aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorAlexander Kabui2021-09-16 08:54:01 +0300
committerAlexander Kabui2021-09-16 08:54:01 +0300
commit38cbc95f216548d4a2f46b8e25cd328ff8c52d62 (patch)
treefaf532a5ff4d91cd61d73a24af52abeb29b823bf
parenta3ef298678b32ee83cac7bd7462d3d92f8eaec26 (diff)
downloadgenenetwork3-38cbc95f216548d4a2f46b8e25cd328ff8c52d62.tar.gz
add function to compose and run wgcna script
-rw-r--r--gn3/computations/wgcna.py17
1 files changed, 16 insertions, 1 deletions
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)