loops_to_beddb


chr3d.utils.loops_to_beddb(
    loops_csv: str,
    peaks_path: str,
    output_bedpe: str,
    output_bedpedb: str,
    assembly: str = "hg38",
    p_value_col: str = "p_adj_fdr_bh",
    significant_col: str = "significant_fdr_bh",
    canonical_chroms_only: bool = True,
    max_score: float = 300.0,
    chromsizes_path: str = None,
    skip_verify: bool = False,
) -> Dict[str, Any]

Convert significant-loops CSV + narrowPeak → BEDPE → bedpedb (HiGlass).

One-call wrapper that chains csv_to_bedpe, bedpe_to_bedpedb, and optionally verify_positions.

Parameters

Parameter	Type	Description
loops_csv	`str`	Path to significant loops CSV file
peaks_path	`str`	Path to narrowPeak file
output_bedpe	`str`	Path for intermediate BEDPE output
output_bedpedb	`str`	Path for final bedpedb (HiGlass SQLite) output
assembly	`str`	Genome assembly name (default: `"hg38"`)
p_value_col	`str`	Column name for p-values in loops CSV (default: `"p_adj_fdr_bh"`)
significant_col	`str`	Column name for significance flag in loops CSV (default: `"significant_fdr_bh"`)
canonical_chroms_only	`bool`	Keep only canonical chromosomes (default: `True`)
max_score	`float`	Maximum -log10(p) score (default: 300)
chromsizes_path	`str`	Path to chromosome sizes file (needed for verification)
skip_verify	`bool`	Skip position verification step (default: `False`)

Returns:

Dict[str, Any] — Combined statistics from all conversion steps, plus "verification_passed" key if verification was run.

Example:


from chr3d.utils import loops_to_beddb
 
stats = loops_to_beddb(
    loops_csv="significant_loops.csv",
    peaks_path="peaks.narrowPeak",
    output_bedpe="loops.bedpe",
    output_bedpedb="loops.bedpedb",
    chromsizes_path="hg38.chrom.sizes",
)
 
print(f"Final loops: {stats['n_final']}")
print(f"Verification: {stats['verification_passed']}")