bsxplorer.BinomialData.read_total_stats

classmethod BinomialData.read_total_stats(file: str | Path, report_type: Literal['bismark', 'cgmap', 'bedgraph', 'coverage', 'binom'], block_size_mb: int = 20, use_threads: bool = True, **kwargs)[source]

Get methylation stats from methylation reports file.

Parameters:

  • file – Path to cytosine report.

  • report_type – Type of report. Possible types: “bismark”, “cgmap”, “bedgraph”, “coverage”.

  • block_size_mb – Block size for reading. (Block size ≠ amount of RAM used. Reader allocates approx. Block size * 20 memory for reading.)

  • use_threads – Do multi-threaded or single-threaded reading. If multi-threaded option is used, number of threads is defined by multiprocessing.cpu_count()

  • kwargs – Keyword agruements for reader (e.g. sequence)