Cooler API#

class hictkpy.cooler.SingleCellFile#

Class representing a file handle to a .scool file.

__init__#: Open a single-cell Cooler file (.scool).

attributes#: Get file attributes as a dictionary.

bins#: Get bins as a pandas DataFrame.

cells#: Get the list of available cells.

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

path#: Get the file path.

resolution#: Get the bin size in bp.

class hictkpy.cooler.FileWriter#

Class representing a file handle to create .cool files.

__init__#: Open a .cool 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 resolution in bp.