obikmer/benchmark/compare_all_dist.py

#!/usr/bin/env python3
"""Compare all reference distance matrices against obikmer phylo outputs.

Reads from:
  reference_dist/   — ground-truth matrices computed by build_reference_dist.py
  obikmer_dist/     — matrices produced by `obikmer phylo`

Handles label reordering: both matrices are sorted by genome label before
element-wise comparison, so column/row order differences are irrelevant.

Output: stats/dist_comparison/summary.csv
  comparison,max_abs,mean_abs,rmse,n_pairs,status
"""
import csv
import sys
from pathlib import Path

import numpy as np


# ── CSV loading ───────────────────────────────────────────────────────────────

def load_matrix(path: Path) -> tuple[list[str], np.ndarray]:
    """Load a distance-matrix CSV; return (sorted_labels, matrix_float64)."""
    with path.open() as fh:
        reader = csv.reader(fh)
        header = next(reader)[1:]     # skip 'genome' column
        raw: dict[str, list[float]] = {}
        for row in reader:
            raw[row[0]] = [float(x) for x in row[1:]]

    label_to_col = {h: i for i, h in enumerate(header)}
    labels = sorted(raw.keys())
    n = len(labels)
    mat = np.zeros((n, n), dtype=np.float64)
    for i, ri in enumerate(labels):
        for j, cj in enumerate(labels):
            mat[i, j] = raw[ri][label_to_col[cj]]
    return labels, mat


# ── comparison ────────────────────────────────────────────────────────────────

def compare(label: str,
            ref_path: Path,
            obi_path: Path,
            tol: float = 1e-4) -> dict:
    if not ref_path.exists():
        return {'comparison': label, 'status': 'REF_MISSING',
                'max_abs': '', 'mean_abs': '', 'rmse': '', 'n_pairs': ''}
    if not obi_path.exists():
        return {'comparison': label, 'status': 'OBI_MISSING',
                'max_abs': '', 'mean_abs': '', 'rmse': '', 'n_pairs': ''}

    ref_labels, ref_mat = load_matrix(ref_path)
    obi_labels, obi_mat = load_matrix(obi_path)

    if ref_labels != obi_labels:
        only_ref = sorted(set(ref_labels) - set(obi_labels))
        only_obi = sorted(set(obi_labels) - set(ref_labels))
        print(f'  [{label}] label mismatch — '
              f'only_ref={only_ref}  only_obi={only_obi}', file=sys.stderr)
        return {'comparison': label, 'status': 'LABEL_MISMATCH',
                'max_abs': '', 'mean_abs': '', 'rmse': '', 'n_pairs': ''}

    n = len(ref_labels)
    # Off-diagonal mask
    mask = ~np.eye(n, dtype=bool)
    diff = np.abs(ref_mat[mask] - obi_mat[mask])
    n_pairs = diff.size

    max_abs  = float(diff.max())
    mean_abs = float(diff.mean())
    rmse     = float(np.sqrt((diff ** 2).mean()))
    status   = 'PASS' if max_abs <= tol else 'FAIL'

    print(f'  [{label}] n={n_pairs}  '
          f'max={max_abs:.3e}  mean={mean_abs:.3e}  rmse={rmse:.3e}  {status}',
          file=sys.stderr)
    return {
        'comparison': label,
        'max_abs':    f'{max_abs:.6e}',
        'mean_abs':   f'{mean_abs:.6e}',
        'rmse':       f'{rmse:.6e}',
        'n_pairs':    str(n_pairs),
        'status':     status,
    }


# ── comparison table ──────────────────────────────────────────────────────────

# (label, ref_csv, obikmer_csv)
# The reference jaccard/shared is presence-based, which should match both
# presence/jaccard and count/jaccard (threshold=1).
COMPARISONS = [
    # ── presence index ────────────────────────────────────────────────────────
    ('presence/jaccard_dist',
     'reference_dist/jaccard_dist.csv',
     'obikmer_dist/presence/jaccard_dist.csv'),

    ('presence/jaccard_shared',
     'reference_dist/shared_kmers.csv',
     'obikmer_dist/presence/jaccard_shared.csv'),

    ('presence/hamming_dist',
     'reference_dist/hamming_dist.csv',
     'obikmer_dist/presence/hamming_dist.csv'),

    # ── count index (jaccard cross-check) ─────────────────────────────────────
    ('count/jaccard_dist',
     'reference_dist/jaccard_dist.csv',
     'obikmer_dist/count/jaccard_dist.csv'),

    ('count/jaccard_shared',
     'reference_dist/shared_kmers.csv',
     'obikmer_dist/count/jaccard_shared.csv'),

    # ── count index (count-based metrics) ────────────────────────────────────
    ('count/bray_curtis_dist',
     'reference_dist/bray_curtis_dist.csv',
     'obikmer_dist/count/bray_curtis_dist.csv'),

    ('count/relfreq_bray_curtis_dist',
     'reference_dist/relfreq_bray_curtis_dist.csv',
     'obikmer_dist/count/relfreq_bray_curtis_dist.csv'),

    ('count/euclidean_dist',
     'reference_dist/euclidean_dist.csv',
     'obikmer_dist/count/euclidean_dist.csv'),

    ('count/relfreq_euclidean_dist',
     'reference_dist/relfreq_euclidean_dist.csv',
     'obikmer_dist/count/relfreq_euclidean_dist.csv'),

    ('count/hellinger_dist',
     'reference_dist/hellinger_dist.csv',
     'obikmer_dist/count/hellinger_dist.csv'),

    ('count/hellinger_euclidean_dist',
     'reference_dist/hellinger_euclidean_dist.csv',
     'obikmer_dist/count/hellinger_euclidean_dist.csv'),
]


# ── main ─────────────────────────────────────────────────────────────────────

def main() -> None:
    import argparse
    ap = argparse.ArgumentParser(description=__doc__,
                                 formatter_class=argparse.RawDescriptionHelpFormatter)
    ap.add_argument('--tol', type=float, default=1e-4,
                    help='Max abs diff threshold for PASS/FAIL (default 1e-4)')
    ap.add_argument('--run-dir', default='run',
                    help='Root directory holding reference_dist/ and obikmer_dist/ (default: run)')
    ap.add_argument('--out', default='run/stats/dist_comparison/summary.csv',
                    help='Output summary CSV path')
    args = ap.parse_args()

    out_path = Path(args.out)
    out_path.parent.mkdir(parents=True, exist_ok=True)

    run_dir = Path(args.run_dir)
    print(f'Comparing {len(COMPARISONS)} matrix pairs…', file=sys.stderr)
    rows = []
    for label, ref, obi in COMPARISONS:
        rows.append(compare(label, run_dir / ref, run_dir / obi, tol=args.tol))

    fields = ['comparison', 'max_abs', 'mean_abs', 'rmse', 'n_pairs', 'status']
    with out_path.open('w', newline='') as fh:
        w = csv.DictWriter(fh, fieldnames=fields)
        w.writeheader()
        w.writerows(rows)

    print(f'\n→ {out_path}', file=sys.stderr)

    n_fail = sum(1 for r in rows if r.get('status') == 'FAIL')
    n_pass = sum(1 for r in rows if r.get('status') == 'PASS')
    print(f'Summary: {n_pass} PASS  {n_fail} FAIL  '
          f'{len(rows) - n_pass - n_fail} SKIP', file=sys.stderr)
    if n_fail:
        sys.exit(1)


if __name__ == '__main__':
    main()