def compute_k_gwa_with_loco_and_cavar(chromosomes, maf, token): """k-gwa-compute; Loco with 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: phenofile, snpsfile, covarfile = [ os.path.join(working_dir, _dict.get(x)) for x in ["pheno", "snps", "covar"] ] genofile = cache_ipfs_file( ipfs_file=_dict.get("geno"), cache_dir=current_app.config.get('CACHEDIR')) 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, chromosomes=chromosomes) gemma_kwargs["c"] = covarfile gemma_kwargs["maf"] = float(maf) 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={ "loco": ("--input " f"{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'), job_queue=current_app.config.get("REDIS_JOB_QUEUE"), cmd=(f"{gemma_k_cmd.get('gemma_cmd')} && " f"{gemma_gwa_cmd.get('gemma_cmd')}")), status="queued", output_file=gemma_gwa_cmd.get("output_file")) # pylint: disable=W0703 except Exception: return jsonify( status=128, # use better message message="Metadata file non-existent!")
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: phenofile, snpsfile, covarfile = [ os.path.join(working_dir, _dict.get(x)) for x in ["pheno", "snps", "covar"] ] genofile = cache_ipfs_file( ipfs_file=_dict.get("geno"), cache_dir=current_app.config.get('CACHEDIR')) 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'), job_queue=current_app.config.get("REDIS_JOB_QUEUE"), cmd=(f"{gemma_k_cmd.get('gemma_cmd')} && " f"{gemma_gwa_cmd.get('gemma_cmd')}")), status="queued", output_file=gemma_gwa_cmd.get("output_file")) # pylint: disable=W0703 except Exception: return jsonify( status=128, # use better message message="Metadata file non-existent!")
def compute_gwa_with_loco_covar(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: phenofile, snpsfile, covarfile = [ os.path.join(working_dir, _dict.get(x)) for x in ["pheno", "snps", "covar"] ] genofile = cache_ipfs_file( ipfs_file=_dict.get("geno"), cache_dir=current_app.config.get('CACHEDIR')) if not do_paths_exist([genofile, phenofile, snpsfile, covarfile]): raise FileNotFoundError gemma_kwargs = { "g": genofile, "p": phenofile, "a": snpsfile, "c": covarfile, "lmm": _dict.get("lmm", 9), "maf": float(maf) } results = 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={ "loco": f"--input {os.path.join(working_dir, k_filename)}" }) 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=results.get("gemma_cmd")), status="queued", output_file=results.get("output_file")) # pylint: disable=W0703 except Exception: return jsonify( status=128, # use better message message="Metadata file non-existent!")
def test_compute_k_values_without_loco(self, mock_get_hash): """Test computing k values without loco""" mock_get_hash.return_value = "my-hash" self.assertEqual( generate_gemma_cmd(gemma_cmd="gemma-wrapper", output_dir="/tmp", token="my-token", gemma_kwargs={ "g": "genofile", "p": "phenofile", "a": "snpsfile" }), { "output_file": "my-hash-output.json", "gemma_cmd": ("gemma-wrapper --json -- -g genofile " "-p phenofile -a snpsfile " "-gk > /tmp/my-token/my-hash-output.json") })
def compute_gwa(k_filename, token): """Compute GWA values. No loco no covariates provided. """ working_dir = os.path.join(current_app.config.get("TMPDIR"), token) _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json")) try: phenofile, snpsfile = [ os.path.join(working_dir, _dict.get(x)) for x in ["pheno", "snps"] ] genofile = cache_ipfs_file( ipfs_file=_dict.get("geno"), cache_dir=current_app.config.get('CACHEDIR')) gemma_kwargs = { "g": genofile, "p": phenofile, "a": snpsfile, "lmm": _dict.get("lmm", 9) } results = 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, k_filename) }) 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=results.get("gemma_cmd")), status="queued", output_file=results.get("output_file")) # pylint: disable=W0703 except Exception: return jsonify( status=128, # use better message message="Metadata file non-existent!")
def test_generate_gemma_cmd_with_loco(self, mock_get_hash): """Test computing k values with loco""" mock_get_hash.return_value = "my-hash" self.assertEqual( generate_gemma_cmd(gemma_cmd="gemma-wrapper", output_dir="/tmp", token="my-token", chromosomes="1,2,3,4,5", gemma_kwargs={ "g": "genofile", "p": "phenofile", "a": "snpsfile" }), { "output_file": "my-hash-r+gF5a-output.json", "gemma_cmd": ("gemma-wrapper --json " "--loco 1,2,3,4,5 " "-- -g genofile " "-p phenofile -a snpsfile " "-gk > /tmp/my-token/" "my-hash-r+gF5a-output.json") })
def compute_k_loco(chromosomes, token): """Similar to 'compute_k' with the extra option of using loco given chromosome values. """ working_dir = os.path.join(current_app.config.get("TMPDIR"), token) _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json")) try: phenofile, snpsfile = [ os.path.join(working_dir, _dict.get(x)) for x in ["pheno", "snps"] ] genofile = cache_ipfs_file( ipfs_file=_dict.get("geno"), cache_dir=current_app.config.get('CACHEDIR')) if not do_paths_exist([genofile, phenofile, snpsfile]): raise FileNotFoundError gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile} results = 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, chromosomes=chromosomes) 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=results.get("gemma_cmd")), status="queued", output_file=results.get("output_file")) # pylint: disable=W0703 except Exception: return jsonify( status=128, # use better message message="Metadata file non-existent!")