Source code for proteobench.io.params.piprimenovo

"""
Pi-PrimeNovo parameter parsing.
"""

from __future__ import annotations

import yaml

from proteobench.io.params import ProteoBenchParameters




def extract_params(file_path: str) -> ProteoBenchParameters:
    """
    Extract parameters from the config file.

    Parameters
    ----------
    file_path : str
        The path to the config file.

    Returns
    -------
    ProteoBenchParameters
        The extracted parameters as a ProteoBenchParameters object.
    """
    params = ProteoBenchParameters(json_path="denovo/denovo_lfq_DDA_HCD.json")

    try:
        file = yaml.safe_load(file_path)
    except:
        with open(file_path) as f:
            file = yaml.load(f, yaml.SafeLoader)

    params.software_name = "Pi-PrimeNovo"
    params.checkpoint = file["load_file_name"]
    params.n_beams = file["n_beams"]
    params.n_peaks = file["n_peaks"]
    params.precursor_mass_tolerance = file["precursor_mass_tol"]
    # params.min_peptide_length = file["min_peptide_len"]
    params.max_peptide_length = file["max_length"]
    params.min_mz = file["min_mz"]
    params.max_mz = file["max_mz"]
    params.min_intensity = file["min_intensity"]
    params.tokens = "; ".join(list(file["residues"].keys()))
    params.max_precursor_charge = file["max_charge"]
    params.remove_precursor_tol = file["remove_precursor_tol"]
    params.isotope_error_range = str(file["isotope_error_range"])

    if file["PMC_enable"]:
        if file["n_beams"] > 1:
            params.decoding_strategy = f"beam search + PMC [{file['mass_control_tol']} Da]"
        else:
            params.decoding_strategy = f"greedy search + PMC [{file['mass_control_tol']} Da]"
    else:
        if file["n_beams"] > 1:
            params.decoding_strategy = f"beam search"
        else:
            params.decoding_strategy = f"greedy search"

    params.fill_none()
    return params