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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| { | ||
| "populations": [ | ||
| "CAU" | ||
| ], | ||
| "freq_trim_threshold": 1e-5, | ||
| "priority": { | ||
| "alpha": 0.4999999, | ||
| "eta": 0, | ||
| "beta": 1e-7, | ||
| "gamma": 1e-7, | ||
| "delta": 0.4999999 | ||
| }, | ||
| "UNK_priors": "SR", | ||
| "FULL_LOCI": "ABCQR", | ||
| "loci_map": { | ||
| "A": 1, | ||
| "B": 2, | ||
| "C": 3, | ||
| "DQB1": 4, | ||
| "DRB1": 5 | ||
| }, | ||
|
|
||
| "factor_missing_data": 0.0001, | ||
| "Plan_B_Matrix": [ | ||
| [[1, 2, 3, 4, 5]], | ||
| [[1, 2, 3], [4, 5]], | ||
| [[1], [2, 3], [4, 5]], | ||
| [[1, 2, 3], [4], [5]], | ||
| [[1], [2, 3], [4], [5]], | ||
| [[1], [2], [3], [4], [5]] | ||
| ], | ||
| "planb": true, | ||
| "number_of_options_threshold": 100000, | ||
| "epsilon": 1e-3, | ||
| "number_of_results": 10, | ||
| "number_of_pop_results": 100, | ||
| "output_MUUG": true, | ||
| "output_haplotypes": true, | ||
| "freq_data_dir": "data/freqs" , | ||
| "freq_file": "output/hpf.csv" , | ||
| "graph_files_path": "graph_generation/output/csv/" , | ||
| "node_csv_file": "nodes.csv", | ||
| "edges_csv_file": "edges.csv", | ||
| "info_node_csv_file": "info_node.csv", | ||
| "top_links_csv_file": "top_links.csv", | ||
| "imputation_in_file": "data/subjects/donor.csv", | ||
| "imputation_out_umug_freq_filename": "don.umug", | ||
| "imputation_out_umug_pops_filename": "don.umug.pops", | ||
| "imputation_out_hap_freq_filename": "don.pmug", | ||
| "imputation_out_hap_pops_filename": "don.pmug.pops", | ||
| "imputation_out_miss_filename": "don.miss", | ||
| "imputation_out_problem_filename": "don.problem", | ||
| "max_haplotypes_number_in_phase": 100, | ||
| "imuptation_out_path": "output" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,127 @@ | ||
| import argparse | ||
| import cProfile | ||
| import json | ||
| import pathlib | ||
| import sys | ||
| import os | ||
|
|
||
| sys.path.insert(0, os.path.dirname(os.path.realpath(__file__))) | ||
|
|
||
| from .imputation.impute import Imputation | ||
| from .imputation.networkx_graph import Graph | ||
|
|
||
| # Profiler start | ||
| #pr = cProfile.Profile() | ||
| #pr.enable() | ||
|
|
||
| def run_impute(conf_file = "../conf/minimal-configuration.json", project_dir_graph = "", project_dir_in_file = ""): | ||
|
|
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| configuration_file = conf_file | ||
|
|
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| #project_dir = ""# "../" | ||
| #output_dir = "output/" | ||
|
|
||
|
|
||
| # Read configuration file and load properties | ||
| with open(configuration_file) as f: | ||
| json_conf = json.load(f) | ||
|
|
||
| graph_files_path = json_conf.get("graph_files_path") | ||
| if graph_files_path[-1] != '/': | ||
| graph_files_path += '/' | ||
| output_dir = json_conf.get("imuptation_out_path", "output") | ||
| if output_dir[-1] != '/': | ||
| output_dir += '/' | ||
| config = { | ||
| "planb": json_conf.get('planb', True), | ||
| "pops": json_conf.get('populations'), | ||
| "priority": json_conf.get('priority'), | ||
| "epsilon": json_conf.get('epsilon', 1e-3), | ||
| "number_of_results": json_conf.get('number_of_results', 1000), | ||
| "number_of_pop_results": json_conf.get('number_of_pop_results', 100), | ||
| "output_MUUG": json_conf.get("output_MUUG", True), | ||
| "output_haplotypes": json_conf.get("output_haplotypes", False), | ||
| "node_file": project_dir_graph + graph_files_path + json_conf.get("node_csv_file"), | ||
| "top_links_file": project_dir_graph + graph_files_path + json_conf.get("top_links_csv_file"), | ||
| "edges_file": project_dir_graph + graph_files_path +json_conf.get("edges_csv_file"), | ||
| "imputation_input_file": project_dir_in_file + json_conf.get("imputation_in_file"), | ||
| "imputation_out_umug_freq_file": output_dir + json_conf.get("imputation_out_umug_freq_filename"), | ||
| "imputation_out_umug_pops_file": output_dir + json_conf.get("imputation_out_umug_pops_filename"), | ||
| "imputation_out_hap_freq_file": output_dir + json_conf.get("imputation_out_hap_freq_filename"), | ||
| "imputation_out_hap_pops_file": output_dir + json_conf.get("imputation_out_hap_pops_filename"), | ||
| "imputation_out_miss_file": output_dir + json_conf.get("imputation_out_miss_filename"), | ||
| "imputation_out_problem_file": output_dir + json_conf.get("imputation_out_problem_filename"), | ||
| "factor_missing_data": json_conf.get("factor_missing_data", 0.01), | ||
| "loci_map": json_conf.get("loci_map", {"A": 1, "B":3, "C": 2, "DQB1": 4, "DRB1": 5} ), | ||
| "matrix_planb": json_conf.get("Plan_B_Matrix", [ | ||
| [[1, 2, 3, 4, 5]], | ||
| [[1, 2, 3], [4, 5]], | ||
| [[1], [2, 3], [4, 5]], | ||
| [[1, 2, 3], [4], [5]], | ||
| [[1], [2, 3], [4], [5]], | ||
| [[1], [2], [3], [4], [5]] | ||
| ]), | ||
| "pops_count_file": project_dir_graph + json_conf.get("pops_count_file",'' ), | ||
| "use_pops_count_file": json_conf.get("pops_count_file",False), | ||
| "number_of_options_threshold": json_conf.get("number_of_options_threshold", 100000), | ||
| "max_haplotypes_number_in_phase": json_conf.get("max_haplotypes_number_in_phase",100 ), | ||
| "bin_imputation_input_file": project_dir_in_file + json_conf.get("bin_imputation_in_file", "None"), | ||
| "nodes_for_plan_A": json_conf.get("Plan_A_Matrix", []), | ||
| "save_mode": json_conf.get("save_space_mode", False), | ||
| "UNK_priors" : json_conf.get("UNK_priors", "MR") | ||
|
|
||
| } | ||
|
|
||
| # Display the configurations we are using | ||
| print('****************************************************************************************************') | ||
| print("Performing imputation based on:") | ||
| print("\tPopulation: {}".format(config["pops"])) | ||
| print("\tPriority: {}".format(config["priority"])) | ||
| print("\tUNK priority: {}".format(config["UNK_priors"])) | ||
| print("\tEpsilon: {}".format(config["epsilon"])) | ||
| print("\tPlan B: {}".format(config["planb"])) | ||
| print("\tNumber of Results: {}".format(config["number_of_results"])) | ||
| print("\tNumber of Population Results: {}".format(config["number_of_pop_results"])) | ||
| print("\tNodes File: {}".format(config["node_file"])) | ||
| print("\tTop Links File: {}".format(config["edges_file"])) | ||
| print("\tInput File: {}".format(config["imputation_input_file"])) | ||
| print("\tOutput UMUG Format: {}".format(config["output_MUUG"])) | ||
| print("\tOutput UMUG Freq Filename: {}".format(config["imputation_out_umug_freq_file"])) | ||
| print("\tOutput UMUG Pops Filename: {}".format(config["imputation_out_umug_pops_file"])) | ||
| print("\tOutput Haplotype Format: {}".format(config["output_haplotypes"])) | ||
| print("\tOutput HAP Freq Filename: {}".format(config["imputation_out_hap_freq_file"])) | ||
| print("\tOutput HAP Pops Filename: {}".format(config["imputation_out_hap_pops_file"])) | ||
| print("\tOutput Miss Filename: {}".format(config["imputation_out_miss_file"])) | ||
| print("\tOutput Problem Filename: {}".format(config["imputation_out_problem_file"])) | ||
| print("\tFactor Missing Data: {}".format(config["factor_missing_data"])) | ||
| print("\tLoci Map: {}".format(config["loci_map"])) | ||
| print("\tPlan B Matrix: {}".format(config["matrix_planb"])) | ||
| print("\tPops Count File: {}".format(config["pops_count_file"])) | ||
| print("\tUse Pops Count File: {}".format(config["use_pops_count_file"])) | ||
| print("\tNumber of Options Threshold: {}".format(config["number_of_options_threshold"])) | ||
| print("\tMax Number of haplotypes in phase: {}".format(config["max_haplotypes_number_in_phase"])) | ||
| if config["nodes_for_plan_A"]: | ||
| print("\tNodes in plan A: {}".format(config["nodes_for_plan_A"])) | ||
| print("\tSave space mode: {}".format(config["save_mode"])) | ||
| print('****************************************************************************************************') | ||
|
|
||
|
|
||
| all_loci_set = set() | ||
| for _, val in config["loci_map"].items(): | ||
| all_loci_set.add(str(val)) | ||
|
|
||
| config["full_loci"] = ''.join(sorted(all_loci_set)) | ||
| # Perform imputation | ||
| graph = Graph(config) | ||
| graph.build_graph(config["node_file"], config["top_links_file"], config["edges_file"]) | ||
| imputation = Imputation(graph, config) | ||
|
|
||
| # Create output directory if it doesn't exist | ||
| pathlib.Path(output_dir).mkdir(parents=False, exist_ok=True) | ||
|
|
||
| # Write out the results from imputation | ||
| imputation.impute_file(config) | ||
|
|
||
| # Profiler end | ||
| #pr.disable() | ||
| #pr.print_stats(sort="time") |
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