parse output data

2 files changed, 39 insertions, 10 deletions

diff --git a/gn3/computations/rust_correlation.py b/gn3/computations/rust_correlation.py
index a3802ae..e739382 100644
--- a/gn3/computations/rust_correlation.py
+++ b/gn3/computations/rust_correlation.py
@@ -4,10 +4,30 @@ from gn3.settings import CORRELATION_COMMAND
 from gn3.settings import TMPDIR
 
 
-def run_correlation(file_name: & str, outputdir: str = TMPDIR):
+def run_correlation(file_name: str, outputdir: str = TMPDIR):
 
     command_list = [CORRELATION_COMMAND, file_name, outputdir]
 
     results = subprocess.run(command_list, check=True)
 
     return results
+
+
+def parse_correlation_output(result_file: str):
+
+    corr_results = []
+
+    with open(result_file, "r") as file_reader:
+
+        for line in file_reader:
+
+            (trait_name, corr_coeff, p_val) = line.rstrip().split(",")
+            corr_data = {
+                "trait_name": trait_name,
+                "corr_coeff": corr_coeff,
+                "p_val": p_val
+            }
+
+            corr_results.append(corr_data)
+
+    return corr_results
diff --git a/tests/unit/computations/test_rust_correlation.py b/tests/unit/computations/test_rust_correlation.py
index 1398645..121c330 100644
--- a/tests/unit/computations/test_rust_correlation.py
+++ b/tests/unit/computations/test_rust_correlation.py
@@ -2,23 +2,32 @@ import pytest
 
 from gn3.computations.rust_correlation import CORRELATION_COMMAND
 from gn3.computations.rust_correlation import run_correlation
+from gn3.computations.rust_correlation import parse_correlation_output
 
 
 @pytest.mark.unit_test
+def test_run_correlation():
+    """test calling rusts' correlation """
 
-def test_equality():
-	"""initial test for sum """
-
-	assert 4 == 4
+    results = run_correlation(
+        file_name="/home/kabui/correlation_rust/tests/data/sample_json_file.json", outputdir="/")
 
+    assert results == "hello"
 
 
 @pytest.mark.unit_test
+def test_parse_results():
 
-def test_run_correlation():
-	"""test calling rusts' correlation """
-
+    raw_data = [
+        ["63.62", "0.97", "0.00"],
+        ["19", "-0.96", "0.22"],
+        ["77.92", "-0.94", "0.31"],
+        ["84.04", "0.94", "0.11"],
+        ["23", "-0.91", "0.11"]
+    ]
 
-	results =  run_correlation("./tests/data/sample_json_file.json")
+    expected_results = [{"trait_name": name, "corr_coeff": corr,
+                         "p_val": pval} for (name, corr, pval) in raw_data]
 
-	assert results == "hello"
+    assert parse_correlation_output(
+        "tests/unit/computations/data/correlation/sorted_results.txt") == expected_results