casanovoutils.summarize_mgf =========================== .. py:module:: casanovoutils.summarize_mgf .. autoapi-nested-parse:: MGF file visualization tools. fragment-coverage: Calculate the proportion of total fragment ion intensity explained by b- and y-ions (including neutral losses of NH3 and H2O) for each spectrum in an annotated MGF file. The peptide annotation is read from the SEQ= field (ProForma notation). Outputs: 1. A TSV with columns: scan, filename, sequence, charge, n_peaks, n_matched, proportion_matched 2. A histogram (PNG) of the proportion distribution. charge-distribution: Compute the global charge state distribution from an MGF file. Outputs: 1. A TSV with columns: charge, count 2. A bar chart (PNG) of the distribution. peak-counts: Count the number of peaks per spectrum in an MGF file. Outputs: 1. A TSV with columns: n_peaks, count 2. A histogram (PNG) of the distribution. peptide-lengths: Measure peptide lengths for annotated spectra in an MGF file. Requires SEQ= field in ProForma notation. Outputs: 1. A TSV with columns: length, count 2. A histogram (PNG) of the distribution. summarize-mgf: Produce a self-contained HTML summary of an MGF file with basic statistics and embedded histograms for charge state distribution, peaks per spectrum, peptide lengths, and fragment ion coverage. Requires: pyteomics, spectrum_utils, numpy, matplotlib Attributes ---------- .. autoapisummary:: casanovoutils.summarize_mgf.COMMANDS Functions --------- .. autoapisummary:: casanovoutils.summarize_mgf.count_charge_states casanovoutils.summarize_mgf.charge_distribution casanovoutils.summarize_mgf.count_peaks casanovoutils.summarize_mgf.peak_counts casanovoutils.summarize_mgf.measure_peptide_lengths casanovoutils.summarize_mgf.peptide_lengths casanovoutils.summarize_mgf.fragment_coverage casanovoutils.summarize_mgf.summarize_mgf casanovoutils.summarize_mgf.main Module Contents --------------- .. py:function:: count_charge_states(spectra: Iterable) -> tuple[dict[int, int], int] Count precursor charge states across spectra. :param spectra: Iterable of pyteomics spectrum dicts. :type spectra: iterable :returns: * **counts** (*dict[int, int]*) -- Mapping of charge state to count. * **n_skipped** (*int*) -- Number of spectra skipped (missing, empty, or multiple charge states). .. py:function:: charge_distribution(mgf_file: os.PathLike, output_tsv: os.PathLike = 'charge_distribution.tsv', output_plot: os.PathLike = 'charge_distribution.png') -> None Charge state distribution for an MGF file. :param mgf_file: Input MGF file. :type mgf_file: PathLike :param output_tsv: Output TSV path (default: charge_distribution.tsv). :type output_tsv: PathLike :param output_plot: Output bar chart path (default: charge_distribution.png). :type output_plot: PathLike .. py:function:: count_peaks(spectra: Iterable) -> list[int] Return the number of peaks for each spectrum. :param spectra: Iterable of pyteomics spectrum dicts. :type spectra: Iterable :returns: Peak count for each spectrum, in input order. :rtype: list[int] .. py:function:: peak_counts(mgf_file: os.PathLike, output_tsv: os.PathLike = 'peak_counts.tsv', output_plot: os.PathLike = 'peak_counts.png') -> None Number of peaks per spectrum in an MGF file. :param mgf_file: Input MGF file. :type mgf_file: PathLike :param output_tsv: Output TSV path (default: peak_counts.tsv). :type output_tsv: PathLike :param output_plot: Output histogram path (default: peak_counts.png). :type output_plot: PathLike .. py:function:: measure_peptide_lengths(spectra: Iterable) -> tuple[list[int], int] Return (lengths, n_skipped) for annotated spectra. Spectra without SEQ= or with invalid ProForma sequences are counted as skipped. .. py:function:: peptide_lengths(mgf_file: os.PathLike, output_tsv: os.PathLike = 'peptide_lengths.tsv', output_plot: os.PathLike = 'peptide_lengths.png') -> None Peptide length distribution for annotated spectra in an MGF file. :param mgf_file: Input MGF file. :type mgf_file: PathLike :param output_tsv: Output TSV path (default: peptide_lengths.tsv). :type output_tsv: PathLike :param output_plot: Output histogram path (default: peptide_lengths.png). :type output_plot: PathLike .. py:function:: fragment_coverage(mgf_file, tolerance=0.05, tolerance_unit='Da', output_tsv='fragment_coverage.tsv', output_full_tsv='fragment_coverage.full.tsv', output_plot='fragment_coverage.png', workers=1, max_charge='1less', neutral_losses=True) Fragment ion intensity coverage for annotated MGF spectra. :param mgf_file: Annotated MGF file (with SEQ= in ProForma notation). :type mgf_file: str :param tolerance: Mass tolerance (default: 10). :type tolerance: float :param tolerance_unit: Tolerance unit: 'ppm' or 'Da' (default: ppm). :type tolerance_unit: str :param output_tsv: Output TSV path (default: fragment_coverage.tsv). :type output_tsv: str :param output_full_tsv: Output per-spectrum TSV path (default: fragment_coverage.full.tsv). :type output_full_tsv: str :param output_plot: Output histogram path (default: fragment_coverage.png). :type output_plot: str :param workers: Number of parallel worker processes (default: 1). :type workers: int :param max_charge: Maximum charge state for fragment ions: 'max' (precursor charge) or '1less' (precursor charge minus one, default). :type max_charge: str :param neutral_losses: Include neutral losses in annotation (default: True). :type neutral_losses: bool .. py:function:: summarize_mgf(mgf_file: os.PathLike, output_root: os.PathLike = 'mgf_summary', tolerance: float = 0.05, tolerance_unit: str = 'Da', workers: int = 1, max_charge: str = '1less', neutral_losses: bool = True) -> None Produce a self-contained HTML summary of an MGF file. :param mgf_file: Input MGF file. :type mgf_file: PathLike :param output_root: Output directory name; the HTML file inside will share this basename (default: mgf_summary). :type output_root: PathLike :param tolerance: Fragment mass tolerance for coverage calculation (default: 10). :type tolerance: float :param tolerance_unit: Tolerance unit: 'ppm' or 'Da' (default: ppm). :type tolerance_unit: str :param workers: Number of parallel worker processes for coverage annotation (default: 1). :type workers: int :param max_charge: Maximum charge state for fragment ions: 'max' (precursor charge) or '1less' (precursor charge minus one, default). :type max_charge: str :param neutral_losses: Include neutral losses in annotation (default: True). :type neutral_losses: bool .. py:data:: COMMANDS .. py:function:: main() -> None