Not able to run DCA from command line

[gufranca]

Dear Gökçen,

Thanks a lot for developing DCA. I am really looking forward to use your method in my data, however, I am not being able to run from command line (although the installation was successful). Here is my try:

dca test.csv dca_test

Using TensorFlow backend. WARNING: This might be very slow. Consider passing cache=True`, which enables much faster reading from a cache file.
Traceback (most recent call last):
File "/home/gu/miniconda3/envs/work/bin/dca", line 11, in
load_entry_point('DCA==0.1', 'console_scripts', 'dca')()
File "/home/gu/miniconda3/envs/work/lib/python3.5/site-packages/DCA/main.py", line 135, in main
train.train_with_args(args)
File "/home/gu/miniconda3/envs/work/lib/python3.5/site-packages/DCA/train.py", line 108, in train_with_args
test_split=args.testsplit)
File "/home/gu/miniconda3/envs/work/lib/python3.5/site-packages/DCA/io.py", line 64, in read_dataset
assert 'n_count' not in adata.obs, norm_error
AttributeError: 'AnnData' object has no attribute 'obs'

---

0:00:01.420 - total wall time
`
Attached is the example of my input (first 100 rows and 100 columns). The error is the same with the full dataset.

test.csv.zip

I appreciate any help on how to fix this.
Thanks
Gustavo

[gokceneraslan]

There are some fixes about this in the last release. Can you try upgrading to last version using pip install dca -U command?

[gufranca]

Unfortunately I still get a similar error even after updating DCA:

dca test.csv dca_test

Using TensorFlow backend.
WARNING: This might be very slow. Consider passing `cache=True`, which enables much faster reading from a cache file.
Traceback (most recent call last):
  File "/home/gu/miniconda3/envs/work/bin/dca", line 11, in <module>
    sys.exit(main())
  File "/home/gu/miniconda3/envs/work/lib/python3.5/site-packages/DCA/__main__.py", line 138, in main
    train.train_with_args(args)
  File "/home/gu/miniconda3/envs/work/lib/python3.5/site-packages/DCA/train.py", line 108, in train_with_args
    test_split=args.testsplit)
  File "/home/gu/miniconda3/envs/work/lib/python3.5/site-packages/DCA/io.py", line 64, in read_dataset
    assert 'n_count' not in adata.obs, norm_error
AttributeError: 'AnnData' object has no attribute 'obs'
_____________________________
0:00:03.109 - total wall time

It looks like it's expecting a kind of Annotation information, but I guess the only input is the expression matrix in .csv format, right?

I appreciate any help on that.
Gustavo

pip show dca
Name: DCA
Version: 0.1.1
Summary: Count autoencoder for scRNA-seq denoising
Home-page: https://github.com/gokceneraslan/countae
Author: Gokcen Eraslan
Author-email: gokcen.eraslan@gmail.com
License: Apache License 2.0
Location: /home/gu/miniconda3/envs/work/lib/python3.5/site-packages
Requires: numpy, scanpy, six, kopt, pandas, scikit-learn, keras, h5py
Required-by: 

[gokceneraslan]

Hmm, this works for me on the zip file you sent, interesting. Can you also try upgrading scanpy and anndata packages? pip install scanpy anndata -U

[gufranca]

Oh! Now it worked!! Thanks a lot for the help!