tidytcells.aa

Functions to manage amino acid sequence data.

Functions

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

Alias for tidytcells.aa.standardize().

Return type:

str | None

tidytcells.aa.standardize(seq, on_fail=None, log_failures=None, suppress_warnings=None)

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

Parameters:

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

• on_fail (str) – Behaviour when standardization fails. If set to "reject", returns None on failure. If set to "keep", returns the original input. Defaults to "reject".

• log_failures (bool) – Report standardisation failures through logging (at level WARNING). Defaults to True.

• suppress_warnings (bool) – Disable warnings that are usually logged when standardisation fails. Deprecated in favour of log_failures.

Returns:

Capitalised version of seq, if seq is a valid amino acid sequence. Otherwise follow behaviour set by on_fail.

Return type:

Optional[str]

Example usage

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

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

Decision Logic

To provide an easy way to gauge the scope and limitations of standardization, below is a simplified overview of the decision logic employed when attempting to standardize an amino acid sequence. For more detail, please refer to the source code.

IF input sequence contains non-amino acid symbols:
    set standardization status to failed
ELSE:
    set standardization status to successful

IF standardization status is set to successful:
    RETURN standardized sequence

ELSE:
    IF on_fail is set to "reject":
        RETURN None
    IF on_fail is set to "keep":
        RETURN original sequence