def test_format_function_arguments(self):
app = MothurClassifySeqs({
'reference': '/home/myuser/ref-seqs.fasta',
'taxonomy': '/home/MyUser/data/tax.txt',
'cutoff': 80,
})
obs_args = app._format_function_arguments(
['reference', 'taxonomy', 'cutoff', 'iters'])
exp_args = ("reference=/home/myuser/ref\\-seqs.fasta, "
"taxonomy=/home/MyUser/data/tax.txt, cutoff=80")
self.assertEqual(obs_args, exp_args)
def test_format_function_arguments(self):
app = MothurClassifySeqs({
'reference': '/home/myuser/ref-seqs.fasta',
'taxonomy': '/home/MyUser/data/tax.txt',
'cutoff': 80,
})
obs_args = app._format_function_arguments(
['reference', 'taxonomy', 'cutoff', 'iters'])
exp_args = (
"reference=/home/myuser/ref\\-seqs.fasta, "
"taxonomy=/home/MyUser/data/tax.txt, cutoff=80")
self.assertEqual(obs_args, exp_args)
def test_compile_mothur_script(self):
app = MothurClassifySeqs({
'reference': '/home/myuser/ref-seqs.fasta',
'taxonomy': '/home/MyUser/data/tax.txt',
'cutoff': 80,
})
app._input_filename = "/my/input.fasta"
exp_script = ("#classify.seqs(fasta=/my/input.fasta, "
"reference=/home/myuser/ref\-seqs.fasta, "
"taxonomy=/home/MyUser/data/tax.txt, "
"cutoff=80)")
self.assertEqual(app._compile_mothur_script(), exp_script)
def test_compile_mothur_script(self):
app = MothurClassifySeqs({
'reference': '/home/myuser/ref-seqs.fasta',
'taxonomy': '/home/MyUser/data/tax.txt',
'cutoff': 80,
})
app._input_filename = "/my/input.fasta"
exp_script = (
"#classify.seqs(fasta=/my/input.fasta, "
"reference=/home/myuser/ref\-seqs.fasta, "
"taxonomy=/home/MyUser/data/tax.txt, "
"cutoff=80)")
self.assertEqual(app._compile_mothur_script(), exp_script)
def test_app(self):
app = MothurClassifySeqs({
'reference': self.ref_file.name,
'taxonomy': self.tax_file.name,
})
res = app(mothur_seqs)
assignments = res['assignments'].read()
self.assertEqual(assignments, mothur_assignments)
summary = res['summary'].read()
self.assertEqual(summary, mothur_summary)
