SNP dosages to numpy/pandas?

Hail Query & hailctl
21

This is a bit grody, but I would re-write BlockMatrix.to_numpy yourself:

import os
import numpy as np
from hail.linalg import BlockMatrix
from hail.utils import new_local_temp_file, local_path_uri

def to_numpy(bm, _force_blocking=False):
    if bm.n_rows * bm.n_cols > 1 << 31 or _force_blocking:
        path = new_temp_file()
        bm.export_blocks(path, binary=True)
        return BlockMatrix.rectangles_to_numpy(path, binary=True)

    path = new_local_temp_file()
    try:
        uri = local_path_uri(path)
        bm.tofile(uri)
        return np.fromfile(path).reshape((bm.n_rows, bm.n_cols))
    finally:
        try:
            os.remove(path)
        except FileNotFoundError:
            pass