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'''Genotype database reader
This module is a tiny Python library to read a GeneNetwork genotype
database. It exports the following functions.
* open - Open a genotype database
* matrix - Get current matrix
* row - Get row of matrix
* column - Get column of matrix
Here is a typical invocation to read row 17 and column 13 from a genotype
database at `/tmp/bxd`.
from gn3 import genodb
with genodb.open('/tmp/bxd') as db:
matrix = genodb.matrix(db)
print(genodb.row(matrix, 17))
print(genodb.column(matrix, 13))
'''
from collections import namedtuple
from contextlib import contextmanager
import lmdb
import numpy as np
# pylint: disable=invalid-name,redefined-builtin
GenotypeDatabase = namedtuple('GenotypeDatabase', 'txn hash_length')
Matrix = namedtuple('Matrix', 'db nrows ncols row_pointers column_pointers')
@contextmanager
def open(path):
'''Open genotype database.'''
env = lmdb.open(path, readonly=True, create=False)
txn = env.begin()
yield GenotypeDatabase(txn, 32) # 32 bytes in a SHA256 hash
txn.abort()
env.close()
def get(db, key):
'''Get value associated with key in genotype database.'''
return db.txn.get(key)
def get_metadata(db, hash, metadata):
'''Get metadata associated with hash in genotype database.'''
return db.txn.get(hash + b':' + metadata.encode())
def matrix(db):
'''Get current matrix from genotype database.'''
hash = get(db, b'current')[0:db.hash_length]
nrows = int.from_bytes(get_metadata(db, hash, 'nrows'), byteorder='little')
ncols = int.from_bytes(get_metadata(db, hash, 'ncols'), byteorder='little')
row_column_pointers = get(db, hash)
return Matrix(db, nrows, ncols,
row_column_pointers[0 : nrows*db.hash_length],
row_column_pointers[nrows*db.hash_length :])
def vector_ref(db, index, pointers):
'''Get vector from byte array of pointers.'''
start = index * db.hash_length
end = start + db.hash_length
return np.frombuffer(get(db, pointers[start:end]), dtype=np.uint8)
def row(matrix, index):
'''Get row of matrix.'''
# pylint: disable=redefined-outer-name
return vector_ref(matrix.db, index, matrix.row_pointers)
def column(matrix, index):
'''Get column of matrix.'''
# pylint: disable=redefined-outer-name
return vector_ref(matrix.db, index, matrix.column_pointers)
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