Cleavage Profile

finaletoolkit.frag.cleavage_profile(input_file: str, chrom_size: int, contig: str, start: int, stop: int, left: int = 0, right: int = 0, fraction_low: int = 1, fraction_high: int = 10000000, quality_threshold: int = 30, verbose: bool | int = 0) → ndarray

Cleavage profile calculated over a single interval.

Parameters:

• input_file (str) – SAM, BAM, CRAM, or FRAG file with fragment information.

• chrom_size (int) – length of contig.

• contig (str) – Chromosome or contig

• start (int) – 0-based start coordinate

• stop (int) – 1-based end coordinate

• left (int) – Amount to subtract from start coordinate. Useful if only given coordinates of CpG.

• right (int) – Amount to add to stop coordinate.

• fraction_low (int) – Minimum fragment size to include

• fraction_high (int) – Maximum fragment size to include

• quality_threshold (int) – Minimum MAPQ

• verbose (bool or in)

Returns:

cleavage_proportions – Array of cleavage proportions over given interval.

Return type:

NDArray