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authorBonfaceKilz2021-03-08 14:23:53 +0300
committerBonfaceKilz2021-03-08 21:09:58 +0300
commit504cd5748e5fa71a539b095958fe71a20f5ca443 (patch)
tree150f8b829c19dc0e239e4fbba3b67296dcb8fe8e /gn3/api
parent79f931b0fbe0712954201a15278f9088fd7cdb8a (diff)
downloadgenenetwork3-504cd5748e5fa71a539b095958fe71a20f5ca443.tar.gz
Add "/k-gwa-compute/covars/<token>"
Diffstat (limited to 'gn3/api')
-rw-r--r--gn3/api/gemma.py33
1 files changed, 33 insertions, 0 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index 2d1fedf..d141e18 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -400,11 +400,44 @@ covars; lmm defaults to 9!
status=128,
# use better message
message="Metadata file non-existent!")
+
+
+@gemma.route("/k-gwa-compute/covars/<token>", methods=["POST"])
+def compute_k_gwa_with_covars_only(token):
+ """Given a genofile, traitfile, snpsfile, and the token, compute the k-values
+and return <hash-of-inputs>.json with a UNIQUE-ID of the job. The genofile,
+traitfile, and snpsfile are extracted from a metadata.json file. No Loco no
+covars; lmm defaults to 9!
+
+ """
+ working_dir = os.path.join(current_app.config.get("TMPDIR"), token)
+ _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json"))
+ try:
+ genofile, phenofile, snpsfile, covarfile = [
+ os.path.join(working_dir, _dict.get(x))
+ for x in ["geno", "pheno", "snps", "covar"]
+ ]
+ if not do_paths_exist([genofile, phenofile, snpsfile]):
+ raise FileNotFoundError
+ gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
+ gemma_k_cmd = generate_gemma_cmd(
gemma_cmd=current_app.config.get("GEMMA_"
"WRAPPER_CMD"),
output_dir=current_app.config.get('TMPDIR'),
token=token,
gemma_kwargs=gemma_kwargs)
+ gemma_kwargs["c"] = covarfile
+ gemma_kwargs["lmm"] = _dict.get("lmm", 9)
+ gemma_gwa_cmd = generate_gemma_cmd(
+ gemma_cmd=current_app.config.get("GEMMA_"
+ "WRAPPER_CMD"),
+ output_dir=current_app.config.get('TMPDIR'),
+ token=token,
+ gemma_kwargs=gemma_kwargs,
+ gemma_wrapper_kwargs={
+ "input": os.path.join(working_dir,
+ gemma_k_cmd.get("output_file"))
+ })
return jsonify(unique_id=queue_cmd(
conn=redis.Redis(),
email=(request.get_json() or {}).get('email'),