bsxplorer.UniversalReader

class UniversalReader(file: str | Path, report_type: Literal['bismark', 'cgmap', 'bedgraph', 'coverage', 'binom'], use_threads: bool = False, bar: bool = True, **kwargs)

Class for batched reading methylation reports.

Parameters:

• file – Path to the methylation report file.

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

• use_threads – Will reading be multithreaded.

• bar – Indicate the progres bar while reading.

• kwargs – Specific keyword arguments to the reader.

• cytosine_file (str | Path) – Instance of Sequence for reading bedGraph or .coverage reports.

• methylation_pvalue (float) – Pvalue with which cytosine will be considered methylated.

• block_size_mb (int) – Size of batch in bytes, which will be read from report file (for report types other than “binom”).

Examples

>>> reader = UniversalReader("path/to/file.txt", report_type="bismark", use_threads=True)
>>> for batch in reader:
>>>     do_something(batch)

Methods

__init__

property batch_size

returns: Size of batch in bytes. :rtype: int

property file_size

returns: File size in bytes. :rtype: int