mirror of
https://github.com/chanzuckerberg/cellxgene.git
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f69d141336
This will give us the ability to specify different config options for different dataroots. the key of the dataroot dictionary is no longer the same as the dataroot_url. Previously key==dataroot_url, and now those are separated. Added an "is_multi_dataset" function to simplify logic where it branched on single vs multi. Simplified the rest.py interface by no longer passing in the user annotations object, since that can be retrieved from the dataset.
118 lines
3.9 KiB
Python
118 lines
3.9 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_cxg as diffexp_cxg
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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, help="number of rows in group A")
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parser.add_argument("-nb", "--numB", type=int, help="number of rows in group B")
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parser.add_argument("-va", "--varA", help="obs variable:value to use for group A")
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parser.add_argument("-vb", "--varB", help="obs variable:value to use for 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", "cxg"), 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.update_server_config(single_dataset__datapath=args.dataset)
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app_config.update_server_config(app__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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random.seed(args.seed)
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np.random.seed(args.seed)
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rows = adaptor.get_shape()[0]
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if args.numA:
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filterA = random.sample(range(rows), args.numA)
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elif args.varA:
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vname, vval = args.varA.split(":")
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filterA = get_filter_from_obs(adaptor, vname, vval)
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else:
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print("must supply numA or varA")
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sys.exit(1)
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if args.numB:
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filterB = random.sample(range(rows), args.numB)
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elif args.varB:
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vname, vval = args.varB.split(":")
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filterB = get_filter_from_obs(adaptor, vname, vval)
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else:
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print("must supply numB or varB")
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sys.exit(1)
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for i in range(args.trials):
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if args.new_selection:
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if args.numA:
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filterA = random.sample(range(rows), args.numA)
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if args.numB:
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filterB = random.sample(range(rows), args.numB)
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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 == "cxg":
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if not isinstance(adaptor, CxgAdaptor):
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print("cxg only works with CxgAdaptor")
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sys.exit(1)
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results = diffexp_cxg.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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def get_filter_from_obs(adaptor, obsname, obsval):
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attrs = adaptor.get_obs_columns()
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if obsname not in attrs:
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print(f"Unknown obs attr {obsname}: expected on of {attrs}")
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sys.exit(1)
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obsvals = adaptor.query_obs_array(obsname)[:]
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obsval = type(obsvals[0])(obsval)
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vfilter = np.where(obsvals == obsval)[0]
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if len(vfilter) == 0:
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u = np.unique(obsvals)
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print(f"Unknown value in variable {obsname}:{obsval}: expected one of {list(u)}")
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sys.exit(1)
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return vfilter
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if __name__ == "__main__":
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main()
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