mirror of
https://github.com/chanzuckerberg/cellxgene.git
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45 lines
1.6 KiB
Python
45 lines
1.6 KiB
Python
import anndata
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import argparse
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import random
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import scipy
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import numpy as np
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def main():
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parser = argparse.ArgumentParser("A command to generate test h5ad files")
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parser.add_argument("output", help="Name of the output file")
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parser.add_argument("nobs", type=int, help="Number of observations (rows)")
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parser.add_argument("nvar", type=int, help="Number of variables (columns)")
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parser.add_argument("-n", "--nnz-percent", type=float, default=100, help="percent of non-zeros")
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parser.add_argument("-c", "--col-shift", action="store_true", help="add a random value to each column")
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parser.add_argument("--seed", type=int, default=None, help="add a random value to each column")
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args = parser.parse_args()
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create_test_h5ad(args.output, args.nobs, args.nvar, args.nnz_percent, args.col_shift, args.seed)
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def create_test_h5ad(outfile, nobs, nvar, nnz_percent=100, apply_col_shift=False, seed=None):
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random.seed(seed)
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np.random.seed(seed)
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x = create_X_array(nobs, nvar, nnz_percent, apply_col_shift)
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obsm = {"X_random": np.random.rand(nobs, 2).astype(np.float32)}
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adata = anndata.AnnData(x, obsm=obsm)
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adata.write(outfile)
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def create_X_array(nobs, nvar, nnz_percent, apply_col_shift):
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if nnz_percent < 100:
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array = scipy.sparse.random(nobs, nvar, nnz_percent * 0.01, dtype=np.float32, format="csc")
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else:
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array = np.random.rand(nobs, nvar).astype(np.float32)
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if apply_col_shift:
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col_shift = np.random.rand((nvar))
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array += col_shift
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return array
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if __name__ == "__main__":
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main()
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