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andersen-lab / Freyja

Depth-weighted De-Mixing
BSD 2-Clause "Simplified" License
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Pandas update breaks demixing #179

Closed gabimuir closed 9 months ago

gabimuir commented 10 months ago

Upgrading pandas from version 2.0.3 to the newest 2.1.0 gives a TypeError in deconvolution.

The error is:

File "/home/ubuntu/miniconda3/envs/freyja/lib/python3.10/site-packages/freyja/sample_deconv.py", line 71, in build_mix_and_depth_arrays df['mutName'] = df['REF'] + df['POS'].astype(str) + df['ALT'] ... TypeError: unsupported operand type(s) for +: 'float' and 'str'

Downgrading back to pandas 2.0.3 fixed the issue

dylanpilz commented 10 months ago

Would you mind sharing the steps to reproduce the error (i.e. command, freyja version, input files)? If you prefer, you're welcome to reach out via email (dpilz@scripps.edu) in case you'd rather not post the files publicly.

dylanpilz commented 9 months ago

Closing as stale