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labdevgen / 3Dpredictor

3DPredictor - a computational approch to predict spatial interactions of chromatin based on epigenetic data
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unexpected keyword argument 'expected_binsize' in example_generate_data_K562_train.py #57

Closed chenkenbio closed 3 years ago

chenkenbio commented 4 years ago

Hello, recently I'm interested in you work published on Genome Research. But when I tried to reproduce the results in your paper, I found the following bug:

user@localhost:~/Documents/3Dpredictor/source$ python example_generate_data_K562_train.py 1,3,5,7,9 contacts.gz
DEBUG:__main__:Using input folder input/K562/
Traceback (most recent call last):
  File "example_generate_data_K562_train.py", line 66, in <module>
    expected_binsize = 25000)
TypeError: read_files() got an unexpected keyword argument 'expected_binsize'

It seems that the keyword expected_binsize only appears in source/example_generate_data_K562_train.py and is not defined in any other scripts, which confuses me a lot. Can you give any more advice on reproducing 3Dpredictor? Thanks a lot!

polyaB commented 3 years ago

Hello, recently I'm interested in you work published on Genome Research. But when I tried to reproduce the results in your paper, I found the following bug:

user@localhost:~/Documents/3Dpredictor/source$ python example_generate_data_K562_train.py 1,3,5,7,9 contacts.gz
DEBUG:__main__:Using input folder input/K562/
Traceback (most recent call last):
  File "example_generate_data_K562_train.py", line 66, in <module>
    expected_binsize = 25000)
TypeError: read_files() got an unexpected keyword argument 'expected_binsize'

It seems that the keyword expected_binsize only appears in source/example_generate_data_K562_train.py and is not defined in any other scripts, which confuses me a lot. Can you give any more advice on reproducing 3Dpredictor? Thanks a lot!

Hello, I suppose that it was version incompatibility. We are constantly update our code so please, use commit de22c741325a44385aad184634ed6506a465ab62 to reproduce results. If you have any questions we will glad to help.