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facebookresearch / esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins
MIT License
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Make sure extract.py refuses MSA inputs, closes #148 #179

Closed tomsercu closed 2 years ago

tomsercu commented 2 years ago

Thanks for flagging. This should be handled with a proper error message. The problem here is that this fasta file does not contain an MSA, and therefore is not meant for input to MSATransformer. Things go awry in the MSABatchConverter. We should just raise an error since the whole extract.py script is written for efficient batched computation of single-sequence language models.

tomsercu commented 2 years ago

Sure that would work, I guess the MSABatchConverter is the more general place if we release more models with MSA-inputs. But probably more straightforward as you say, let me update