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| -rw-r--r-- | gn3/genodb.py | 34 |
1 files changed, 34 insertions, 0 deletions
diff --git a/gn3/genodb.py b/gn3/genodb.py new file mode 100644 index 0000000..71e9994 --- /dev/null +++ b/gn3/genodb.py @@ -0,0 +1,34 @@ +import lmdb +import numpy as np + +class GenotypeDatabase: + def __init__(self, path): + self.env = lmdb.open(path) + 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() + b'\0') + def matrix(self): + hash = self.get(b'current\0') + return Matrix(self, hash) + +class Matrix(): + def __init__(self, db, hash): + # TODO: Decide on endianness. + 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) |