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XiaoTaoWang / NeoLoopFinder

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
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Getting a bug while running vis.plot_genes() #61

Open walidabualafia opened 5 months ago

walidabualafia commented 5 months ago

Hi all,

Thanks for your work developing this great tool. We're currently trying to run vis.plot_genes(), but we are getting the following error:

image

I installed neoloopfinder from mamba, given the instructions provided in the README. Seems to me like the issue has to do with the renaming of polars.toggle_string_cache() to polars.enable_string_cache() in August (see here: https://github.com/pola-rs/polars/issues/8631)

I did not try editing */read_gtf.py, given polars.enable_string_cache() is the new function name. Mamba seems to be installing an older version of polars. Do you recommend I upgrade polars to latest, or I swap the function calls to use the old nomenclature?

Thanks! Walid

XiaoTaoWang commented 5 months ago

I believe this is something related to the pyensembl version issue. pyensembl v2.1.0 is the latest version that I have tested. Can you downgrade your pyensembl to this version or older versions and try again?