Hi-C API#

class hictkpy.hic.FileWriter#

Class representing a file handle to create .hic files.

__init__#

Overloaded function.

__init__(self, path: str, chromosomes: dict, resolution: int, assembly: str = 'unknown', n_threads: int = 1, chunk_size: int = 10000000, tmpdir: str = '/tmp', compression_lvl: int = 9, skip_all_vs_all_matrix: bool = False) -> None

Open a .hic file for writing.

__init__(self, path: str, chromosomes: dict, resolutions: list[int], assembly: str = 'unknown', n_threads: int = 1, chunk_size: int = 10000000, tmpdir: str = '/tmp', compression_lvl: int = 9, skip_all_vs_all_matrix: bool = False) -> None

Open a .hic file for writing.

add_pixels#: Add pixels from a pandas DataFrame containing pixels in COO or BG2 format (i.e. either with columns=[bin1_id, bin2_id, count] or with columns=[chrom1, start1, end1, chrom2, start2, end2, count].

chromosomes#: Get chromosomes sizes as a dictionary mapping names to sizes.

finalize#: Write interactions to file.

path#: Get the file path.

resolutions#: Get the list of resolutions in bp.