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| """Input sequence cleaning/validation (integration guide section 5).""" | |
| from .errors import SequenceError | |
| STANDARD_AA = frozenset("ACDEFGHIKLMNPQRSTVWY") | |
| def clean_sequence(raw: str, min_length: int, max_length: int, | |
| limit_reason: str = "the structure predictor: ESMFold API") -> str: | |
| """Strip one optional FASTA header and all whitespace, uppercase, then validate.""" | |
| lines = (raw or "").strip().splitlines() | |
| headers = [line for line in lines if line.lstrip().startswith(">")] | |
| if len(headers) > 1: | |
| raise SequenceError(f"Only one sequence per request is supported (found {len(headers)} FASTA records).") | |
| sequence = "".join("".join(line for line in lines if not line.lstrip().startswith(">")).split()).upper() | |
| if not sequence: | |
| raise SequenceError("Sequence is empty.") | |
| invalid = [(i + 1, aa) for i, aa in enumerate(sequence) if aa not in STANDARD_AA] | |
| if invalid: | |
| shown = ", ".join(f"'{aa}' at {pos}" for pos, aa in invalid[:5]) | |
| more = f" (+{len(invalid) - 5} more)" if len(invalid) > 5 else "" | |
| raise SequenceError( | |
| f"Sequence may only contain the 20 standard amino acids (ACDEFGHIKLMNPQRSTVWY). " | |
| f"Found {shown}{more}. Non-standard residues such as X, U, B, Z, O are not supported." | |
| ) | |
| if len(sequence) < min_length: | |
| raise SequenceError(f"Sequence has {len(sequence)} residues; the minimum is {min_length}.") | |
| if len(sequence) > max_length: | |
| raise SequenceError( | |
| f"Sequence has {len(sequence)} residues; the maximum is {max_length} " | |
| f"(limit of {limit_reason}).", | |
| too_long=True, | |
| ) | |
| return sequence | |