preprocess_features.py file is generating empty output bed files

[ranijames]

Hi All,
Thanks for the tool. I am a beginner in deep learning. I was trying to reproduce the tutorials with the provided datasets. I have started with this https://github.com/davek44/Basset/blob/master/tutorials/prepare_compendium.ipynb for preparing the data. The first python script (preprocess_features.py) for that is just generating empty bed files with given default settings. I am running the script in python 3.

While running the script it is throwing the following warning message for every chromosome.

<_io.TextIOWrapper name='err_1_+.bed' mode='w' encoding='UTF-8'> 1	39761285.5	39761286.5	ENSG00000084072	

Any pointers would be of great help.
Thank you!

[davek44]

Although I have begun moving some of the scripts to python3 compatibility, there is still some code that is only python2.

[shtoneyan]

Hey all, I've redone the script for python 3 excluding a couple of print statements that still need rewriting:
https://github.com/shtoneyan/Basset_data_collection/blob/master/preprocess_features.py
With the settings in the tutorial it should work fine though. I came across the same issue with empty BED files and at least for me this was resolved by having integer start and end coordinates.