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https://github.com/chanzuckerberg/cellxgene.git
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98c2a1359b
* Specialize diffexp for tiledb This patch adds a new diffexp algorithm which is tuned for tiledb. This algorithm was written by Bruce and is adapted here to plug into the current framework. The anndata_adaptor still calls the original algotithm (which was move from diffexp.py to diffexp_generic.py). The cxg_adaptor now calls the new diffexp_tiledb version. Some code is shared between the two. This is part 1 of the diffexp for tiledb. Further tuning and global throttles are still needed. A script to run and time diffexp with various options is also added: test/run_diffexp.py.
89 lines
3.0 KiB
Python
89 lines
3.0 KiB
Python
import sys
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import argparse
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import random
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import time
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import numpy as np
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import server.compute.diffexp_tiledb as diffexp_tiledb
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import server.compute.diffexp_generic as diffexp_generic
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from server.common.app_config import AppConfig
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from server.data_common.matrix_loader import MatrixDataLoader
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from server.data_cxg.cxg_adaptor import CxgAdaptor
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def main():
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parser = argparse.ArgumentParser("A command to test diffexp")
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parser.add_argument("dataset", help="name of a dataset to load")
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parser.add_argument("-na", "--numA", type=int, required=True, help="number of rows in group A")
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parser.add_argument("-nb", "--numB", type=int, required=True, help="number of rows in group B")
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parser.add_argument("-t", "--trials", default=1, type=int, help="number of trials")
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parser.add_argument(
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"-a", "--alg", choices=("default", "generic", "tiledb"), default="default", help="algorithm to use"
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)
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parser.add_argument("-s", "--show", default=False, action="store_true", help="show the results")
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parser.add_argument(
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"-n", "--new-selection", default=False, action="store_true", help="change the selection between each trial"
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)
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parser.add_argument("--seed", default=1, type=int, help="set the random seed")
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args = parser.parse_args()
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app_config = AppConfig()
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app_config.data_locator__s3__region_name = "us-west-2"
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app_config.adaptor__cxg_adaptor__tiledb_ctx["vfs.s3.region"] = "us-west-2"
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app_config.single_dataset__datapath = args.dataset
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app_config.server__verbose = True
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app_config.complete_config()
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loader = MatrixDataLoader(args.dataset)
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adaptor = loader.open(app_config)
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if args.show:
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if isinstance(adaptor, CxgAdaptor):
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adaptor.open_array("X").schema.dump()
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numA = args.numA
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numB = args.numB
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rows = adaptor.get_shape()[0]
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random.seed(args.seed)
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if not args.new_selection:
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samples = random.sample(range(rows), numA + numB)
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filterA = samples[:numA]
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filterB = samples[numA:]
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for i in range(args.trials):
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if args.new_selection:
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samples = random.sample(range(rows), numA + numB)
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filterA = samples[:numA]
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filterB = samples[numA:]
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maskA = np.zeros(rows, dtype=bool)
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maskA[filterA] = True
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maskB = np.zeros(rows, dtype=bool)
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maskB[filterB] = True
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t1 = time.time()
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if args.alg == "default":
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results = adaptor.compute_diffexp_ttest(maskA, maskB)
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elif args.alg == "generic":
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results = diffexp_generic.diffexp_ttest(adaptor, maskA, maskB)
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elif args.alg == "tiledb":
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if not isinstance(adaptor, CxgAdaptor):
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print("tiledb only works with CxgAdaptor")
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sys.exit(1)
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results = diffexp_tiledb.diffexp_ttest(adaptor, maskA, maskB)
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t2 = time.time()
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print("TIME=", t2 - t1)
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if args.show:
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for res in results:
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print(res)
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if __name__ == "__main__":
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main()
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