tidytcells.aa

Functions to clean and standardise amino acid sequence data.

Functions

tidytcells.aa.standardise(seq: str, suppress_warnings: bool = False)

Ensures that a string value looks like a valid amino acid sequence.

Parameters:

• seq (str) – String value representing an amino acid sequence.

• suppress_warnings (bool) – Disable warnings that are usually emitted when standardisation fails. Defaults to False.

Returns:

Capitalised version of seq, if seq is a valid amino acid sequence. Otherwise the input is rejected and None is returned.

Return type:

str or None

Example usage

Strings that look like amino acid sequences will be accepted, and returned in capitalised form.

>>> tt.aa.standardise("sqllnakyl")
'SQLLNAKYL'

Any strings that contain characters that cannot be recognised as amino acids will be rejected, and the function will return None.

>>> result = tt.aa.standardise("sqll?akyl")
UserWarning: Input sqll?akyl was rejected as it is not a valid amino acid sequence.
>>> print(result)
None

tidytcells.aa.standardize(*args, **kwargs)

Alias for tidytcells.aa.standardise().