select_good.py

#!/usr/bin/env python
from __future__ import print_function
import os
from IMP import ArgumentParser


__doc__ = "List/extract good-scoring models from a set of sampling runs."""


def parse_args():
    parser = ArgumentParser(
        description="List and extract good-scoring models from a set of "
        "sampling runs. Example of usage: "
        "%(prog)s -rd <run_directory_for_sampling> -rp <run_prefix> -sl "
        "ExcludedVolumeSphere_None GaussianEMRestraint_None "
        "-pl CrossLinkingMassSpectrometryDataScore|"
        "XLDSS CrossLinkingMassSpectrometryDataScore|XLEDC -agl -9999999.0 "
        "-99999.0 -aul 99999999.0 999999.0 -mlt 0 0 -mut 0 0. Flag -h "
        "for more details.")

    parser.add_argument("-rd", "--run_directory", dest="run_dir",
                        help="directory in which sampling results are stored",
                        required=True)

    parser.add_argument("-rp", "--run_prefix", dest="run_prefix",
                        help="prefix of runs", required=True)

    parser.add_argument("-sl", "--selection_keywords_list", nargs='+',
                        type=str, dest="selection_keywords_list",
                        help="list of stat file keywords corresponding to "
                             "selection criteria")
    parser.add_argument("-pl", "--printing_keywords_list", nargs='+',
                        type=str, dest="printing_keywords_list",
                        help="list of stat file keywords whose values are "
                             "printed out for selected models")

    # thresholds only apply to selection keywords
    parser.add_argument("-alt", "--aggregate_lower_thresholds", nargs='+',
                        type=float, dest="aggregate_lower_thresholds",
                        help="aggregate lower thresholds")
    parser.add_argument("-aut", "--aggregate_upper_thresholds", nargs='+',
                        type=float, dest="aggregate_upper_thresholds",
                        help="aggregate upper thresholds")
    parser.add_argument("-mlt", "--member_lower_thresholds", nargs='+',
                        type=float, dest="member_lower_thresholds",
                        help="member lower thresholds")
    parser.add_argument("-mut", "--member_upper_thresholds", nargs='+',
                        type=float, dest="member_upper_thresholds",
                        help="member upper thresholds")

    parser.add_argument("-e", "--extract", default=False, dest="extract",
                        action='store_true',
                        help="Type -e to extract all good scoring model "
                             "RMFs from the trajectory files")
    parser.add_argument("-sf", "--score_file", default="scores", type=str,
                        dest="score_file_prefix",
                        help="Score file prefix for samples A and B. "
                             "Default is %(default)r")
    result = parser.parse_args()

    return result


def select_good_scoring_models():
    from IMP.sampcon.good_scoring_model_selector \
            import GoodScoringModelSelector

    # process input
    arg = parse_args()

    gsms = GoodScoringModelSelector(arg.run_dir, arg.run_prefix)

    subsets = gsms.get_good_scoring_models(
        selection_keywords_list=arg.selection_keywords_list,
        printing_keywords_list=arg.printing_keywords_list,
        aggregate_lower_thresholds=arg.aggregate_lower_thresholds,
        aggregate_upper_thresholds=arg.aggregate_upper_thresholds,
        member_lower_thresholds=arg.member_lower_thresholds,
        member_upper_thresholds=arg.member_upper_thresholds,
        extract=arg.extract)
    return subsets, arg.extract


def create_score_files(subsets, field="Total_Score"):
    arg = parse_args()

    score_dir = os.path.join(arg.run_dir, "good_scoring_models")
    scoreA = open(os.path.join(score_dir, arg.score_file_prefix + "A.txt"),
                  "w")
    scoreB = open(os.path.join(score_dir, arg.score_file_prefix + "B.txt"),
                  "w")
    model_file = open(os.path.join(score_dir, "model_ids_scores.txt"), "r")

    print("Creating input files for Total_Score convergence test")

    for line_index, each_model_line in enumerate(model_file.readlines()):

        # Find index of the field we want to use for model score convergence
        if line_index == 0:
            field_headers = each_model_line.strip().split()

            try:
                ts_ix = field_headers.index(field)
                _ = field_headers.index("Run_id")
                model_ix = field_headers.index("Model_index")

            except ValueError:
                print("create_scores_file: model_ids_scores.txt file has "
                      "an incorrect format.")
                exit()

        else:
            fields = each_model_line.strip().split()

            score = fields[ts_ix]

            model = int(fields[model_ix])
            print(score, file=scoreA if model in subsets[0] else scoreB)

    scoreA.close()
    scoreB.close()


def main():
    subsets, extract = select_good_scoring_models()

    print("Filtered model scores ready")

    if extract:

        # Create Score Files
        create_score_files(subsets)

        print("Ready to calculate sampling precision with "
              "Master_Sampling_Exhaustiveness_Analysis.py")


if __name__ == "__main__":
    main()