cell2net.preprocessing.calculate_depth#

cell2net.preprocessing.calculate_depth(chrom_size, starts, ends)#

Calculate genome depth for a given chromosome.

This function computes the depth (coverage) at each base pair of a chromosome based on start and end positions of genomic fragments.

Parameters:

  • chrom_size (int) – The size of the chromosome (total number of base pairs).

  • starts (ndarray) – An array of start positions for the genomic fragments. Each value specifies the zero-based position where a fragment begins.

  • ends (ndarray) – An array of end positions for the genomic fragments. Each value specifies the zero-based position where a fragment ends (exclusive).

Return type:

ndarray

Returns:

A one-dimensional array of length chrom_size, where each position contains the depth (coverage) at that base pair.

Notes

  • The starts and ends arrays must have the same length, as each pair defines a single fragment.

  • The depth is calculated as the count of overlapping fragments for each base pair.

  • This function uses Numba’s Just-In-Time (JIT) compilation to optimize performance, making it suitable for processing large datasets.

Examples

>>> import numpy as np
>>> import cell2net as cn
>>> chrom_size = 10
>>> starts = np.array([0, 2, 4])
>>> ends = np.array([3, 6, 8])
>>> depth = cn.pp.calculate_depth(chrom_size, starts, ends)
>>> print(depth)
array([1, 1, 2, 1, 2, 2, 1, 1, 0, 0], dtype=uint32)