diff options
Diffstat (limited to 'gn3/api/gemma.py')
| -rw-r--r-- | gn3/api/gemma.py | 33 |
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'), |