gunz_cm.converters package
Submodules
gunz_cm.converters.coo module
Module for converting contact matrix data from standard formats (like .hic or .cool) into a tabular, sparse COO (Coordinate List) text format.
Examples
>>> from gunz_cm.converters.coo import convert_to_cm_coo
>>> convert_to_cm_coo("sample.cool", "output.csv", resolution=10000)
gunz_cm.converters.gnz module
gunz_cm.converters.memmap module
Module for converting various contact matrix formats into a memory-mapped (memmap) file for efficient, on-disk matrix operations.
Examples
- gunz_cm.converters.memmap.convert_to_memmap(data: Path | DataFrame | Tuple[_Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | complex | bytes | str | _NestedSequence[complex | bytes | str], ...], output_fpath: Path, **kwargs) None
Converts contact matrix data to a NumPy memory-mapped file (memmap).
This is a polymorphic function that dispatches to the appropriate implementation based on the type of the data argument.
- datapathlib.Path or pd.DataFrame or tuple
The input data to convert. Can be: - A path to a standard contact matrix file (.hic, .cool, etc.). - A pandas DataFrame in COO format. - A tuple of (rows, cols, values) arrays.
- output_fpathpathlib.Path
The base path for the output memmap file.
- **kwargs :
Additional arguments specific to the conversion type, such as resolution, balancing, output_full_matrix, etc.
Examples