RunnerIOConfig

class pyprophet._config.RunnerIOConfig(infile: str, outfile: str, subsample_ratio: float, level: str, context: str, runner: RunnerConfig)

Bases: BaseIOConfig

Wrapper configuration class for I/O and runner parameters.

infile

Input file path (.osw, .parquet, or .tsv).

Type:

str

outfile

Output file path (same format as input).

Type:

str

level

Scoring level (‘ms1’, ‘ms2’, ‘ms1ms2’, ‘transition’, or ‘alignment’).

Type:

str

context

Optional scoring context (e.g. ‘experiment-wide’, not commonly used).

Type:

str

prefix

Derived from outfile, used as prefix for output artifacts.

Type:

str

runner

All scoring and learning configuration settings.

Type:

RunnerConfig

extra_writes

Dictionary of named output paths (e.g., report, weights, summary).

Type:

dict

__eq__(other)

Return self==value.

__hash__ = None

__init__(infile: str, outfile: str, subsample_ratio: float, level: str, context: str, runner: RunnerConfig) → None

__post_init__()

Initialize the file_type and prefix attributes based on the input file.

__repr__()

Return repr(self).

__str__()

Return str(self).

_extra_writes()

Generates paths for various output files based on the prefix provided.

Yields:

Tuple[str, str] – A tuple containing the name of the output file type and the corresponding file path.

classmethod from_cli_args(infile, outfile, subsample_ratio, level, context, classifier, autotune, xeval_fraction, xeval_num_iter, ss_initial_fdr, ss_iteration_fdr, ss_num_iter, ss_main_score, ss_score_filter, ss_scale_features, group_id, parametric, pfdr, pi0_lambda, pi0_method, pi0_smooth_df, pi0_smooth_log_pi0, lfdr_truncate, lfdr_monotone, lfdr_transformation, lfdr_adj, lfdr_eps, ipf_max_peakgroup_rank, ipf_max_peakgroup_pep, ipf_max_transition_isotope_overlap, ipf_min_transition_sn, add_alignment_features, glyco, density_estimator, grid_size, tric_chromprob, threads, test, color_palette, main_score_selection_report)

Creates a configuration object from command-line arguments.