restriction_site_generator


chr3d.utils.restriction_site_generator(
    enzyme: Union[str, List[str]],
    genome_fasta: str,
    output_file: str,
    min_frag_size: int = 20,
    max_frag_size: int = 1_000_000,
) -> Dict[str, Any]

Generate restriction fragment BED from a genome FASTA.

One-call wrapper around RestrictionSiteGenerator. Convenient function API for generating restriction fragments without instantiating a class.

Parameters

Parameter	Type	Description
enzyme	`Union[str, List[str]]`	Enzyme name (e.g., `'MboI'`), recognition site (e.g., `'^GATC'`), or list for multiple enzymes
genome_fasta	`str`	Path to genome FASTA file (must be indexed with samtools faidx or pyfaidx)
output_file	`str`	Path to output fragment BED file
min_frag_size	`int`	Minimum fragment length to keep (default: 20 bp)
max_frag_size	`int`	Maximum fragment length to keep (default: 1 Mb)

Returns:

Dict[str, Any] — Statistics dictionary with fragment counts per chromosome.

Example:

generate_fragments.py


from chr3d.utils import restriction_site_generator
 
stats = restriction_site_generator(
    enzyme="MboI",
    genome_fasta="/data/genomes/hg38.fa",
    output_file="hg38_MboI_fragments.bed",
)
 
print(f"Fragments: {stats['total_fragments']:,}")