Unexpected truncation of HGVS variant string when using strip()

[chrisxu2016]

When attempting to remove the prefix p. from an HGVS protein variant string (e.g., p.Gly34Asp) using the str.strip() method, the trailing character of the amino acid abbreviation is incorrectly removed if it matches any character in the strip set.

>>> variant = "p.Gly34Asp"
>>> variant.strip("p.")
'Gly34As'
>>> variant.strip().removeprefix("p.")
'Gly34Asp'

BIAS-2015/src/preprocessing/extract_from_avada_track.py

Line 100 in 8f74048

clean_variant = variant.strip("p.") # Remove the p. if its present

[chrisEisenhartBitscopic]

Does this modify the preprocessing file generated for Avada?

[chrisxu2016]

This will result in missing data due to an error in the conversion of protein abbreviation codes.

[chrisEisenhartBitscopic]

Since this is part of preprocessing it doesn't directly affect the algorithm logic. That being said this is still a valuable addition. To properly close this we need to re produce the avada file, verify that it is different than the existing, then make available to users.