From 38cbc95f216548d4a2f46b8e25cd328ff8c52d62 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 16 Sep 2021 08:54:01 +0300
Subject: add  function to compose and run wgcna script

---
 gn3/computations/wgcna.py | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

(limited to 'gn3/computations')

diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
index 3819b62..bcd3a0a 100644
--- a/gn3/computations/wgcna.py
+++ b/gn3/computations/wgcna.py
@@ -5,8 +5,10 @@ import json
 import uuid
 from gn3.settings import TMPDIR
 
+from gn3.commands import run_cmd
 
-def dump_wgcna_data(request_data):
+
+def dump_wgcna_data(request_data: dict):
     """function to dump request data to json file"""
     filename = f"{str(uuid.uuid4())}.json"
 
@@ -16,3 +18,16 @@ def dump_wgcna_data(request_data):
         json.dump(request_data, output_file)
 
     return temp_file_path
+
+
+def compose_wgcna_cmd(rscript_path: str, temp_file_path: str):
+    """function to componse wgcna cmd"""
+    cmd = f"Rscript {rscript_path}  {temp_file_path}"
+    return cmd
+
+
+def call_wgcna_script(rscript_path: str, request_data: dict):
+    """function to call wgcna script"""
+    generated_file = dump_wgcna_data(request_data)
+    cmd = compose_gemma_cmd(rscript_path, generated_file)
+    run_cmd(cmd=cmd)
-- 
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