predict_dir.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

"""
predict_models_dir.py

Predict for all models in models_dir on a folder of FASTA genomes.
Optionally annotate with ground truth from a TSV and compute the same metrics
as in your original script (overall + Isolate + MAG + AUC).

Inputs:
  --genomes_dir   Folder with FASTA files (.fna/.fa/.fasta)
  --models_dir    Folder with model_*.joblib + feature_columns_*.json
  --outdir        Output folder
  --truth_tsv     OPTIONAL: genomes-all_metadata_with_genetic_code_id_noNA.tsv
                  (must contain Genome, Genome_type, Genetic_code_ID)

Ground truth (if provided):
  ALT = Genetic_code_ID != 11
  STD = Genetic_code_ID == 11

Outputs:
  - <outdir>/<model>__pred.csv                          (per model, per genome)
  - <outdir>/all_models_predictions_long.csv            (long: model x genome)
  - <outdir>/prediction_summary.csv                     (ONLY if truth_tsv is provided)
  - <outdir>/top_models_by_pr_auc.txt                   (ONLY if truth_tsv is provided)

Requires:
  - aragorn in PATH (or pass --aragorn)
"""

import os
import re
import json
import time
import argparse
import subprocess
from pathlib import Path
from collections import Counter

import numpy as np
import pandas as pd
from joblib import load as joblib_load

from sklearn.metrics import (
    confusion_matrix,
    accuracy_score,
    precision_score,
    recall_score,
    f1_score,
    roc_auc_score,
    average_precision_score,
)

from sklearn.base import BaseEstimator, ClassifierMixin, clone


# =========================
# PU class (for joblib load)
# =========================
class PUBaggingClassifier(BaseEstimator, ClassifierMixin):
    def __init__(self, base_estimator, n_bags=15, u_ratio=3.0, random_state=42):
        self.base_estimator = base_estimator
        self.n_bags = int(n_bags)
        self.u_ratio = float(u_ratio)
        self.random_state = int(random_state)
        self.models_ = None
        self.classes_ = np.array([0, 1], dtype=int)

    def fit(self, X, y, sample_weight=None):
        y = np.asarray(y).astype(int)
        pos_idx = np.where(y == 1)[0]
        unl_idx = np.where(y == 0)[0]
        if pos_idx.size == 0:
            raise ValueError("PU training requires at least one positive sample (y==1).")

        rng = np.random.RandomState(self.random_state)
        self.models_ = []

        if unl_idx.size == 0:
            m = clone(self.base_estimator)
            try:
                if sample_weight is not None:
                    m.fit(X, y, sample_weight=np.asarray(sample_weight))
                else:
                    m.fit(X, y)
            except TypeError:
                m.fit(X, y)
            self.models_.append(m)
            return self

        k_u = int(min(unl_idx.size, max(1, round(self.u_ratio * pos_idx.size))))
        for _ in range(self.n_bags):
            u_b = rng.choice(unl_idx, size=k_u, replace=(k_u > unl_idx.size))
            idx_b = np.concatenate([pos_idx, u_b])
            X_b = X.iloc[idx_b] if hasattr(X, "iloc") else X[idx_b]
            y_b = y[idx_b]

            sw_b = None
            if sample_weight is not None:
                sw_b = np.asarray(sample_weight)[idx_b]

            m = clone(self.base_estimator)
            try:
                if sw_b is not None:
                    m.fit(X_b, y_b, sample_weight=sw_b)
                else:
                    m.fit(X_b, y_b)
            except TypeError:
                m.fit(X_b, y_b)

            self.models_.append(m)
        return self

    def predict_proba(self, X):
        if not self.models_:
            raise RuntimeError("PUBaggingClassifier not fitted")
        probs = [m.predict_proba(X) for m in self.models_]
        return np.mean(np.stack(probs, axis=0), axis=0)

    def predict(self, X):
        return (self.predict_proba(X)[:, 1] >= 0.5).astype(int)


# =========================
# Feature extraction
# =========================
CODON_RE = re.compile(r"\(([ACGTUacgtu]{3})\)")

def set_single_thread_env():
    os.environ["OMP_NUM_THREADS"] = "1"
    os.environ["OPENBLAS_NUM_THREADS"] = "1"
    os.environ["MKL_NUM_THREADS"] = "1"
    os.environ["VECLIB_MAXIMUM_THREADS"] = "1"
    os.environ["NUMEXPR_NUM_THREADS"] = "1"

def list_fasta_files(genomes_dir: str):
    exts = (".fna", ".fa", ".fasta")
    paths = []
    for fn in os.listdir(genomes_dir):
        p = os.path.join(genomes_dir, fn)
        if not os.path.isfile(p):
            continue
        if fn.endswith(exts):
            paths.append(p)
    return sorted(paths)

def calc_gc_and_tetra(fasta_path):
    bases = ["A", "C", "G", "T"]
    all_kmers = ["".join([a, b, c, d]) for a in bases for b in bases for c in bases for d in bases]
    tetra_counts = {k: 0 for k in all_kmers}

    A = C = G = T = 0
    tail = ""

    with open(fasta_path, "r") as fh:
        for line in fh:
            if line.startswith(">"):
                continue
            s = line.strip().upper().replace("U", "T")
            s = re.sub(r"[^ACGT]", "N", s)
            if not s:
                continue

            seq = tail + s

            for ch in s:
                if ch == "A": A += 1
                elif ch == "C": C += 1
                elif ch == "G": G += 1
                elif ch == "T": T += 1

            for i in range(len(seq) - 3):
                k = seq[i:i+4]
                if "N" in k:
                    continue
                tetra_counts[k] += 1

            tail = seq[-3:] if len(seq) >= 3 else seq

    total_acgt = A + C + G + T
    gc_percent = (float(G + C) / float(total_acgt) * 100.0) if total_acgt > 0 else 0.0

    windows_total = sum(tetra_counts.values())
    denom = float(windows_total) if windows_total > 0 else 1.0
    tetra_freq = {f"tetra_{k}": float(v) / denom for k, v in tetra_counts.items()}

    features = {
        "gc_percent": float(gc_percent),
        "genome_length": float(total_acgt),
    }
    features.update(tetra_freq)
    return features

def run_aragorn(aragorn_bin, fasta_path, out_txt):
    cmd = [aragorn_bin, "-t", "-l", "-gc1", "-w", "-o", out_txt, fasta_path]
    with open(os.devnull, "w") as devnull:
        subprocess.run(cmd, stdout=devnull, stderr=devnull, check=False)

def parse_anticodons_from_aragorn(aragorn_txt):
    counts = Counter()
    if not os.path.isfile(aragorn_txt):
        return counts
    with open(aragorn_txt, "r") as fh:
        for line in fh:
            for m in CODON_RE.finditer(line):
                cod = m.group(1).upper().replace("U", "T")
                if re.fullmatch(r"[ACGT]{3}", cod):
                    counts[cod] += 1
    return counts

def build_ac_features(anticodon_counts):
    bases = ["A", "C", "G", "T"]
    feats = {}
    for a in bases:
        for b in bases:
            for c in bases:
                cod = f"{a}{b}{c}"
                feats[f"ac_{cod}"] = float(anticodon_counts.get(cod, 0))
    return feats

def build_plr_features(ac_features, needed_plr_cols, eps=0.5):
    plr_feats = {}
    for col in needed_plr_cols:
        core = col[len("plr_"):]
        left, right = core.split("__")
        a = ac_features.get(f"ac_{left}", 0.0)
        b = ac_features.get(f"ac_{right}", 0.0)
        plr_feats[col] = float(np.log((a + eps) / (b + eps)))
    return plr_feats

def build_features_for_genome(fasta_path, aragorn_bin, feature_columns, reuse_aragorn=True):
    acc = os.path.splitext(os.path.basename(fasta_path))[0]

    feat_gc_tetra = calc_gc_and_tetra(fasta_path)

    tmp_aragorn = fasta_path + ".aragorn.txt"
    if reuse_aragorn and os.path.isfile(tmp_aragorn):
        try:
            if os.path.getmtime(tmp_aragorn) < os.path.getmtime(fasta_path):
                run_aragorn(aragorn_bin, fasta_path, tmp_aragorn)
        except Exception:
            run_aragorn(aragorn_bin, fasta_path, tmp_aragorn)
    else:
        run_aragorn(aragorn_bin, fasta_path, tmp_aragorn)

    anticodon_counts = parse_anticodons_from_aragorn(tmp_aragorn)
    ac_feats = build_ac_features(anticodon_counts)

    plr_cols = [c for c in feature_columns if c.startswith("plr_")]
    plr_feats = build_plr_features(ac_feats, plr_cols) if plr_cols else {}

    all_feats = {}
    all_feats.update(ac_feats)
    all_feats.update(plr_feats)
    all_feats.update(feat_gc_tetra)

    row = {col: float(all_feats.get(col, 0.0)) for col in feature_columns}
    return acc, row


# =========================
# Ground truth from TSV (optional)
# =========================
def load_truth_tsv(tsv_path: str) -> pd.DataFrame:
    df = pd.read_csv(tsv_path, sep="\t", dtype=str)

    for col in ["Genome", "Genome_type", "Genetic_code_ID"]:
        if col not in df.columns:
            raise ValueError(f"TSV missing column '{col}'. Columns: {list(df.columns)}")

    df["Genome"] = df["Genome"].astype(str)
    df["Genome_type"] = df["Genome_type"].astype(str)
    df["Genetic_code_ID"] = pd.to_numeric(df["Genetic_code_ID"], errors="coerce").astype("Int64")

    # ALT ground truth: != 11
    df["y_true_alt"] = df["Genetic_code_ID"].apply(lambda x: (pd.notna(x) and int(x) != 11)).astype(int)
    df["true_label"] = df["y_true_alt"].map({0: "STD", 1: "ALT"})

    return df[["Genome", "Genome_type", "Genetic_code_ID", "y_true_alt", "true_label"]]


# =========================
# Metrics (only if truth exists)
# =========================
def safe_confusion(y_true, y_pred):
    cm = confusion_matrix(y_true, y_pred, labels=[0, 1])
    tn, fp, fn, tp = int(cm[0,0]), int(cm[0,1]), int(cm[1,0]), int(cm[1,1])
    return tn, fp, fn, tp

def compute_metrics_block(y_true, y_pred, y_score=None):
    y_true = np.asarray(y_true, dtype=int)
    y_pred = np.asarray(y_pred, dtype=int)

    tn, fp, fn, tp = safe_confusion(y_true, y_pred)
    n = int(len(y_true))
    pos = int(np.sum(y_true == 1))

    out = {
        "n": n,
        "positives": pos,
        "tn": tn, "fp": fp, "fn": fn, "tp": tp,
        "accuracy": float(accuracy_score(y_true, y_pred)) if n else np.nan,
        "precision": float(precision_score(y_true, y_pred, zero_division=0)) if n else np.nan,
        "recall": float(recall_score(y_true, y_pred, zero_division=0)) if n else np.nan,
        "f1": float(f1_score(y_true, y_pred, zero_division=0)) if n else np.nan,
        "specificity": float(tn / (tn + fp)) if (tn + fp) > 0 else np.nan,
        "fn_rate": float(fn / (fn + tp)) if (fn + tp) > 0 else np.nan,   # 1 - recall
        "fp_rate": float(fp / (fp + tn)) if (fp + tn) > 0 else np.nan,
    }

    if y_score is not None:
        y_score = np.asarray(y_score, dtype=float)
        if n > 0 and len(np.unique(y_true)) == 2:
            try:
                out["roc_auc"] = float(roc_auc_score(y_true, y_score))
            except Exception:
                out["roc_auc"] = np.nan
            try:
                out["pr_auc"] = float(average_precision_score(y_true, y_score))
            except Exception:
                out["pr_auc"] = np.nan
        else:
            out["roc_auc"] = np.nan
            out["pr_auc"] = np.nan
    else:
        out["roc_auc"] = np.nan
        out["pr_auc"] = np.nan

    return out


# =========================
# Model discovery
# =========================
def find_models(models_dir: Path):
    return sorted(models_dir.glob("model_*.joblib"))

def pick_feature_cols(models_dir: Path, feature_cols_arg: str | None):
    if feature_cols_arg:
        return Path(feature_cols_arg)
    p = models_dir / "feature_columns_64log_gc_tetra.json"
    if p.exists():
        return p
    candidates = sorted(models_dir.glob("feature_columns_*.json"))
    if not candidates:
        raise FileNotFoundError(f"No feature_columns_*.json found in {models_dir}")
    return candidates[0]


# =========================
# Main
# =========================
def main():
    ap = argparse.ArgumentParser(
        description="Predict for all models in a directory; optionally annotate truth from TSV and compute metrics."
    )
    ap.add_argument("--genomes_dir", required=True, help="Folder with FASTA genomes (.fna/.fa/.fasta).")
    ap.add_argument("--models_dir", required=True, help="Folder with model_*.joblib + feature_columns_*.json.")
    ap.add_argument("--outdir", required=True, help="Output folder for CSV predictions.")
    ap.add_argument("--aragorn", default="aragorn", help="Path to ARAGORN binary.")
    ap.add_argument("--feature_cols", default=None, help="Optional: force a specific feature_columns_*.json.")
    ap.add_argument("--reuse_aragorn", action="store_true", help="Reuse *.aragorn.txt if it exists and is fresh.")
    ap.add_argument(
        "--truth_tsv",
        default=None,
        help="OPTIONAL: genomes-all_metadata_with_genetic_code_id_noNA.tsv (Genome, Genome_type, Genetic_code_ID).",
    )
    args = ap.parse_args()

    set_single_thread_env()

    genomes_dir = Path(args.genomes_dir)
    models_dir = Path(args.models_dir)
    outdir = Path(args.outdir)
    outdir.mkdir(parents=True, exist_ok=True)

    fasta_files = list_fasta_files(str(genomes_dir))
    if not fasta_files:
        raise SystemExit(f"No FASTA files found in {genomes_dir}")

    models = find_models(models_dir)
    if not models:
        raise SystemExit(f"No model_*.joblib found in {models_dir}")

    feat_cols_path = pick_feature_cols(models_dir, args.feature_cols)

    print(f"[INFO] Genomes : {len(fasta_files)} in {genomes_dir}")
    print(f"[INFO] Models  : {len(models)} in {models_dir}")
    print(f"[INFO] FeatCols: {feat_cols_path}")
    print(f"[INFO] Truth   : {args.truth_tsv if args.truth_tsv else '(none)'}")

    # Load feature columns
    with open(feat_cols_path, "r") as fh:
        feature_columns = json.load(fh)

    # Optional truth
    truth = None
    if args.truth_tsv:
        truth = load_truth_tsv(args.truth_tsv)

    # Build features once (shared across all models)
    t_feat0 = time.time()
    rows, accs = [], []
    for i, fasta in enumerate(fasta_files, 1):
        if i % 50 == 0 or i == 1 or i == len(fasta_files):
            print(f"[FEAT] {i}/{len(fasta_files)} {os.path.basename(fasta)}")
        acc, feats = build_features_for_genome(
            fasta_path=fasta,
            aragorn_bin=args.aragorn,
            feature_columns=feature_columns,
            reuse_aragorn=args.reuse_aragorn
        )
        accs.append(acc)
        rows.append(feats)

    X = pd.DataFrame(rows, index=accs)[feature_columns]
    print(f"[FEAT] Built X={X.shape} in {(time.time()-t_feat0):.1f}s")

    # Annotation base table (always exists)
    ann = pd.DataFrame({"Genome": accs})

    if truth is not None:
        ann = ann.merge(truth, how="left", on="Genome")
        n_annot = int(ann["y_true_alt"].notna().sum())
        n_missing = int(len(ann) - n_annot)
        print(f"[TRUTH] Annotated: {n_annot}/{len(ann)}  Missing_in_TSV: {n_missing}")
    else:
        # Ensure columns exist for consistent outputs
        ann["Genome_type"] = pd.NA
        ann["Genetic_code_ID"] = pd.NA
        ann["y_true_alt"] = pd.NA
        ann["true_label"] = pd.NA

    long_rows = []
    summary_rows = []

    for mi, model_path in enumerate(models, 1):
        model_name = model_path.stem
        print("\n" + "="*80)
        print(f"[{mi}/{len(models)}] MODEL: {model_path.name}")
        print("="*80)

        t0 = time.time()
        model = joblib_load(model_path)

        # Probabilities (if possible)
        proba = None
        if hasattr(model, "predict_proba"):
            try:
                proba = model.predict_proba(X)[:, 1]
            except Exception:
                proba = None

        # Pred class
        if hasattr(model, "predict"):
            try:
                yhat = model.predict(X)
            except Exception:
                yhat = (proba >= 0.5).astype(int) if proba is not None else np.zeros(len(X), dtype=int)
        else:
            yhat = (proba >= 0.5).astype(int) if proba is not None else np.zeros(len(X), dtype=int)

        elapsed = time.time() - t0

        df_pred = ann.copy()
        df_pred["model"] = model_name
        df_pred["y_pred_alt"] = np.asarray(yhat).astype(int)
        df_pred["pred_label"] = df_pred["y_pred_alt"].map({0: "STD", 1: "ALT"})
        df_pred["proba_alt"] = np.asarray(proba, dtype=float) if proba is not None else np.nan

        out_csv = outdir / f"{model_name}__pred.csv"
        df_pred.to_csv(out_csv, index=False)
        print(f"[WRITE] {out_csv} rows={len(df_pred)} time={(elapsed/60):.2f} min")

        # Long output
        keep_cols = ["model", "Genome", "Genome_type", "Genetic_code_ID", "y_true_alt", "y_pred_alt", "proba_alt"]
        keep_cols = [c for c in keep_cols if c in df_pred.columns]
        long_rows.extend(df_pred[keep_cols].to_dict(orient="records"))

        # Metrics only if we have truth annotations
        if truth is not None:
            df_eval = df_pred[df_pred["y_true_alt"].notna()].copy()
            if df_eval.shape[0] == 0:
                print("[METRICS] No annotated genomes for this run (truth TSV did not match Genome names).")
                continue

            y_true = df_eval["y_true_alt"].astype(int).values
            y_pred = df_eval["y_pred_alt"].astype(int).values
            y_score = df_eval["proba_alt"].astype(float).values if proba is not None else None

            overall = compute_metrics_block(y_true, y_pred, y_score=y_score)

            def subset_metrics(gen_type: str):
                sub = df_eval[df_eval["Genome_type"] == gen_type]
                if sub.shape[0] == 0:
                    return None
                yt = sub["y_true_alt"].astype(int).values
                yp = sub["y_pred_alt"].astype(int).values
                ys = sub["proba_alt"].astype(float).values if proba is not None else None
                return compute_metrics_block(yt, yp, y_score=ys)

            iso = subset_metrics("Isolate")
            mag = subset_metrics("MAG")

            srow = {
                "model": model_name,
                "model_file": str(model_path),
                "feature_cols": str(feat_cols_path),
                "n_genomes_total": int(len(df_pred)),
                "n_annotated": int(df_eval.shape[0]),
                "n_missing_truth": int(len(df_pred) - df_eval.shape[0]),
                "elapsed_sec": float(elapsed),
                "elapsed_min": float(elapsed/60.0),
            }

            for k, v in overall.items():
                srow[f"overall_{k}"] = v

            if iso is not None:
                for k, v in iso.items():
                    srow[f"isolate_{k}"] = v

            if mag is not None:
                for k, v in mag.items():
                    srow[f"mag_{k}"] = v

            summary_rows.append(srow)

    # Write combined outputs
    long_csv = outdir / "all_models_predictions_long.csv"
    pd.DataFrame(long_rows).to_csv(long_csv, index=False)
    print(f"\n[WRITE] {long_csv} rows={len(long_rows)}")

    if truth is not None:
        summary_csv = outdir / "prediction_summary.csv"
        df_sum = pd.DataFrame(summary_rows)
        df_sum.to_csv(summary_csv, index=False)
        print(f"[WRITE] {summary_csv} rows={len(df_sum)}")

        # Top models report
        if not df_sum.empty and "overall_pr_auc" in df_sum.columns:
            df_rank = df_sum.sort_values(["overall_pr_auc", "overall_roc_auc"], ascending=False, na_position="last")
            report_path = outdir / "top_models_by_pr_auc.txt"
            cols = [
                "model",
                "n_annotated",
                "overall_positives",
                "overall_precision",
                "overall_recall",
                "overall_f1",
                "overall_pr_auc",
                "overall_roc_auc",
                "isolate_fn", "isolate_fp", "mag_fn", "mag_fp",
                "elapsed_min",
            ]
            cols = [c for c in cols if c in df_rank.columns]
            with open(report_path, "w", encoding="utf-8") as f:
                f.write("Top models by overall PR-AUC (ALT = Genetic_code_ID != 11)\n")
                f.write(df_rank[cols].head(25).to_string(index=False))
                f.write("\n")
            print(f"[WRITE] {report_path}")

    print("[DONE]")


if __name__ == "__main__":
    main()