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authorzsloan2021-10-12 20:56:31 +0000
committerzsloan2021-10-12 20:56:31 +0000
commit6e211182354fb4d6941e3a44ec1ec9d378b0e4ef (patch)
tree60d9aaf382eefbb47cdbab9c74d98481cf0983de /gn3/computations/wgcna.py
parentb815236123ff8e144bd84f349357a1852df95651 (diff)
parent77c274b79c3ec01de60e90db3299763cb58f715b (diff)
downloadgenenetwork3-6e211182354fb4d6941e3a44ec1ec9d378b0e4ef.tar.gz
Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into bug/fix_rqtl_covariates
Diffstat (limited to 'gn3/computations/wgcna.py')
-rw-r--r--gn3/computations/wgcna.py51
1 files changed, 51 insertions, 0 deletions
diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
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+"""module contains code to preprocess and call wgcna script"""
+
+import os
+import json
+import uuid
+from gn3.settings import TMPDIR
+
+from gn3.commands import run_cmd
+
+
+def dump_wgcna_data(request_data: dict):
+ """function to dump request data to json file"""
+ filename = f"{str(uuid.uuid4())}.json"
+
+ temp_file_path = os.path.join(TMPDIR, filename)
+
+ with open(temp_file_path, "w") as output_file:
+ 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"""
+ # (todo):issue relative paths to abs paths
+ cmd = f"Rscript ./scripts/{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_wgcna_cmd(rscript_path, generated_file)
+
+ try:
+
+ run_cmd_results = run_cmd(cmd)
+
+ with open(generated_file, "r") as outputfile:
+
+ if run_cmd_results["code"] != 0:
+ return run_cmd_results
+ return {
+ "data": json.load(outputfile),
+ **run_cmd_results
+ }
+ except FileNotFoundError:
+ # relook at handling errors gn3
+ return {
+ "output": "output file not found"
+ }