mniellab / nettcr Goto Github PK

When running the default test script python scripts/netTCR.py -infile test_data/data.txt -outfile NetTCR_predictions.txt using either Python 2.7.17 or Python 3.6.9 I get the following output:

Traceback (most recent call last): File "scripts/netTCR.py", line 170, in <module> best_params = np.load(param_dir + "params.t." + str(t) + ".v." + str(v) + ".s." + str(s) + ".npz")['arr_0'] File "/home/local/ASUAD/mrcai/.local/lib/python2.7/site-packages/numpy/lib/npyio.py", line 262, in __getitem__ pickle_kwargs=self.pickle_kwargs) File "/home/local/ASUAD/mrcai/.local/lib/python2.7/site-packages/numpy/lib/format.py", line 696, in read_array raise ValueError("Object arrays cannot be loaded when " ValueError: Object arrays cannot be loaded when allow_pickle=False

As a workaround at the moment you can downgrade numpy to 1.16.1 to be able to run the script successfully.

I think the default value in numpy has changed and allow_pickle needs to be directly assigned as True.

Hi,

Would it be possible for you to share the training data, especially the negative set, since all known (positive) set seems to be under: https://github.com/mnielLab/netTCR/blob/master/parameters/iedb_mira_pos_uniq.txt

Thank you very much!

Can you please list in the README.md the dependencies?
Test example won't work with the latest tensorflow 2.x. I've managed to run it with:

numpy==1.16.1
tensorflow==1.13.1

Are these OK or you recommend some other versions?
Thanks!