Comments (2)
davek44
commented on June 23, 2024
Although I have begun moving some of the scripts to python3 compatibility, there is still some code that is only python2.
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shtoneyan
commented on June 23, 2024
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.
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Related Issues (20)
- Training aways converges after 2 or 3 epochs HOT 4
- Training takes too long HOT 3
- Pre-trained Weights? HOT 1
- Torch-HDF5 Failure during Writing Output by basset_motifs_predict.lua HOT 3
- First Epoch Loss is Bigger than Expected HOT 2
- Nucleotide Order in Motif Heatmap Reversed HOT 1
- how are filters combined HOT 2
- Error in running basset_sat_vcf.py HOT 1
- Convolutional layers - padding and bias HOT 1
- input and target size mismatch when running test.lua HOT 3
- Citation on README HOT 1
- Prediction tasks specification HOT 1
- install_data.py requires more than 30 GiB of memory HOT 2
- Docker image Lua and Python setups wrong
- how to install 'convnet' module HOT 1
- ENUM error when running basset_train.lua HOT 7
- bedtools getfasta skipping problem HOT 1
- Used in non human species HOT 1
- Original dataset Basset is trained on HOT 1
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