File size: 2,100 Bytes
cd0c7a9 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 | from Bio import SeqIO
from io import StringIO
from dataclasses import dataclass, field
from typing import List
PROTEIN_ALPHABET = "ACDEFGHIKLMNPQRSTVWYUBZXOJ"
NUCLEOTIDE_ALPHABET = "ACGUTNRSWYKMBDHV"
@dataclass
class ValidationResult:
valid: bool = True
error: str = ""
sequences: List = field(default_factory=list)
def _sequence_type_of(seq_str: str) -> str:
from app.services.sequence_utils import detect_sequence_type
clean = "".join(c for c in seq_str if c.isalpha()).upper()
return detect_sequence_type(clean)
def _validate_sequence(seq_str: str) -> tuple[bool, str]:
if len(seq_str) < 6:
return False, f"Sequence too short: {len(seq_str)} residues"
seq_type = _sequence_type_of(seq_str)
if seq_type == "protein":
ok = set(seq_str.upper()).issubset(set(PROTEIN_ALPHABET))
return (ok, "" if ok else "Invalid amino acid characters found")
if seq_type in ("dna", "rna"):
ok = set(seq_str.upper()).issubset(set(NUCLEOTIDE_ALPHABET))
return (ok, "" if ok else "Invalid nucleotide characters found")
return False, "Sequence contains unrecognized characters"
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:
ok, err = _validate_sequence(str(rec.seq))
if not ok:
return ValidationResult(valid=False, error=err)
return ValidationResult(sequences=records)
# Plain sequence (no FASTA header)
clean = "".join(c for c in text if c.isalpha()).upper()
ok, err = _validate_sequence(clean)
if not ok:
return ValidationResult(valid=False, error=err)
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
record = SeqRecord(Seq(clean), id="query", description="")
return ValidationResult(sequences=[record])
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