def test_vquest_main_custom_arg(self):
"""Try an extra argument given as though on the command line."""
with tempfile.TemporaryDirectory() as tempdir:
os.chdir(tempdir)
main(["--IMGTrefdirSet", "1", str(self.path / "config.yml")])
self.assertTrue(Path("vquest_airr.tsv").exists())
self.assertTrue(Path("Parameters.txt").exists())
def test_vquest_main_no_collapse(self):
"""Test command-line interface with --no-collapse."""
with tempfile.TemporaryDirectory() as tempdir:
os.chdir(tempdir)
main(["--no-collapse", str(self.path / "config.yml")])
self.assertTrue(Path("001/vquest_airr.tsv").exists())
self.assertTrue(Path("001/Parameters.txt").exists())
def test_vquest_main(self):
"""Test that the command-line interface gives the expected response."""
with tempfile.TemporaryDirectory() as tempdir:
os.chdir(tempdir)
main([str(self.path / "config.yml")])
self.assertTrue(Path("vquest_airr.tsv").exists())
self.assertTrue(Path("Parameters.txt").exists())
def test_vquest_main(self):
"""Test that an html file with an error message is parsed correctly for cmd-line usage."""
with self.assertRaises(VquestError) as err_cm:
with tempfile.TemporaryDirectory() as tempdir:
os.chdir(tempdir)
main([str(self.path / "config.yml")])
self.assertEqual(
err_cm.exception.server_messages,
["The receptor type or locus is not available for this species"])
def test_vquest_main_no_args(self):
"""Test how the command-line interface handles no arguments.
It should exit with a nonzero exit code and write the help text to
stdout.
"""
self.check_missing_defaults_main(lambda: main([]))
def test_vquest_main_alignment(self):
"""Try using the --align feature.
In this case the regular output files should not be created and instead
FASTA text should be written to stdout.
"""
expected = """>IGKV2-ACR*02
gacattgtgatgacccagactccactctccctgcccgtcacccctggagagccagcctccatctcctgcaggtctagtcagagcctcttggatagt...gacgggtacacctgtttggactggtacctgcagaagccaggccagtctccacagctcctgatctatgaggtt.....................tccaaccgggtctctggagtccct...gacaggttcagtggcagtggg......tcagncactgatttcacactgaaaatcagccgggtggaagctgaggatgttggggtgtattactgtatgcaaagtatagagtttcctcc
"""
out = StringIO()
err = StringIO()
with redirect_stdout(out), redirect_stderr(err):
with tempfile.TemporaryDirectory() as tempdir:
os.chdir(tempdir)
main([str(self.path / "config.yml"), "--align"])
self.assertFalse(Path("vquest_airr.tsv").exists())
self.assertFalse(Path("Parameters.txt").exists())
self.assertEqual(out.getvalue(), expected)
self.assertEqual(err.getvalue(), "")
def test_vquest_main_alignment(self):
self.check_missing_defaults_main(lambda: main(["--align"]))
def test_vquest_main_no_collapse(self):
self.check_missing_defaults_main(lambda: main(["--no-collapse"]))
def test_vquest_main(self):
self.check_missing_defaults(
lambda: main([str(self.path / "config.yml")]))