diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/api/gemma.py | 49 |
1 files changed, 49 insertions, 0 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py index acaec68..7fcf2a2 100644 --- a/gn3/api/gemma.py +++ b/gn3/api/gemma.py @@ -7,10 +7,12 @@ from flask import current_app from flask import jsonify from flask import request +from gn3.commands import compose_gemma_cmd from gn3.commands import queue_cmd from gn3.commands import run_cmd from gn3.file_utils import get_hash_of_files from gn3.file_utils import jsonfile_to_dict +from gn3.computations.gemma import do_paths_exist from gn3.computations.gemma import generate_hash_of_string from gn3.computations.gemma import generate_pheno_txt_file from gn3.computations.gemma import generate_gemma_computation_cmd @@ -252,3 +254,50 @@ def compute_gwa_with_covar(k_filename, token): return jsonify(status=128, # use better message message="Metadata file non-existent!") + + +@gemma.route("/gwa-compute/<k_filename>/loco/maf/<maf>/<token>", + methods=["POST"]) +def compute_gwa_with_loco_maf(k_filename, maf, token): + """Compute GWA values. No Covariates provided. Only loco and maf vals given. + + """ + 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 = [ + os.path.join(working_dir, + _dict.get(x)) + for x in ["geno", "pheno", "snps"]] + if not do_paths_exist([genofile, phenofile, snpsfile]): + raise FileNotFoundError + gemma_kwargs = {"g": genofile, "p": phenofile, + "a": snpsfile, "lmm": _dict.get("lmm", 9), + 'maf': float(maf)} + _hash = get_hash_of_files([genofile, phenofile, snpsfile]) + _output_filename = f"{_hash}-gwa-output.json" + return jsonify( + unique_id=queue_cmd( + conn=redis.Redis(), + email=(request.get_json() or {}).get('email'), + job_queue=current_app.config.get("REDIS_JOB_QUEUE"), + cmd=compose_gemma_cmd( + gemma_wrapper_cmd=current_app.config.get("GEMMA_" + "WRAPPER_CMD"), + gemma_wrapper_kwargs={ + "loco": ("--input " + f"{os.path.join(working_dir, k_filename)}") + }, + gemma_kwargs=gemma_kwargs, + gemma_args=["-gk", ">", + (f"{current_app.config.get('TMPDIR')}/" + f"{token}/{_output_filename}")])), + status="queued", + output_file=_output_filename) + # pylint: disable=W0703 + except Exception: + return jsonify(status=128, + # use better message + message="Metadata file non-existent!") |