Separated fit and transform steps. #4
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If one sequence has e.g. only CGT the old code will inconsistently assign integers to each letter if other sequences have all letters.
i.e. integer_encoder.fit_transform(list('CGT')) != integer_encoder.fit_transform(list('ACGT'))
Solution: grab alphabet of all letters in all sequences first and fit before transforming each sequence in loop.
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If one sequence has e.g. only CGT the old code will inconsistently assign integers to each letter if other sequences have a different set of letters (i.e. ACG or ACGT). Not problematic for long sequences which are very unlikely to not use all 4 letters, but if e.g. applying to small k-mers very likely to produce errors.
i.e. integer_encoder.fit_transform(list('CGT')) != integer_encoder.fit_transform(list('ACGT'))
Solution: grab alphabet of all letters in all sequences first and fit before transforming each sequence in loop.