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SNPs with wildcard values fail to be recognised within piezo-predict.py #1

Closed JeremyWesthead closed 2 years ago

JeremyWesthead commented 3 years ago

Using the piezo-predict.py script, and attempting to predict for wildcard values such as tlyA@N236? causes an error as it does not correctly check if ? is valid. This is due to validation of SNP values being based on the isupper() function, which returns False for ? values.

Similarly, if the before value is a wildcard (e.g tlyA@?236K) fails as checks for wildcard values here do no occur, and instead the ? is considered as an amino acid (given the same error as if this amino acid mutation is not in the catalogue).

Furthermore, checking for mutations such as rpoB@*? fail due to the script attempting to convert * to an int rather than considering the wildcard as detailed in GARC.

JeremyWesthead commented 2 years ago

This is intended behaviour. Mutations given to predict should not contain wildcards.