Running the evodiff/generate.py script

[Amelie-Schreiber]

I've been having trouble with getting the conda environment to work properly, so this may be exacerbating the issue below.

(evodiff3) ubuntu@209-20-159-77:~/evodiff_repo$ python evodiff/generate.py --model-type oa_dm_38M --num-seqs 100
Traceback (most recent call last):
  File "evodiff/generate.py", line 323, in <module>
    main()
  File "evodiff/generate.py", line 40, in main
    data = UniRefDataset('data/uniref50/', 'train', structure=False, max_len=2048)
  File "/home/ubuntu/miniconda3/envs/evodiff3/lib/python3.8/site-packages/sequence_models/datasets.py", line 330, in __init__
    with open(data_dir + 'splits.json', 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: 'data/uniref50/splits.json'
(evodiff3) ubuntu@209-20-159-77:~/evodiff_repo$ 

[chAwater]

@Amelie-Schreiber I ran to the same error and I found that you have to download the uniref50 (from #10 (comment)) to run the code.

I believe it's not necessary, you can hack the code to bypass it.

• Comment out the code
  

  evodiff/evodiff/generate.py

  Lines 40 to 41 in 32e3bd8

  	data = UniRefDataset('data/uniref50/', 'train', structure=False, max_len=2048)
  	data_valid = UniRefDataset('data/uniref50/', 'rtest', structure=False, max_len=2048)

  
  

  evodiff/evodiff/generate.py

  Lines 128 to 129 in 32e3bd8

  	r_idx = np.random.choice(len(data))
  	seq_len = len(data[r_idx][0]) # randomly sample a sequence length from train data

  
  

  evodiff/evodiff/generate.py

  Line 148 in 32e3bd8

  aa_reconstruction_parity_plot(home, out_fpath, 'generated_samples_string.csv')

• Add one line of code
  

  evodiff/evodiff/generate.py

  Line 130 in 32e3bd8

+ # the sequence length you want to sample from, for example (30, 200)
+ seq_len = np.random.choice(np.arange(30, 200))

• run the bash command

export AMLT_OUTPUT_DIR=YOUR_OUTPUT_DIR; python evodiff/generate.py --model-type oa_dm_38M --num-seqs 10 --amlt`