File size: 2,642 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 | """BLAST program / database matrix and sequence-type-aware resolution.
Programs map to the NCBI QBLAST PROGRAMS. Databases are validated against the
program's valid target types so a protein-only db (nr) is never sent for a
nucleotide program (blastn) and vice versa.
"""
from app.services.sequence_utils import detect_sequence_type
PROTEIN_PROGRAMS = ["blastp", "tblastn"]
NUCLEOTIDE_PROGRAMS = ["blastn", "blastx", "tblastx"]
ALL_PROGRAMS = ["blastp", "blastn", "blastx", "tblastn", "tblastx"]
PROGRAM_DATABASES = {
"blastp": ["nr", "swissprot", "pdb", "pdbaa", "refseq_protein", "env_nr"],
"blastn": ["nt", "refseq_rna", "refseq_genomic", "est", "gss"],
"blastx": ["nr", "swissprot", "pdb", "pdbaa", "refseq_protein"],
"tblastn": ["nt", "refseq_rna", "refseq_genomic", "est", "gss"],
"tblastx": ["nt", "refseq_rna", "refseq_genomic", "est", "gss"],
}
DEFAULT_PROGRAM = {"protein": "blastp", "dna": "blastn", "rna": "blastn"}
DEFAULT_DATABASE = {"protein": "nr", "dna": "nt", "rna": "nt"}
FAST_DATABASE = {"protein": "swissprot", "dna": "refseq_rna", "rna": "refseq_rna"}
def resolve_blast_params(
sequence: str,
program: str | None = None,
database: str | None = None,
fast_mode: bool = False,
) -> tuple[str, str, str]:
"""Return (program, database, seq_type) with safe normalization.
An explicitly requested program that doesn't match the query's detected
type raises ValueError (the caller surfaces it as a clear job error).
An incompatible or missing database falls back to the program's default so
the frontend's permissive defaults (e.g. nr sent for a DNA query) degrade
gracefully instead of erroring.
"""
seq_type = detect_sequence_type(sequence)
if seq_type not in ("protein", "dna", "rna"):
raise ValueError(f"Could not determine sequence type for BLAST (detected: {seq_type})")
if not program:
program = DEFAULT_PROGRAM[seq_type]
program = program.lower().strip()
if program not in ALL_PROGRAMS:
raise ValueError(f"Unsupported BLAST program: {program}")
allowed = PROTEIN_PROGRAMS if seq_type == "protein" else NUCLEOTIDE_PROGRAMS
if program not in allowed:
raise ValueError(f"Program '{program}' cannot be used with a {seq_type} query")
if not database:
database = FAST_DATABASE[seq_type] if fast_mode else DEFAULT_DATABASE[seq_type]
database = database.lower().strip()
valid_dbs = PROGRAM_DATABASES[program]
if database not in valid_dbs:
database = FAST_DATABASE[seq_type] if fast_mode else DEFAULT_DATABASE[seq_type]
return program, database, seq_type
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