casanovoutils.constants

Shared constants for column names and sentinel values used across the package.

Classes

Constants

Global constants for column names and sentinel values.

Module Contents

class casanovoutils.constants.Constants

Global constants for column names and sentinel values.

ground_truth_sequence_columnstr

Name of the column holding ground truth peptide sequences.

aa_scores_columnstr

Name of the column holding per-amino-acid score strings.

pep_score_columnstr

Name of the column holding peptide-level search engine scores.

aa_idx_columnstr

Name of the column holding per-amino-acid positional indices, added during alignment and explosion.

precision_columnstr

Name of the column holding cumulative precision values computed by calc_precision_coverage.

coverage_columnstr

Name of the column holding cumulative coverage values computed by calc_precision_coverage.

min_scorefloat

Sentinel score assigned to gap positions during sequence alignment.

ground_truth_sequence_column: str = 'mgf_seq'

aa_scores_column: str = 'mztab_opt_ms_run[1]_aa_scores'

pep_score_column: str = 'mztab_search_engine_score[1]'

aa_idx_column: str = 'pc_aa_idx'

precision_column: str = 'pc_precision'

coverage_column: str = 'pc_coverage'

predicted_tokens: str = 'mztab_tokens'

ground_truth_tokens: str = 'mgf_tokens'

min_score: float = -1.0

static get_pred_sequence_column(df: polars.DataFrame) → str

Determine the name of the predicted sequence column.

Checks for the presence of a ProForma-formatted prediction column first, falling back to the plain mzTab sequence column if it is absent.

Parameters:

df (pl.DataFrame) – A DataFrame expected to contain either "mztab_opt_ms_run[1]_proforma" or "mztab_sequence".

Returns:

The name of the predicted sequence column.

Return type:

str