zipoop 0.1.0__py3-none-any.whl

zipoop/__init__.py

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+"""Zipoop: decoder and reader for the per-window teacher shards (merged per-chromosome npz)."""
+from .dataset import Dataset, verify
+from .decoder import Decoder
+from .evaluation import calibrate, restore_real, summarize, window_pearson
+from .panel import panel_tracks, zero_tracks
+from .shard import Shard, read_shard
+from .teacher import TeacherWindow, load_window
+
+__version__ = "0.1.0"
+__all__ = ["Dataset", "verify", "Decoder", "Shard", "read_shard", "TeacherWindow", "load_window",
+           "panel_tracks", "zero_tracks", "calibrate", "restore_real", "summarize", "window_pearson"]

zipoop/cli.py

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+import argparse
+import sys
+
+from .dataset import Dataset, verify
+
+
+def main(argv=None):
+    parser = argparse.ArgumentParser(prog="zipoop", description="Zipoop teacher-shard dataset tools")
+    sub = parser.add_subparsers(dest="cmd", required=True)
+    v = sub.add_parser("verify", help="check <root>/*.npz against MANIFEST.tsv (size + sha256)")
+    v.add_argument("root")
+    v.add_argument("--chroms", default="", help="comma-separated subset")
+    v.add_argument("--workers", type=int, default=4, help="files hashed in parallel")
+    s = sub.add_parser("show", help="decode one window and print its shapes")
+    s.add_argument("root")
+    s.add_argument("window")
+    args = parser.parse_args(argv)
+    if args.cmd == "verify":
+        chroms = set(args.chroms.split(",")) if args.chroms else None
+        bad = verify(args.root, chroms, workers=args.workers, progress=lambda c, problem: print(f"{c}: {problem or 'ok'}", flush=True))
+        print(f"{len(bad)} problem(s)" if bad else "all files verified")
+        return 1 if bad else 0
+    with Dataset(args.root) as ds:
+        w = ds.load_window(args.window)
+    print(f"{w.key}: dna {tuple(w.dna.shape)}, signal {tuple(w.signal.shape)}, valid fraction {w.valid.float().mean():.4f}")
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())