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Without digging into the issue too much, I have a feeling this might be caused by strange PyRanges stranded vs. unstranded behavior that I've been encountering lately (see this issue). Either way, I recommend installing my version of PyRanges for use with Cerberus. Try this and let me know if it solves your issue!
This indeed solves this issue, thanks.
Unfortunately, for me, the agg_ics function throws the following error:
File "/Users/emilvorsteveld/miniforge3/envs/cerberus/lib/python3.9/site-packages/pandas/core/internals/base.py", line 57, in _validate_set_axis
raise ValueError(
ValueError: Length mismatch: Expected axis has 4 elements, new values have 3 elements
I have tried older pandas versions (1.3.0 and 1.5.3), but not luck...
Using GTF files from GENCODE, I get the following error:
Exception: Cannot compute TSSes or TESes without strand info. Perhaps use extend() or subsequence() or spliced_subsequence() instead?
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