def test_unclassifiable_sequence(self): query_file = StringIO( ">MostlyTs\nTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT" "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTT" "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n") res = mothur_classify_file( query_file, self.ref_file.name, self.tax_file.name) exp_res = { 'MostlyTs': (['Unknown'], 0.0), } self.assertEqual(res, exp_res)
def test_mothur_classify_file(self): query_file = StringIO(mothur_seqs) res = mothur_classify_file( query_file, self.ref_file.name, self.tax_file.name) exp_res = { 'A': (['k__Bacteria', 'p__Firmicutes', 'c__Clostridia', 'o__Clostridale', 'f__Eubacteriaceae', 'g__Eubacterium', 's__Eubacteriumfoedans'], 1.0), 'Very': (['k__Bacteria', 'p__Bacteriodetes'], 1.0), '01': (['k__Bacteria', 'p__Firmicutes'], 1.0), } self.assertEqual(res, exp_res)
def __call__(self, seq_path, result_path=None, log_path=None): seq_file = open(seq_path) percent_confidence = int(self.Params['Confidence'] * 100) result = mothur.mothur_classify_file( query_file=seq_file, ref_fp=self.Params['reference_sequences_fp'], tax_fp=self.Params['id_to_taxonomy_fp'], cutoff=percent_confidence, iters=self.Params['Iterations'], ksize=self.Params['KmerSize'], output_fp=result_path, ) if log_path: self.writeLog(log_path) return result
def __call__(self, seq_path, result_path=None, log_path=None): seq_file = open(seq_path) percent_confidence = int(self.Params['Confidence'] * 100) result = mothur.mothur_classify_file( query_file=seq_file, ref_fp=self.Params['reference_sequences_fp'], tax_fp=self.Params['id_to_taxonomy_fp'], cutoff=percent_confidence, iters=self.Params['Iterations'], ksize=self.Params['KmerSize'], output_fp=result_path, ) if log_path: self.writeLog(log_path) return result