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This is an attempt to fix the error encountered when running predict.py using the MSA Transformer on the example data provided in examples/variant-prediction/data (#458)
The reason for the current error appears to be that the example MSA has an EVMutation-specific usage of lower-case columns to signify low-coverage (nonfocus) columns and not insertions. In this case the desired behaviour is presumably to coerce such columns to upper-case for scoring. This was the original behaviour of predict.py, before the PR https://github.com/facebookresearch/esm/issues/230, which seems to be intended to support the standard usage of lower-case residues to designate insertions in user-supplied a2m/a3m files and inadvertently breaks the example.
This PR supports both options via the lowercase-type flag. The default treats the lower-case columns as EVMutation style nonfocus (i.e. low coverage) columns for compatibility with the example MSA.