tidytcells.junction

Functions to clean and standardize junction (CDR3) data.

Functions

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

Alias for tidytcells.junction.standardize().

tidytcells.junction.standardize(seq: str, strict: bool = False, on_fail: str = 'reject', suppress_warnings: bool = False)

Ensures that a string value looks like a valid junction (CDR3) amino acid sequence. This function is a special variant of tidytcells.aa.standardize().

A valid junction sequence must:

1. Be a valid amino acid sequence

2. Begin with a cysteine (C)

3. End with a phenylalanine (F) or a tryptophan (W)

Parameters:

• seq (str) – String value representing a junction sequence.

• strict (bool) – If True, any string that does not look like a junction sequence is rejected. If False, any inputs that are valid amino acid sequences but do not start with C and end with F/W are not rejected and instead are corrected by having a C appended to the beginning and an F appended at the end. Defaults to False.

• 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".

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

Returns:

If possible, a standardized version of the input string is returned. If the input string cannot be standardized, the function follows the behaviour as set by on_fail.

Return type:

Union[str, None]

Example usage

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

>>> tt.junction.standardize("csadaff")
'CSADAFF'

Strings that are valid amino acid sequences but do not stard and end with the appropriate residues will have a C and an F appended to its beginning and end respectively.

>>> tt.junction.standardize("sadaf")
'CSADAFF'

However, setting strict to True will cause these cases to be rejected.

>>> result = tt.junction.standardize("sadaf", strict=True)
UserWarning: Input sadaf was rejected as it is not a valid junction sequence.
>>> print(result)
None