Hi,
When training on ATAC-seq data without specifying positive and negative tracks, there is a IndexError
File "/storage/chen/home/zz4/anaconda3/envs/bpnet/lib/python3.6/site-packages/gin/utils.py", line 41, in augment_exception_message_and_reraise
raise proxy.with_traceback(exception.__traceback__) from None
File "/storage/chen/home/zz4/anaconda3/envs/bpnet/lib/python3.6/site-packages/gin/config.py", line 1582, in gin_wrapper
return fn(*new_args, **new_kwargs)
File "/storage/chen/home/zz4/anaconda3/envs/bpnet/lib/python3.6/site-packages/bpnet/cli/train.py", line 469, in train
num_workers=num_workers))
File "/storage/chen/home/zz4/anaconda3/envs/bpnet/lib/python3.6/site-packages/bpnet/utils.py", line 51, in render_ipynb
parameters=params
File "/storage/chen/home/zz4/anaconda3/envs/bpnet/lib/python3.6/site-packages/papermill/execute.py", line 122, in execute_notebook
raise_for_execution_errors(nb, output_path)
File "/storage/chen/home/zz4/anaconda3/envs/bpnet/lib/python3.6/site-packages/papermill/execute.py", line 234, in raise_for_execution_errors
raise error
papermill.exceptions.PapermillExecutionError:
---------------------------------------------------------------------------
Exception encountered at "In [26]":
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
<ipython-input-26-36ba7ef40acb> in <module>
30 # Predicted
31 (f"\nPred", to_neg(pred[f'{task}/profile'][0] * np.exp(pred[f'{task}/counts'][0]))),
---> 32 ] for task_idx, task in enumerate(tasks)])
33
34 sl = slice(*xlim)
<ipython-input-26-36ba7ef40acb> in <listcomp>(.0)
30 # Predicted
31 (f"\nPred", to_neg(pred[f'{task}/profile'][0] * np.exp(pred[f'{task}/counts'][0]))),
---> 32 ] for task_idx, task in enumerate(tasks)])
33
34 sl = slice(*xlim)
<ipython-input-25-040d466e1211> in to_neg(track)
3 """
4 track = track.copy()
----> 5 track[:, 1] = - track[:, 1]
6 return track
IndexError: index 1 is out of bounds for axis 1 with size 1
In call to configurable 'train' (<function train at 0x7f93dcb01b70>)
Could you please provide an example of how to run BPNet on unstrand data type?
Hi, When training on ATAC-seq data without specifying positive and negative tracks, there is a IndexError
Could you please provide an example of how to run BPNet on unstrand data type?