def benchmark(query_protein_id, method=Pfam(), blast_service="plain", max_evalue=None, n_alignments=100):
query_result = method.get_result(query_protein_id)
blast_results = BLAST_Client.blast(
query_protein_id, service=blast_service, max_evalue=max_evalue, n_alignments=n_alignments
)
benchmarks = []
for blast_result in blast_results:
for hit_protein_id in blast_result["subjects"]:
hit_result = method.get_result(hit_protein_id)
b = method.benchmark(query_result, hit_result)
benchmarks.append({"protein_id": hit_protein_id, "benchmark": b, "evalue": blast_result["evalue"]})
return benchmarks
def search_homologs(self, protein_id):
return BLAST_Client.blast(protein_id, max_evalue=self.max_evalue, n_alignments=self.max_alignments)