def load_chunk(group, col_start, col_end):
''' Load a submatrix specified by the given column (barcode) range from an h5 group
Args: col_start, col_end - half-open interval of column indices to load'''
# Check bounds
shape = getattr(group, cr_constants.H5_MATRIX_SHAPE_ATTR).read()
assert col_start >= 0 and col_start < shape[1]
assert col_end >= 0 and col_end <= shape[1]
# Load genes and barcodes
genes = GeneBCMatrix.load_genes_from_h5_group(group)
bcs = GeneBCMatrix.load_bcs_from_h5_group(group)[col_start:col_end]
matrix = GeneBCMatrix(genes, bcs)
# Get views into full matrix
data = getattr(group, cr_constants.H5_MATRIX_DATA_ATTR)
indices = getattr(group, cr_constants.H5_MATRIX_INDICES_ATTR)
indptr = getattr(group, cr_constants.H5_MATRIX_INDPTR_ATTR)
# Determine extents of selected columns
ind_start = indptr[col_start]
if col_end < len(indptr)-1:
# Last index (end-exclusive) is the start of the next column
ind_end = indptr[col_end]
else:
# Last index is the last index in the matrix
ind_end = len(data)
chunk_data = data[ind_start:ind_end]
chunk_indices = indices[ind_start:ind_end]
chunk_indptr = np.append(indptr[col_start:col_end], ind_end) - ind_start
chunk_shape = (shape[0], col_end - col_start)
matrix.m = sp_sparse.csc_matrix((chunk_data, chunk_indices, chunk_indptr), shape=chunk_shape)
return matrix
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