Cleavage Profile#

finaletoolkit.frag.cleavage_profile(input_file: FragFile, chrom_size: int, contig: str, start: int, stop: int, left: int = 0, right: int = 0, min_length: int | None = None, max_length: int | None = None, quality_threshold: int = 30, verbose: bool | int = 0, fraction_low: int | None = None, fraction_high: int | None = None) → np.ndarray#

Cleavage profile calculated over a single interval.

Parameters:

  • input_file (str) – 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.

  • min_length (int) – Minimum fragment size to include

  • max_length (int) – Maximum fragment size to include

  • quality_threshold (int) – Minimum MAPQ

  • verbose (bool or in)

  • fraction_low (int, optional) – Deprecated alias for min_length

  • fraction_high (int, optional) – Deprecated alias for max_length

Returns:

cleavage_proportions – Array of cleavage proportions over given interval.

Return type:

NDArray