eaba077fdba99847a483281aba (patch)
treee4b22a0b7616895e224d04bf47f08dbe385021fc /tests/unit
parentf53a8a98206b4e8aedbf4b86e49f41ea140c9c6a (diff)
downloadgenenetwork3-ce045ec96bf965eaba077fdba99847a483281aba.tar.gz
init tests for wgcna
Diffstat (limited to 'tests/unit')
-rw-r--r--tests/unit/computations/test_wgcna.py36
1 files changed, 28 insertions, 8 deletions
diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py
index 1ce69a1..8a68985 100644
--- a/tests/unit/computations/test_wgcna.py
+++ b/tests/unit/computations/test_wgcna.py
@@ -1,15 +1,35 @@
"""module contains python code for wgcna"""
from unittest import TestCase
-
-
-def compute_sum(rhs_val, lhs_val):
- """function to compute sum of two numbers"""
- return rhs_val+lhs_val
+from gn3.computations.wgcna import dump_wgcna_data
+from gn3.computations.wgcna import compose_wgcna_cmd
class TestWgcna(TestCase):
"""test class for wgcna"""
- def test_compute_sum(self):
- """test for compute sum function"""
- self.assertEqual(compute_sum(1, 2), 3)
+ def test_compose_wgcna_cmd(self):
+ """test for composing wgcna cmd"""
+ wgcna_cmd = compose_wgcna_cmd("/wgcna.r", "/tmp/wgcna.json")
+ self.assertEqual(wgcna_cmd, f"Rscript /wgcna.r /tmp/wgcna.json")
+
+ def test_create_json_data(self):
+ """test for writing the data to a csv file"""
+ # # All the traits we have data for (should not contain duplicates)
+ # All the strains we have data for (contains duplicates)
+
+ trait_sample_data = {"1425642_at": {"129S1/SvImJ": 7.142, "A/J": 7.31, "AKR/J": 7.49,
+ "B6D2F1": 6.899, "BALB/cByJ": 7.172, "BALB/cJ": 7.396},
+ "1457784_at": {"129S1/SvImJ": 7.071, "A/J": 7.05, "AKR/J": 7.313,
+ "B6D2F1": 6.999, "BALB/cByJ": 7.293, "BALB/cJ": 7.117},
+ "1444351_at": {"129S1/SvImJ": 7.221, "A/J": 7.246, "AKR/J": 7.754,
+ "B6D2F1": 6.866, "BALB/cByJ": 6.752, "BALB/cJ": 7.269}
+
+ }
+
+ expected_input = {
+ "trait_sample_data": trait_sample_data,
+ "TOMtype": "unsigned",
+ "minModuleSize": 30
+ }
+
+ _results = dump_wgcna_data(expected_input)