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prihoda / AbNumber

Convenience Python APIs for antibody numbering using ANARCI
MIT License
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Unusual behavior for Chain as the input sequence gets modified when providing the output #8

Closed ahmadpgh closed 2 years ago

ahmadpgh commented 2 years ago

Hi,

Running the snippet below, I expected to see a similar chain.seq to the input sequence but it seems the order of amino acids is modified. Specifically GSEHR is replaced by RHESG. May I ask why we see this change?


from abnumber import Chain

seq = "AVQLVDSGGGTLQAGKSLRLSCAISGLAFDGGAMGSEHRLTAGAMGWFRQAPGKDREFVAAISPRTDETYYAESLEGRFSVSRDAAATMVFLQADNVRLDDTASYYCAADEDVTPRVMGVIPHADHWGQGTLVTVSS"
chain = Chain(seq, scheme='imgt')
print("Sequence:\n", seq)
print("Chain:\n", chain)
assert chain.seq==seq

Thanks for your reply in advance

prihoda commented 2 years ago

Hi @ahmadpgh thanks for reporting this. Turns out we had a bug in ordering the IMGT CDR1 33 and CDR2 61 positions.

Fixed in https://github.com/prihoda/AbNumber/pull/9, the new 0.3.0 abnumber release will be available on Bioconda soon.