def test_build_trim_command_typical(self):
for fwd in self.demux_seqs.sequences.iter_views(FastqGzFormat):
obs = _build_trim_command(self.demux_seqs, fwd[0], None,
self.trimmed_seqs,
cores=0,
adapter_f=['AAAA'],
front_f=['GGGG'],
anywhere_f=['CCCC'],
error_rate=2,
indels=False,
times=3,
overlap=4,
match_read_wildcards=True,
match_adapter_wildcards=False)
obs = ' '.join(obs)
self.assertTrue('-o %s' % str(self.trimmed_seqs.path / fwd[0])
in obs)
self.assertTrue('--cores 0' in obs)
self.assertTrue('--adapter AAAA' in obs)
self.assertTrue('--front GGGG' in obs)
self.assertTrue('--anywhere CCCC' in obs)
self.assertTrue('--error-rate 2' in obs)
self.assertTrue('--times 3' in obs)
self.assertTrue('--overlap 4' in obs)
self.assertTrue('--no-indels' in obs)
self.assertTrue('--match-read-wildcards' in obs)
self.assertTrue('--no-match-adapter-wildcards' in obs)
self.assertTrue(str(self.demux_seqs) in obs)
def test_build_trim_command_typical(self):
df = self.demux_seqs.manifest.view(pd.DataFrame)
for _, fwd in df.itertuples():
obs = _build_trim_command(fwd, None,
self.trimmed_seqs,
cores=0,
adapter_f=['AAAA'],
front_f=['GGGG'],
anywhere_f=['CCCC'],
error_rate=2,
indels=False,
times=3,
overlap=4,
match_read_wildcards=True,
match_adapter_wildcards=False,
minimum_length=2,
discard_untrimmed=True)
obs = ' '.join(obs)
self.assertTrue('-o %s' % str(self.trimmed_seqs.path / fwd[0])
in obs)
self.assertTrue('--cores 0' in obs)
self.assertTrue('--adapter AAAA' in obs)
self.assertTrue('--front GGGG' in obs)
self.assertTrue('--anywhere CCCC' in obs)
self.assertTrue('--error-rate 2' in obs)
self.assertTrue('--times 3' in obs)
self.assertTrue('--overlap 4' in obs)
self.assertTrue('--no-indels' in obs)
self.assertTrue('--match-read-wildcards' in obs)
self.assertTrue('--no-match-adapter-wildcards' in obs)
self.assertTrue('--minimum-length 2' in obs)
self.assertTrue('--discard-untrimmed' in obs)
self.assertTrue(str(self.demux_seqs) in obs)
def test_build_trim_command_no_adapters_or_flags(self):
for fwd in self.demux_seqs.sequences.iter_views(FastqGzFormat):
obs = _build_trim_command(self.demux_seqs, fwd[0], None,
self.trimmed_seqs)
obs = ' '.join(obs)
self.assertTrue('--adapter' not in obs)
self.assertTrue('--front' not in obs)
self.assertTrue('--anywhere' not in obs)
self.assertTrue('--no-indels' not in obs)
self.assertTrue('--match-read-wildcards' not in obs)
self.assertTrue('--no-match-adapter-wildcards' not in obs)
def test_build_trim_command_multiple_adapters(self):
for fwd in self.demux_seqs.sequences.iter_views(FastqGzFormat):
obs = _build_trim_command(self.demux_seqs, fwd[0], None,
self.trimmed_seqs,
adapter_f=['AAAA', 'GGGG', 'CCCC'])
obs = ' '.join(obs)
self.assertTrue('--adapter AAAA' in obs)
self.assertTrue('--adapter GGGG' in obs)
self.assertTrue('--adapter CCCC' in obs)
self.assertTrue('--front' not in obs)
self.assertTrue('--anywhere' not in obs)
def test_build_trim_command_multiple_adapters(self):
df = self.demux_seqs.manifest.view(pd.DataFrame)
for _, fwd in df.itertuples():
obs = _build_trim_command(fwd, None,
self.trimmed_seqs,
adapter_f=['AAAA', 'GGGG', 'CCCC'])
obs = ' '.join(obs)
self.assertTrue('--adapter AAAA' in obs)
self.assertTrue('--adapter GGGG' in obs)
self.assertTrue('--adapter CCCC' in obs)
self.assertTrue('--front' not in obs)
self.assertTrue('--anywhere' not in obs)
def test_build_trim_command_no_adapters_or_flags(self):
df = self.demux_seqs.manifest.view(pd.DataFrame)
for _, fwd in df.itertuples():
obs = _build_trim_command(fwd, None, self.trimmed_seqs)
obs = ' '.join(obs)
self.assertTrue('--adapter' not in obs)
self.assertTrue('--front' not in obs)
self.assertTrue('--anywhere' not in obs)
self.assertTrue('--no-indels' not in obs)
self.assertTrue('--match-read-wildcards' not in obs)
self.assertTrue('--no-match-adapter-wildcards' not in obs)
self.assertTrue('--minimum-length 1' in obs)
self.assertTrue('--discard-untrimmed' not in obs)
def test_build_trim_command_multiple_adapters(self):
itr = self.demux_seqs.sequences.iter_views(FastqGzFormat)
for fwd in itr:
rev = next(itr)
obs = _build_trim_command(self.demux_seqs, fwd[0], rev[0],
self.trimmed_seqs,
adapter_f=['AAAA', 'GGGG', 'CCCC'],
adapter_r=['TTTT', 'CCCC', 'GGGG'])
obs = ' '.join(obs)
self.assertTrue('--adapter AAAA' in obs)
self.assertTrue('--adapter GGGG' in obs)
self.assertTrue('--adapter CCCC' in obs)
self.assertTrue('-A TTTT' in obs)
self.assertTrue('-A CCCC' in obs)
self.assertTrue('-A GGGG' in obs)
self.assertTrue('--front' not in obs)
self.assertTrue('--anywhere' not in obs)
self.assertTrue('-G' not in obs)
self.assertTrue('-B' not in obs)