chansigit
commented
4 years ago It should be asked in pySCENIC repo
Closed chansigit closed 4 years ago
chansigit
commented
4 years ago It should be asked in pySCENIC repo
pyscenic grn 200409-ABM2-totalclustered.scenic.expression.csv /data/hca/public_data/scenic/mm_mgi_tfs.txt -o 200409-ABM2-totalclustered.scenic.adjacencies.tsv --num_workers 1
I got 'DataFrame' object has no attribute 'as_matrix' Do I use the wrong version of pandas?
/var/lib/hcaadmin/anaconda1907/envs/r36/lib/python3.8/site-packages/dask/config.py:161: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. data = yaml.load(f.read()) or {} /var/lib/hcaadmin/anaconda1907/envs/r36/lib/python3.8/site-packages/dask/dataframe/utils.py:13: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead. import pandas.util.testing as tm 2020-05-15 12:48:31,658 - pyscenic.cli.pyscenic - INFO - Loading expression matrix. 2020-05-15 12:48:47,423 - pyscenic.cli.pyscenic - INFO - Inferring regulatory networks. /var/lib/hcaadmin/anaconda1907/envs/r36/lib/python3.8/site-packages/dask/config.py:161: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. data = yaml.load(f.read()) or {} /var/lib/hcaadmin/anaconda1907/envs/r36/lib/python3.8/site-packages/dask/dataframe/utils.py:13: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead. import pandas.util.testing as tm preparing dask client parsing input not shutting down client, client was created externallyfinished Traceback (most recent call last): File "/var/lib/hcaadmin/anaconda1907/envs/r36/bin/pyscenic", line 8, in sys.exit(main())
File "/var/lib/hcaadmin/anaconda1907/envs/r36/lib/python3.8/site-packages/pyscenic/cli/pyscenic.py", line 420, in main
args.func(args)
File "/var/lib/hcaadmin/anaconda1907/envs/r36/lib/python3.8/site-packages/pyscenic/cli/pyscenic.py", line 72, in find_adjacencies_command
network = method(expression_data=ex_mtx, tf_names=tf_names, verbose=True, client_or_address=client, seed=args.seed)
File "/var/lib/hcaadmin/anaconda1907/envs/r36/lib/python3.8/site-packages/arboreto/algo.py", line 39, in grnboost2
return diy(expression_data=expression_data, regressor_type='GBM', regressor_kwargs=SGBM_KWARGS,
File "/var/lib/hcaadmin/anaconda1907/envs/r36/lib/python3.8/site-packages/arboreto/algo.py", line 115, in diy
expression_matrix, gene_names, tf_names = _prepare_input(expression_data, gene_names, tf_names)
File "/var/lib/hcaadmin/anaconda1907/envs/r36/lib/python3.8/site-packages/arboreto/algo.py", line 214, in _prepare_input
expression_matrix = expression_data.as_matrix()
File "/var/lib/hcaadmin/anaconda1907/envs/r36/lib/python3.8/site-packages/pandas/core/generic.py", line 5274, in getattr
return object.getattribute(self, name)
AttributeError: 'DataFrame' object has no attribute 'as_matrix'