sigven / pcgr

Personal Cancer Genome Reporter (PCGR)
https://sigven.github.io/pcgr
MIT License
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Fix for "SyntaxWarning: invalid escape sequence" #236

Closed pdiakumis closed 2 months ago

pdiakumis commented 2 months ago

With the newer Python 3.12 version we're getting multiple SyntaxWarning: invalid escape sequence '\|' warnings from the cpsr_validate_input.py script. This is due to a bug fix for https://github.com/python/cpython/issues/105800. Below I've simply doubled up the \ in the egrep commands, hopefully it still works the same - at least the warnings have stopped for me now.

Also added a couple download scripts for the VEP cache and the refdata bundle (will fix those up a bit more in a future PR).