Cleavage Profile

finaletoolkit.frag.cleavage_profile(input_file, chrom_size, contig, start, stop, left=0, right=0, min_length=None, max_length=None, quality_threshold=30, verbose=0, fraction_low=None, fraction_high=None, reference_file=None)[source]

Compute the cleavage profile over a single interval.

Parameters:

  • input_file (str or pysam handle) – BAM/CRAM/fragment input.

  • chrom_size (int) – Length of contig.

  • contig (str) – Contig name.

  • start (int) – 0-based start coordinate.

  • stop (int) – 1-based stop coordinate.

  • left (int, optional) – Amounts to expand the interval on each side (useful when only CpG coordinates are given).

  • right (int, optional) – Amounts to expand the interval on each side (useful when only CpG coordinates are given).

  • min_length (int, optional) – Fragment-length filter.

  • max_length (int, optional) – Fragment-length filter.

  • quality_threshold (int, optional) – Minimum mapping quality (default 30).

  • verbose (bool or int, optional) – Print progress/timing.

  • fraction_low (int, optional) – Deprecated aliases for min_length/max_length.

  • fraction_high (int, optional) – Deprecated aliases for min_length/max_length.

  • reference_file (str or Path, optional) – Reference genome (required for CRAM).

Returns:

Structured array with fields ('contig', 'pos', 'proportion') where proportion is a percentage in [0, 100].

Return type:

numpy.ndarray

finaletoolkit.frag.multi_cleavage_profile(input_file, interval_file, chrom_sizes, left=0, right=0, min_length=None, max_length=None, quality_threshold=30, output_file='-', workers=1, verbose=0, fraction_low=None, fraction_high=None, reference_file=None)[source]

Compute cleavage profiles over intervals in a (sorted) BED file.

Parameters:

  • input_file (str or path) – BAM/CRAM/fragment input.

  • interval_file (str or path) – Sorted BED of intervals ("-" reads stdin).

  • chrom_sizes (str or path) – .chrom.sizes file (required).

  • left (int, optional) – Interval expansion applied before merging overlaps.

  • right (int, optional) – Interval expansion applied before merging overlaps.

  • min_length (int, optional) – Fragment-length filter.

  • max_length (int, optional) – Fragment-length filter.

  • quality_threshold (int, optional) – Minimum mapping quality (default 30).

  • output_file (str, optional) – .bw or .bed.gz/.bedgraph.gz path (default "-").

  • workers (int, optional) – Worker-process count (default 1).

  • verbose (bool or int, optional) – Print progress/timing.

  • fraction_low (int, optional) – Deprecated aliases for min_length/max_length.

  • fraction_high (int, optional) – Deprecated aliases for min_length/max_length.

  • reference_file (str or Path, optional) – Reference genome (required for CRAM).

Returns:

The output path.

Return type:

str