diff options
Diffstat (limited to 'gn3/computations/rqtl2.py')
| -rw-r--r-- | gn3/computations/rqtl2.py | 64 |
1 files changed, 51 insertions, 13 deletions
diff --git a/gn3/computations/rqtl2.py b/gn3/computations/rqtl2.py index adb6550..7b435ab 100644 --- a/gn3/computations/rqtl2.py +++ b/gn3/computations/rqtl2.py @@ -20,14 +20,15 @@ def generate_rqtl2_files(data, workspace_dir): parsed_files = {} for file_name, data_key in file_to_name_map.items(): if data_key in data: - file_path = write_to_csv(workspace_dir, f"{file_name}.csv", data[data_key]) + file_path = write_to_csv( + workspace_dir, f"{file_name}.csv", data[data_key]) if file_path: parsed_files[file_name] = file_path return {**data, **parsed_files} -def write_to_csv(work_dir, file_name, data:list[dict], - headers= None, delimiter=","): +def write_to_csv(work_dir, file_name, data: list[dict], + headers=None, delimiter=","): """Functions to write data list to csv file if headers is not provided use the keys for first boject. """ @@ -38,15 +39,15 @@ def write_to_csv(work_dir, file_name, data:list[dict], file_path = os.path.join(work_dir, file_name) with open(file_path, "w", encoding="utf-8") as file_handler: writer = csv.DictWriter(file_handler, fieldnames=headers, - delimiter=delimiter) + delimiter=delimiter) writer.writeheader() - for row in data: + for row in data: writer.writerow(row) # return the relative file to the workspace see rqtl2 docs return file_name -def validate_required_keys(required_keys:list, data:dict) -> tuple[bool, str]: +def validate_required_keys(required_keys: list, data: dict) -> tuple[bool, str]: """Check for missing keys in data object""" missing_keys = [key for key in required_keys if key not in data] if missing_keys: @@ -67,15 +68,15 @@ def compose_rqtl2_cmd(rqtl_path, input_file, "threshold": data.get("threshold", 1), "cores": config.get('MULTIPROCESSOR_PROCS', 1) } - rscript_path = config.get("RSCRIPT", "Rscript") - return f"{rscript_path} { rqtl_path } " + " ".join( + rscript_path = config.get("RSCRIPT", "Rscript") + return f"{rscript_path} { rqtl_path } " + " ".join( [f"--{key} {val}" for key, val in params.items()]) def create_file(file_path): """Utility function to create file given a file_path""" try: - with open(file_path, "x",encoding="utf-8") as _file_handler: + with open(file_path, "x", encoding="utf-8") as _file_handler: return True, f"File created at {file_path}" except FileExistsError: return False, "File Already Exists" @@ -83,10 +84,12 @@ def create_file(file_path): def prepare_files(tmpdir): """Prepare necessary files and workspace dir for computation.""" - workspace_dir = os.path.join(tmpdir, str(uuid.uuid4())) # + workspace_dir = os.path.join(tmpdir, str(uuid.uuid4())) Path(workspace_dir).mkdir(parents=False, exist_ok=True) - input_file = os.path.join(workspace_dir, f"rqtl2-input-{uuid.uuid4()}.json") - output_file = os.path.join(workspace_dir, f"rqtl2-output-{uuid.uuid4()}.json") + input_file = os.path.join( + workspace_dir, f"rqtl2-input-{uuid.uuid4()}.json") + output_file = os.path.join( + workspace_dir, f"rqtl2-output-{uuid.uuid4()}.json") # to ensure streaming api has access to file even after computation ends # .. Create the log file outside the workspace_dir @@ -95,12 +98,47 @@ def prepare_files(tmpdir): create_file(file_path) return workspace_dir, input_file, output_file, log_file + def write_input_file(input_file, workspace_dir, data): """ Write input data to a json file to be passed as input to the rqtl2 script """ - with open(input_file,"w+", encoding="UTF-8") as file_handler: + with open(input_file, "w+", encoding="UTF-8") as file_handler: # todo choose a better variable name rqtl2_files = generate_rqtl2_files(data, workspace_dir) json.dump(rqtl2_files, file_handler) + + +def read_output_file(output_path: str) -> dict: + """function to read output file json generated from rqtl2 + see rqtl2_wrapper.R script for the expected output + """ + with open(output_path, "r", encoding="utf-8") as file_handler: + results = json.load(file_handler) + return results + + +def fetch_significance_results(file_path: str): + """ + Processes the 'significance_file' from the given data object to extract + phenotypes and significance values. + thresholds values are: (0.05, 0.01) + Args: + file_path (str): file_Path for the significance output + + Returns: + tuple: A tuple containing + * phenotypes (list): List of phenotypes + * significances (dict): A dictionary where keys + ...are threshold values and values are lists + of significant results corresponding to each threshold. + """ + with open(file_path, "r", encoding="utf-8") as file_handler: + reader = csv.reader(file_handler) + results = {} + phenotypes = next(reader)[1:] + for line in enumerate(reader): + threshold, significance = line[0], line[1:] + results[threshold] = significance + return (phenotypes, significance) |