detect_restriction_enzyme


chr3d.utils.detect_restriction_enzyme(
    fastq_path: str,
    max_reads: int = 1_000_000,
) -> None

Detect which restriction enzyme was used in a Hi-C/HiChIP sample.

Analyzes the first N reads of a paired-end FASTQ to identify which restriction enzyme(s) were used in the library preparation.

Logic:

Enrichment test — A restriction-enzyme cut site should appear at the start of reads far more often than at background positions (because biotin pull-down enriches for ligation junctions).
Junction test — After fill-in and ligation, two identical overhangs are joined, producing a site+site junction (e.g., GATCGATC for MboI). The presence of these junctions at the read start is a definitive signature.
Positional profile — The true enzyme shows a characteristic dual-peak pattern: a large peak at position 0 (cut site) and a second peak offset by len(site)+1 bases (partner ligation site).

This tool is designed for Hi-C and in-situ Hi-C data where reads start at restriction enzyme cut sites. For HiChIP / ChIA-PET data, reads start at linker/adapter sequences. Run this tool on trimmed reads or after the linker-filtering step for accurate detection.

Parameters

Parameter	Type	Description
fastq_path	`str`	Path to FASTQ file (R1 recommended)
max_reads	`int`	Maximum reads to analyze (default: 1,000,000)

Example:


from chr3d.utils import detect_restriction_enzyme
 
# Analyze first 500k reads
detect_restriction_enzyme(
    fastq_path="sample_R1.fastq.gz",
    max_reads=500_000
)
 
# Output includes:
# - Positional profile for each candidate enzyme
# - Enrichment fold-change at position 0
# - Junction counts
# - Recommended enzyme