def test_cull_seqs_degen_one(self):
# Test params: mnum_degenerates = 2
# Only seqs without degen bases returned
obs = cull_seqs(self.seqs1, num_degenerates=1, homopolymer_length=9)
obs_ids = {seq.metadata['id'] for seq in obs.view(DNAIterator)}
exp_ids = {'Hpoly8', 'cleanseq'}
self.assertEqual(obs_ids, exp_ids)
def test_cull_seqs_degen_seven_hpoly_nine(self):
# Test params: num_degenerates = 7, homopolymer_length = 9
# All seqs should pass.
obs = cull_seqs(self.seqs1, num_degenerates=7, homopolymer_length=9)
obs_ids = {seq.metadata['id'] for seq in obs.view(DNAIterator)}
exp_ids = {'Ambig6', 'Ambig2', 'Hpoly8', 'Hpoly8Ambig1', 'cleanseq'}
self.assertEqual(obs_ids, exp_ids)
def test_cull_seqs_degen_seven_hpoly_seven(self):
# Test params: num_degenerates = 7, homopolymer_length = 7
# Keep seq with 2 ambigs, and 7 hpoly
obs = cull_seqs(self.seqs1, num_degenerates=7, homopolymer_length=7)
obs_ids = {seq.metadata['id'] for seq in obs.view(DNAIterator)}
exp_ids = {'Ambig2', 'Ambig6', 'cleanseq'}
self.assertEqual(obs_ids, exp_ids)
def test_cull_seqs_rna_default_params(self):
# Test default params work with RNA seqs as input
rna_path = self.get_data_path('cleanseq-test-1-rna.fasta')
rna_seqs = RNAFASTAFormat(rna_path, mode='r').view(DNAIterator)
obs = cull_seqs(rna_seqs)
obs_ids = {seq.metadata['id'] for seq in obs.view(DNAIterator)}
exp_ids = {'Ambig2', 'cleanseq'}
self.assertEqual(obs_ids, exp_ids)
def test_cull_seqs_default_params(self):
# Test default params: num_degenerates = 5, homopolymer_length = 8
obs = cull_seqs(self.seqs1)
obs_ids = {seq.metadata['id'] for seq in obs.view(DNAIterator)}
exp_ids = {'Ambig2', 'cleanseq'}
self.assertEqual(obs_ids, exp_ids)