from .._utils.abstract_functions import standardize_aa_template
[docs]def standardize(seq: str, on_fail: str = "reject", suppress_warnings: bool = False):
"""
Ensures that a string value looks like a valid amino acid sequence.
:param seq:
String value representing an amino acid sequence.
:type seq:
str
:param on_fail:
Behaviour when standardization fails.
If set to ``"reject"``, returns ``None`` on failure.
If set to ``"keep"``, returns the original input.
Defaults to ``"reject"``.
:type on_fail:
str
:param suppress_warnings:
Disable warnings that are usually emitted when standardisation fails.
Defaults to ``False``.
:type suppress_warnings:
bool
:return:
Capitalised version of ``seq``, if seq is a valid amino acid sequence.
Otherwise follow behaviour set by ``on_fail``.
:rtype:
Union[str, None]
.. topic:: 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")
UserWarning: Input sqll?akyl was rejected as it is not a valid amino acid sequence.
>>> print(result)
None
"""
return standardize_aa_template(
seq=seq, on_fail=on_fail, suppress_warnings=suppress_warnings
)