def test_extract_reads_fail_identity(self): with self.assertRaisesRegex(RuntimeError, "No matches found"): extract_reads(self.sequences, f_primer=self.f_primer, r_primer=self.r_primer, min_length=4, identity=1)
def test_extract_reads_expected(self): results = extract_reads(self.sequences, f_primer=self.f_primer, r_primer=self.r_primer, min_length=4) self._test_results(results)
def test_extract_reads_two_jobs(self): results = extract_reads(self.sequences, f_primer=self.f_primer, r_primer=self.r_primer, min_length=4, n_jobs=2) self._test_results(results)
def test_extract_reads_manual_batch_size(self): results = extract_reads(self.sequences, f_primer=self.f_primer, r_primer=self.r_primer, min_length=4, batch_size=10) self._test_results(results)
def test_extract_reads_expected_reverse(self): reverse_sequences = Artifact.import_data( 'FeatureData[Sequence]', self.get_data_path('dna-sequences-reverse.fasta')) results = extract_reads( reverse_sequences, f_primer=self.f_primer, r_primer=self.r_primer, min_length=4, read_orientation='reverse') self._test_results(results)
def test_extract_reads_expected_degenerate_primers(self): degenerate_f_primer = 'WWWWW' degenerate_r_primer = 'SSSSS' degenerate_sequences = Artifact.import_data( 'FeatureData[Sequence]', self.get_data_path('dna-sequences-degenerate-primers.fasta')) results = extract_reads( degenerate_sequences, f_primer=degenerate_f_primer, r_primer=degenerate_r_primer, min_length=4) self._test_results(results)
def test_extract_reads_expected_degenerate_primers(self): degenerate_f_primer = 'WWWWW' degenerate_r_primer = 'SSSSS' degenerate_seqs = skbio.io.read( self.get_data_path('dna-sequences-degenerate-primers.fasta'), format='fasta', constructor=skbio.DNA) degenerate_tmp_seqs = os.path.join(self.temp_dir.name, 'degenerate-tmp-seqs.fasta') skbio.io.write((s for s in degenerate_seqs), 'fasta', degenerate_tmp_seqs) degenerate_sequences = Artifact.import_data('FeatureData[Sequence]', degenerate_tmp_seqs) results = extract_reads(degenerate_sequences, f_primer=degenerate_f_primer, r_primer=degenerate_r_primer, min_length=4) self._test_results(results)
def test_extract_reads_fail_min_len_greater_than_trunc_len(self): with self.assertRaisesRegex(ValueError, "minimum length setting"): extract_reads(self.sequences, f_primer=self.f_primer, r_primer=self.r_primer, trunc_len=1)
def test_extract_reads_fail_trim_entire_read(self): with self.assertRaisesRegex(RuntimeError, "No matches found"): extract_reads(self.sequences, f_primer=self.f_primer, r_primer=self.r_primer, trim_left=4)
def test_extract_reads_expected_forward(self): results = extract_reads( self.sequences, f_primer=self.f_primer, r_primer=self.r_primer, min_length=4, read_orientation='forward') self._test_results(results)