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BIMSBbioinfo / janggu

Deep learning infrastructure for genomics
GNU General Public License v3.0
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Problem with plotGenomeTrack #9

Closed martynakgajos closed 5 years ago

martynakgajos commented 5 years ago

I want to use the tool, so I have started with the tutorials and the examples provided. When I try to run the "Input attribution" code I get an error in the plotGenomeTrack: "Coverage tracks seems not represent biological sequences. " ValueError: Coverage tracks seems not represent biological sequences. The last dimension must be divisible by the alphabetsize. In this case the alphabet size should be 64 (as the order=3) and the last dimension has a proper size: attr_oct[0].shape Out: (1, 200, 1, 64) I think the problem arises because: len(attr_oct[0]) Out[14]: 1

wkopp commented 5 years ago

Thank you @martynakgajos for pointing out the issue.

Could you provide a minimal example of code that leads to this issue? Also, which version of janggu were you using? I have tried to run ´python src/examples/example_input_importance.py -order 3`, but I couldn't reproduce the error.

martynakgajos commented 5 years ago

OK, I thing the problem is on my side: when I run the code from the command line, it works, when I copy the code to spyder and try to run it, I get to the line with plotting and get the "ValueError: Coverage tracks seems not represent biological sequences. The last dimension must be divisible by the alphabetsize." error.