def test_build_di_demux_command(self):
with tempfile.NamedTemporaryFile() as barcode_fasta_f:
with tempfile.NamedTemporaryFile() as barcode_fasta_r:
obs = _build_demux_command(self.seqs_dir_fmt, {
'fwd': barcode_fasta_f,
'rev': barcode_fasta_r
}, self.per_sample_dir_fmt, self.untrimmed_dir_fmt, 0.1, 2)
self.assertTrue(barcode_fasta_f.name in obs[2])
self.assertTrue('--pair-adapters' == obs[11])
self.assertTrue(barcode_fasta_r.name in obs[13])
def test_build_demux_command(self):
with tempfile.NamedTemporaryFile() as barcode_fasta:
obs = _build_demux_command(self.seqs_dir_fmt, barcode_fasta,
self.per_sample_dir_fmt,
self.untrimmed_dir_fmt, 0.1)
self.assertTrue(barcode_fasta.name in obs[2])
self.assertTrue('0.1' in obs[4])
self.assertTrue(str(self.per_sample_dir_fmt) in obs[6])
self.assertTrue(str(self.untrimmed_dir_fmt) in obs[8])
self.assertEqual(str(self.seqs_dir_fmt.file.view(FastqGzFormat)),
obs[9])
def test_build_demux_command(self):
with tempfile.NamedTemporaryFile() as barcode_fasta:
obs = _build_demux_command(self.seqs_dir_fmt, {
'fwd': barcode_fasta,
'rev': None
}, self.per_sample_dir_fmt, self.untrimmed_dir_fmt, 0.1)
self.assertTrue(barcode_fasta.name in obs[2])
self.assertTrue('0.1' in obs[4])
self.assertTrue(str(self.per_sample_dir_fmt) in obs[6]) # fwd
self.assertTrue(str(self.per_sample_dir_fmt) in obs[10]) # rev
self.assertTrue(str(self.untrimmed_dir_fmt) in obs[8]) # fwd
self.assertTrue(str(self.untrimmed_dir_fmt) in obs[12]) # rev
exp_f = str(self.seqs_dir_fmt.forward_sequences.view(FastqGzFormat))
self.assertEqual(exp_f, obs[13])
exp_r = str(self.seqs_dir_fmt.reverse_sequences.view(FastqGzFormat))
self.assertEqual(exp_r, obs[14])