feat: Add function to process permutation results.

1 files changed, 27 insertions, 0 deletions

diff --git a/gn3/computations/rqtl2.py b/gn3/computations/rqtl2.py
index 7b435ab..e8a5b0f 100644
--- a/gn3/computations/rqtl2.py
+++ b/gn3/computations/rqtl2.py
@@ -119,6 +119,33 @@ def read_output_file(output_path: str) -> dict:
         return results
 
 
+def process_permutation(data):
+    """ This function processses output data from the output results.
+    input: data object  extracted from the output_file
+    returns:
+        dict: A dict containing
+            * phenotypes array
+            * permutations as dict with keys as permutation_id
+            * significance_results with keys as threshold values
+    """
+
+    perm_file = data.get("permutation_file")
+    perm_results = {}
+    with open(perm_file, "r", encoding="utf-8") as file_handler:
+        reader = csv.reader(file_handler)
+        phenotypes = next(reader)[1:]
+        for line in reader:
+            permutation_id, *permutation_values = line
+            perm_results[permutation_id] = permutation_values
+
+    _, significance = fetch_significance_results(data.get("significance_file"))
+    return {
+        "phenotypes": phenotypes,
+        "perm_results": perm_results,
+        "significance": significance,
+    }
+
+
 def fetch_significance_results(file_path: str):
     """
     Processes the 'significance_file' from the given data object to extract