def test_functional_no_hits(self):
out = os.path.join(self.tmpdir, 'test_macsyprofile')
previous_run = self.find_data('functional_test_degenerated_systems')
expected_result = self.find_data('results_macsyprofile_no_hits.tsv')
cmd = f"macsyprofile -o {out} --index-dir {self.tmpdir} --i-evalue-sel 1e-10 --coverage-profile 2.0 {previous_run}"
macsyprofile.main(cmd.split()[1:], log_level='WARNING')
self.assertFileEqual(expected_result, out, comment='#')
def test_functional_best_score(self):
out = os.path.join(self.tmpdir, 'test_macsyprofile')
previous_run = self.find_data('functional_test_degenerated_systems')
expected_result = self.find_data('results_macsyprofile_best_score.tsv')
cmd = f"macsyprofile -o {out} --index-dir {self.tmpdir} --best-hits score {previous_run} "
macsyprofile.main(cmd.split()[1:], log_level='WARNING')
self.assertFileEqual(expected_result, out, comment='#')
def test_functional(self):
old = self.find_data('conf_files', 'macsyfinder-old.conf')
shutil.copyfile(old, os.path.join(self.tmpdir, 'macsyfinder.conf'))
previous_run = self.tmpdir
cmd = f"macsyprofile --index-dir {self.tmpdir} {previous_run}"
with self.assertRaises(ValueError):
macsyprofile.main(cmd.split()[1:], log_level=logging.CRITICAL + 1)
def test_functional_pattern(self):
out = os.path.join(self.tmpdir, 'test_macsyprofile')
previous_run = self.find_data('functional_test_degenerated_systems')
expected_result = self.find_data('results_macsyprofile_pattern.tsv')
# the argument do not need to be protected (we do not use shell)
# as on real command line so '*mpf' => *mpf
cmd = f"macsyprofile -o {out} --index-dir {self.tmpdir} -p *mfp {previous_run} "
macsyprofile.main(cmd.split()[1:], log_level='WARNING')
self.assertFileEqual(expected_result, out, comment='#')
def test_functional_out_exists(self):
out = os.path.join(self.tmpdir, 'test_macsyprofile')
open(out, 'w').close()
previous_run = self.find_data('functional_test_degenerated_systems')
cmd = f"macsyprofile -o {self.tmpdir} --mute --best-hits score {previous_run} "
# we cannot test the log message here
# because the logger are init when main is called
# after that the context is establish
# so when the wrapper is called the handler cannot be substitute by the fake
with self.assertRaises(ValueError):
macsyprofile.main(cmd.split()[1:])
def test_functional_no_previous_run(self):
cmd = "macsyprofile --mute nimportnaoik "
# we cannot test the log message here
# because the logger are init when main is called
# after that the context is establish
# so when the wrapper is called the handler cannot be substitute by the fake
with self.assertRaises(FileNotFoundError):
macsyprofile.main(cmd.split()[1:])
bad_previous_run = os.path.join(self.tmpdir, 'test_macsyprofile')
open(bad_previous_run, 'w').close()
cmd = f"macsyprofile {bad_previous_run} "
with self.assertRaises(ValueError):
macsyprofile.main(cmd.split()[1:], log_level=logging.CRITICAL + 1)