import lmdb import numpy as np class GenotypeDatabase: def __init__(self, path): self.env = lmdb.open(path, readonly=True, create=False) self.txn = self.env.begin() # 32 bytes in a SHA256 hash self.hash_length = 32 def __enter__(self): return self def __exit__(self, type, value, traceback): self.txn.abort() self.env.close() def get(self, hash): return self.txn.get(hash) def get_metadata(self, hash, metadata): return self.txn.get(hash + b':' + metadata.encode()) def matrix(self): hash = self.get(b'current') return Matrix(self, hash) class Matrix(): def __init__(self, db, hash): self.nrows = int.from_bytes(db.get_metadata(hash, 'nrows'), byteorder='little') self.ncols = int.from_bytes(db.get_metadata(hash, 'ncols'), byteorder='little') self.row_pointers = db.get(hash) self.db = db def row(self, index): start = index * self.db.hash_length end = start + self.db.hash_length return np.frombuffer(self.db.get(self.row_pointers[start:end]), dtype=np.uint8)