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| from Bio import SeqIO | |
| from io import StringIO | |
| from dataclasses import dataclass, field | |
| from typing import List | |
| class ValidationResult: | |
| valid: bool = True | |
| error: str = "" | |
| sequences: List = field(default_factory=list) | |
| def validate_fasta(text: str, tool: str = "blast") -> ValidationResult: | |
| if not text or not text.strip(): | |
| return ValidationResult(valid=False, error="Empty sequence") | |
| # Try parsing as FASTA | |
| try: | |
| records = list(SeqIO.parse(StringIO(text), "fasta")) | |
| except Exception: | |
| records = [] | |
| if records: | |
| for rec in records: | |
| seq_str = str(rec.seq) | |
| if len(seq_str) < 6: | |
| return ValidationResult(valid=False, error=f"Sequence too short: {len(seq_str)} residues") | |
| if not set(seq_str.upper()).issubset(set("ACDEFGHIKLMNPQRSTVWYUBZXOJ")): | |
| return ValidationResult(valid=False, error="Invalid amino acid characters found") | |
| return ValidationResult(sequences=records) | |
| # Plain sequence (no FASTA header) | |
| clean = "".join(c for c in text if c.isalpha()).upper() | |
| if len(clean) < 6: | |
| return ValidationResult(valid=False, error=f"Sequence too short: {len(clean)} residues") | |
| if not set(clean).issubset(set("ACDEFGHIKLMNPQRSTVWYUBZXOJ")): | |
| return ValidationResult(valid=False, error="Invalid amino acid characters found") | |
| from Bio.Seq import Seq | |
| from Bio.SeqRecord import SeqRecord | |
| record = SeqRecord(Seq(clean), id="query", description="") | |
| return ValidationResult(sequences=[record]) | |