Generic API#

hictkpy.is_cooler(path: str) → bool#: Test whether path points to a cooler file.

hictkpy.is_mcool_file(path: str) → bool#: Test whether path points to a .mcool file.

hictkpy.is_scool_file(path: str) → bool#: Test whether path points to a .scool file.

hictkpy.is_hic(path: str) → bool#: Test whether path points to a .hic file.

class hictkpy.MultiResFile#

Class representing a file handle to a .hic or .mcool file

__init__#: Open a multi-resolution Cooler file (.mcool).

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

path#: Get the file path.

resolutions#: Get the list of available resolutions.

class hictkpy.File#

Class representing a file handle to a .cool or .hic file.

__init__#: Construct a file object to a .hic, .cool or .mcool file given the file path and resolution. Resolution is ignored when opening single-resolution Cooler files.

attributes#: Get file attributes as a dictionary.

avail_normalizations#: Get the list of available normalizations.

bins#: Get bins as a pandas DataFrame.

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

fetch#: Fetch interactions overlapping a region of interest.

has_normalization#: Check whether a given normalization is available.

is_cooler#: Test whether file is in .cool format.

is_hic#: Test whether file is in .hic format.

nbins#: Get the total number of bins.

nchroms#: Get the total number of chromosomes.

path#: Return the file path.

resolution#: Get the bin size in bp.

uri#: Return the file URI.

weights#: Fetch the balancing weights for the given normalization method.

class hictkpy.PixelSelector#

Class representing pixels overlapping with the given genomic intervals.

coord1#: Get query coordinates for the first dimension.

coord2#: Get query coordinates for the second dimension.

nnz#: Get the number of non-zero entries for the current pixel selection.

sum#: Get the total number of interactions for the current pixel selection.

to_coo#: Retrieve interactions as a scipy.sparse.coo_matrix.

to_df#: Retrieve interactions as a pandas DataFrame.

to_numpy#: Retrieve interactions as a numpy 2D matrix.