def test_get_sequences_error_length(self): seqs = [("151_9240;size=170;", "----tagggcaagactccatg----"), ("151_6640;size=1068;", "--acggaggcgagatgcgtggt----"), ("151_64278;size=200;", "---tactagcaagattcctgg-----")] with self.assertRaises(ValueError): get_sequences(seqs)
def test_get_sequences_error_length(self): seqs = [ ("151_9240;size=170;", "----tagggcaagactccatg----"), ("151_6640;size=1068;", "--acggaggcgagatgcgtggt----"), ("151_64278;size=200;", "---tactagcaagattcctgg-----"), ] with self.assertRaises(ValueError): get_sequences(seqs)
def test_get_sequences(self): exp_seqs = [ Sequence("151_4447;size=1812;", "---aggatgcgagatgcgtggt-----"), Sequence("151_3288;size=1337;", "---ggatgcgagatgcgtggtg-----"), Sequence("151_6640;size=1068;", "---cggaggcgagatgcgtggt-----"), Sequence("151_5155;size=998;", "---gaggatgcgagatgcgtgg-----"), Sequence("151_527;size=964;", "---acggaggatgatgcgcggt-----"), Sequence("151_14716;size=390;", "---gagtgcgagatgcgtggtg-----"), Sequence("151_5777;size=305;", "---ggagtgcaagattccaggt-----"), Sequence("151_64278;size=200;", "---tactagcaagattcctggt-----"), Sequence("151_9240;size=170;", "---tagggcaagactccatggt-----"), Sequence("151_41690;size=157;", "---agg-gcgagattcctagtgg----")] obs_seqs = get_sequences(self.seqs) self.assertEqual(obs_seqs, exp_seqs)
def test_get_sequences(self): exp_seqs = [ Sequence("151_4447;size=1812;", "---aggatgcgagatgcgtggt-----"), Sequence("151_3288;size=1337;", "---ggatgcgagatgcgtggtg-----"), Sequence("151_6640;size=1068;", "---cggaggcgagatgcgtggt-----"), Sequence("151_5155;size=998;", "---gaggatgcgagatgcgtgg-----"), Sequence("151_527;size=964;", "---acggaggatgatgcgcggt-----"), Sequence("151_14716;size=390;", "---gagtgcgagatgcgtggtg-----"), Sequence("151_5777;size=305;", "---ggagtgcaagattccaggt-----"), Sequence("151_64278;size=200;", "---tactagcaagattcctggt-----"), Sequence("151_9240;size=170;", "---tagggcaagactccatggt-----"), Sequence("151_41690;size=157;", "---agg-gcgagattcctagtgg----"), ] obs_seqs = get_sequences(self.seqs) self.assertEqual(obs_seqs, exp_seqs)
def test_get_sequences_error_empty(self): with self.assertRaises(ValueError): get_sequences([])
def test_get_sequences_error_empty(self): self.assertIsNone(get_sequences([]))
def test_get_sequences_empty_file(self): gen = skbio.read(join(self.test_data_dir, 'seqs_empty.fasta'), format='fasta') self.assertEqual(get_sequences(gen), None)