RestrictionSiteGenerator


class chr3d.RestrictionSiteGenerator(
    enzyme: Union[str, List[str]],
    min_frag_size: int = 20,
    max_frag_size: int = 1000000,
)

Generate restriction fragment coordinates from genome FASTA.

This class parses restriction enzyme recognition sites and scans a genome FASTA file to identify all restriction sites, creating fragments between consecutive cut positions.

Parameters

Parameter	Type	Description
enzyme	`Union[str, List[str]]`	Enzyme name (e.g., `'MboI'`) or recognition site (e.g., `'^GATC'`). Can be a list for multiple enzymes.
min_frag_size	`int`	Minimum fragment length to keep (default: 20bp)
max_frag_size	`int`	Maximum fragment length to keep (default: 1Mb)

Class Attributes

COMMON_ENZYMES


RestrictionSiteGenerator.COMMON_ENZYMES = {
    'MboI': '^GATC',
    'HindIII': 'A^AGCTT',
    'DpnII': '^GATC',
    'BglII': 'A^GATCT',
    'Sau3AI': '^GATC',
    'Hinf1': 'G^ANTC',
    'NlaIII': 'CATG^',
    'AluI': 'AG^CT',
    'EcoRI': 'G^AATTC',
    'BamHI': 'G^GATCC',
    'PstI': 'CTGCA^G',
    'SalI': 'G^TCGAC',
    'XbaI': 'T^CTAGA'
}

Dictionary of common restriction enzymes and their recognition sites.

Methods

generate_sites


def generate_sites(
    self,
    genome_fasta: str,
    output_file: str,
) -> Dict[str, Any]

Generate restriction fragment file from genome FASTA.

Parameters:

Parameter	Type	Description
genome_fasta	`str`	Path to genome FASTA file
output_file	`str`	Path to output BED file

Returns:

Dict[str, Any] containing:

'total_fragments': Total fragments found
'filtered_fragments': Fragments filtered by size
'chromosomes': Number of chromosomes processed
'total_sites': Total restriction sites found
'fragments_by_chr': Dictionary mapping chromosome → fragment count

Example:

generate_fragments.py


import chr3d as c3d
 
# Single enzyme
generator = c3d.RestrictionSiteGenerator(
    enzyme="MboI",
    min_frag_size=20,
    max_frag_size=1000000
)
 
stats = generator.generate_sites(
    genome_fasta="/data/genomes/hg38.fa",
    output_file="hg38_MboI_fragments.bed"
)
 
print(f"Generated {stats['total_fragments']:,} fragments")
 
# Multiple enzymes
generator = c3d.RestrictionSiteGenerator(
    enzyme=["MboI", "HindIII"]
)