Complete Workflow Example

import chr3d as c3d
from chr3d.utils import restriction_site_generator, loops_to_beddb
 
# Step 1: Generate restriction fragments
stats = restriction_site_generator(
    enzyme="MboI",
    genome_fasta="/data/genomes/hg38.fa",
    output_file="hg38_MboI_fragments.bed",
)
 
# Step 2: Run Hi-C pipeline
hic = c3d.HiCPipeline(
    genome_index="/data/genomes/hg38.fa",
    chrom_sizes="/data/genomes/hg38.chrom.sizes",
    threads=24,
    fragment_bed="hg38_MboI_fragments.bed",  # Enable fragment-aware processing
)
 
hic_stats = hic.run(
    fastq1="sample_R1.fastq.gz",
    fastq2="sample_R2.fastq.gz",
    output_dir="results/",
)
 
# Step 3: Convert loops to HiGlass format
loop_stats = loops_to_beddb(
    loops_csv="results/loops/significant_loops.csv",
    peaks_path="results/peaks/peaks.narrowPeak",
    output_bedpe="results/loops/loops.bedpe",
    output_bedpedb="results/loops/loops.bedpedb",
    chromsizes_path="/data/genomes/hg38.chrom.sizes",
)