def test_quiet(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.quiet, 0)
cfg = parse_args(['--quiet', 'replicon'])
self.assertEqual(cfg.quiet, 1)
cfg = parse_args(['-qq', 'replicon'])
self.assertEqual(cfg.quiet, 2)
def test_quiet(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.quiet, 0)
cfg = parse_args(['--quiet', 'replicon'])
self.assertEqual(cfg.quiet, 1)
cfg = parse_args(['-qq', 'replicon'])
self.assertEqual(cfg.quiet, 2)
def test_verbose(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.verbose, 0)
cfg = parse_args(['--verbose', 'replicon'])
self.assertEqual(cfg.verbose, 1)
cfg = parse_args(['-vv', 'replicon'])
self.assertEqual(cfg.verbose, 2)
def test_prodigal(self):
cfg = parse_args(['replicon'])
prodigal = 'foo'
self.assertEqual(cfg.prodigal,
distutils.spawn.find_executable('prodigal'))
cfg = parse_args(['--prodigal', prodigal, 'replicon'])
self.assertEqual(cfg.prodigal, prodigal)
def test_hmmsearch(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.hmmsearch,
distutils.spawn.find_executable("hmmsearch"))
hmmsearch = 'foo'
cfg = parse_args(['--hmmsearch', hmmsearch, 'replicon'])
self.assertEqual(cfg.hmmsearch, hmmsearch)
def test_verbose(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.verbose, 0)
cfg = parse_args(['--verbose', 'replicon'])
self.assertEqual(cfg.verbose, 1)
cfg = parse_args(['-vv', 'replicon'])
self.assertEqual(cfg.verbose, 2)
def test_wo_replicon(self):
real_exit = sys.exit
sys.exit = self.fake_exit
with self.catch_io(err=True):
try:
_ = parse_args([])
except TypeError as err:
msg = sys.stderr.getvalue()
msg_end = 'error: the following arguments are required: replicon\n'
self.assertTrue(msg.endswith(msg_end), "{} != {}".format(msg[len(msg) - len(msg_end):], msg_end))
# program exit with returncode = 2
self.assertEqual(str(err), '2')
finally:
sys.exit = real_exit
def test_wo_replicon(self):
real_exit = sys.exit
sys.exit = self.fake_exit
with self.catch_io(err=True):
try:
_ = parse_args([])
except TypeError as err:
msg = sys.stderr.getvalue()
msg_end = 'error: the following arguments are required: replicon\n'
self.assertTrue(msg.endswith(msg_end), "{} != {}".format(msg[len(msg) - len(msg_end):], msg_end))
# program exit with returncode = 2
self.assertEqual(str(err), '2')
finally:
sys.exit = real_exit
def test_cirular_n_linear(self):
real_exit = sys.exit
sys.exit = self.fake_exit
with self.catch_io(err=True):
try:
_ = parse_args(['--circ', '--linear', 'replicon'])
except TypeError as err:
msg = sys.stderr.getvalue()
msg_end = 'error: argument --linear: not allowed with argument --circ\n'
self.assertTrue(msg.endswith(msg_end), "{} != {}".format(msg[len(msg) - len(msg_end):], msg_end))
# program exit with returncode = 2
self.assertEqual(str(err), '2')
finally:
sys.exit = real_exit
def test_cirular_n_linear(self):
real_exit = sys.exit
sys.exit = self.fake_exit
with self.catch_io(err=True):
try:
_ = parse_args(['--circ', '--linear', 'replicon'])
except TypeError as err:
msg = sys.stderr.getvalue()
msg_end = 'error: argument --linear: not allowed with argument --circ\n'
self.assertTrue(msg.endswith(msg_end), "{} != {}".format(msg[len(msg) - len(msg_end):], msg_end))
# program exit with returncode = 2
self.assertEqual(str(err), '2')
finally:
sys.exit = real_exit
def test_version(self):
real_exit = sys.exit
sys.exit = self.fake_exit
from numpy import __version__ as np_vers
from pandas import __version__ as pd_vers
from matplotlib import __version__ as mplt_vers
from Bio import __version__ as bio_vers
from integron_finder import __version__ as if_vers
with self.catch_io(out=True):
try:
_ = cfg = parse_args(['--version'])
except TypeError as err:
msg = sys.stdout.getvalue()
msg_expected = """integron_finder version {i_f}
Using:
- Python {py}
- numpy {np}
- pandas {pd}
- matplolib {mplt}
- biopython {bio}
Authors:
- Jean Cury, Bertrand Neron, Eduardo Rocha,
Citation:
Identification and analysis of integrons and cassette arrays in bacterial genomes
Jean Cury; Thomas Jove; Marie Touchon; Bertrand Neron; Eduardo PC Rocha
Nucleic Acids Research 2016; doi: 10.1093/nar/gkw319
""".format(i_f=if_vers,
py=sys.version.replace('\n', ' '),
np=np_vers,
pd=pd_vers,
mplt=mplt_vers,
bio=bio_vers
)
self.assertEqual(msg.strip(), msg_expected.strip())
# program exit with returncode = 2
self.assertEqual(str(err), '0')
finally:
sys.exit = real_exit
def test_version(self):
real_exit = sys.exit
sys.exit = self.fake_exit
from numpy import __version__ as np_vers
from pandas import __version__ as pd_vers
from matplotlib import __version__ as mplt_vers
from Bio import __version__ as bio_vers
from integron_finder import __version__ as if_vers
with self.catch_io(out=True):
try:
_ = cfg = parse_args(['--version'])
except TypeError as err:
msg = sys.stdout.getvalue()
msg_expected = """integron_finder version {i_f}
Using:
- Python {py}
- numpy {np}
- pandas {pd}
- matplolib {mplt}
- biopython {bio}
Authors:
- Jean Cury, Bertrand Neron, Eduardo Rocha,
Citation:
Identification and analysis of integrons and cassette arrays in bacterial genomes
Jean Cury; Thomas Jove; Marie Touchon; Bertrand Neron; Eduardo PC Rocha
Nucleic Acids Research 2016; doi: 10.1093/nar/gkw319
""".format(i_f=if_vers,
py=sys.version.replace('\n', ' '),
np=np_vers,
pd=pd_vers,
mplt=mplt_vers,
bio=bio_vers
)
self.assertEqual(msg.strip(), msg_expected.strip())
# program exit with returncode = 2
self.assertEqual(str(err), '0')
finally:
sys.exit = real_exit
def test_min_attc_size(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.min_attc_size, 40)
min_attc_size = 50
cfg = parse_args(['--min-attc-size', str(min_attc_size), 'replicon'])
self.assertEqual(cfg.min_attc_size, min_attc_size)
def test_min_attc_size(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.min_attc_size, 40)
min_attc_size = 50
cfg = parse_args(['--min-attc-size', str(min_attc_size), 'replicon'])
self.assertEqual(cfg.min_attc_size, min_attc_size)
def test_circular(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.circular)
cfg = parse_args(['--circ', 'replicon'])
self.assertTrue(cfg.circular)
def test_evalues_attc(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.evalue_attc, 1.0)
evalue = 5.0
cfg = parse_args(['--evalue-attc', str(evalue), 'replicon'])
self.assertEqual(cfg.evalue_attc, evalue)
def test_no_proteins(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.no_proteins)
cfg = parse_args(['--no-proteins', 'replicon'])
self.assertTrue(cfg.no_proteins)
def test_gbk(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.gbk)
cfg = parse_args(['--gbk', 'replicon'])
self.assertTrue(cfg.gbk)
def test_circular(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.circular)
cfg = parse_args(['--circ', 'replicon'])
self.assertTrue(cfg.circular)
def test_pdf(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.pdf)
cfg = parse_args(['--pdf', 'replicon'])
self.assertTrue(cfg.pdf)
def test_gbk(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.gbk)
cfg = parse_args(['--gbk', 'replicon'])
self.assertTrue(cfg.gbk)
def test_keep_palindromes(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.keep_palindromes)
cfg = parse_args(['--keep-palindromes', 'replicon'])
self.assertTrue(cfg.keep_palindromes)
def test_evalues_attc(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.evalue_attc, 1.0)
evalue = 5.0
cfg = parse_args(['--evalue-attc', str(evalue), 'replicon'])
self.assertEqual(cfg.evalue_attc, evalue)
def test_mute(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.mute)
cfg = parse_args(['--mute', 'replicon'])
self.assertTrue(cfg.mute)
def test_topology_file(self):
cfg = parse_args(['replicon'])
self.assertIsNone(cfg.topology_file)
topo = 'foo'
cfg = parse_args(['--topology-file', topo, 'replicon'])
self.assertEqual(cfg.topology_file, topo)
def test_linear(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.linear)
cfg = parse_args(['--linear', 'replicon'])
self.assertTrue(cfg.linear)
def test_mute(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.mute)
cfg = parse_args(['--mute', 'replicon'])
self.assertTrue(cfg.mute)
def test_keep_tmp(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.keep_tmp)
cfg = parse_args(['--keep-tmp', 'replicon'])
self.assertTrue(cfg.keep_tmp)
def test_gembase(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.gembase)
cfg = parse_args(['--gembase', 'replicon'])
self.assertTrue(cfg.gembase)
def test_split_results(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.split_results)
cfg = parse_args(['--split-results', 'replicon'])
self.assertTrue(cfg.split_results)
def test_split_results(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.split_results)
cfg = parse_args(['--split-results', 'replicon'])
self.assertTrue(cfg.split_results)
def test_replicon(self):
replicon = 'foo'
cfg = parse_args([replicon])
self.assertEqual(cfg.input_seq_path, os.path.abspath(replicon))
def test_attc_model(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.model_attc_name, 'attc_4')
model = 'foo'
cfg = parse_args(['--attc-model', model, 'replicon'])
self.assertEqual(cfg.model_attc_name, model)
def test_local_max(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.local_max)
cfg = parse_args(['--local-max', 'replicon'])
self.assertTrue(cfg.local_max)
def test_keep_palindromes(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.keep_palindromes)
cfg = parse_args(['--keep-palindromes', 'replicon'])
self.assertTrue(cfg.keep_palindromes)
def test_func_annot(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.func_annot)
cfg = parse_args(['--func-annot', 'replicon'])
self.assertTrue(cfg.func_annot)
def test_max_attc_size(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.max_attc_size, 200)
max_attc_size = 50
cfg = parse_args(['--max-attc-size', str(max_attc_size), 'replicon'])
self.assertEqual(cfg.max_attc_size, max_attc_size)
def test_cpu(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.cpu, 1)
cpu = 10
cfg = parse_args(['--cpu', str(cpu), 'replicon'])
self.assertEqual(cfg.cpu, cpu)
def test_eagle_eyes(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.local_max)
# eagle option is an "alias" for local_max
cfg = parse_args(['--eagle-eyes', 'replicon'])
self.assertTrue(cfg.local_max)
def test_local_max(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.local_max)
cfg = parse_args(['--local-max', 'replicon'])
self.assertTrue(cfg.local_max)
def test_linear(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.linear)
cfg = parse_args(['--linear', 'replicon'])
self.assertTrue(cfg.linear)
def test_cpu(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.cpu, 1)
cpu = 10
cfg = parse_args(['--cpu', str(cpu), 'replicon'])
self.assertEqual(cfg.cpu, cpu)
def test_topology_file(self):
cfg = parse_args(['replicon'])
self.assertIsNone(cfg.topology_file)
topo = 'foo'
cfg = parse_args(['--topology-file', topo, 'replicon'])
self.assertEqual(cfg.topology_file, topo)
def test_outdir(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.outdir, os.path.abspath('.'))
outdir = 'foo'
cfg = parse_args(['--outdir', outdir, 'replicon'])
self.assertEqual(cfg.outdir, os.path.abspath(outdir))
def test_attc_model(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.model_attc_name, 'attc_4')
model = 'foo'
cfg = parse_args(['--attc-model', model, 'replicon'])
self.assertEqual(cfg.model_attc_name, model)
def test_replicon(self):
replicon = 'foo'
cfg = parse_args([replicon])
self.assertEqual(cfg.input_seq_path, os.path.abspath(replicon))
def test_pdf(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.pdf)
cfg = parse_args(['--pdf', 'replicon'])
self.assertTrue(cfg.pdf)
def test_max_attc_size(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.max_attc_size, 200)
max_attc_size = 50
cfg = parse_args(['--max-attc-size', str(max_attc_size), 'replicon'])
self.assertEqual(cfg.max_attc_size, max_attc_size)
def test_keep_tmp(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.keep_tmp)
cfg = parse_args(['--keep-tmp', 'replicon'])
self.assertTrue(cfg.keep_tmp)
def test_gembase(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.gembase)
cfg = parse_args(['--gembase', 'replicon'])
self.assertTrue(cfg.gembase)
def test_path_func_annot(self):
cfg = parse_args(['replicon'])
self.assertIsNone(cfg.path_func_annot)
func_annot = 'foo'
cfg = parse_args(['--path-func-annot', func_annot, 'replicon'])
self.assertEqual(cfg.path_func_annot, func_annot)
def test_eagle_eyes(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.local_max)
# eagle option is an "alias" for local_max
cfg = parse_args(['--eagle-eyes', 'replicon'])
self.assertTrue(cfg.local_max)
def test_distance_threshold(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.distance_threshold, 4000)
dt = 50
cfg = parse_args(['--distance-thresh', str(dt), 'replicon'])
self.assertEqual(cfg.distance_threshold, dt)
def test_no_proteins(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.no_proteins)
cfg = parse_args(['--no-proteins', 'replicon'])
self.assertTrue(cfg.no_proteins)
def test_func_annot(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.func_annot)
cfg = parse_args(['--func-annot', 'replicon'])
self.assertTrue(cfg.func_annot)
def test_outdir(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.outdir, os.path.abspath('.'))
outdir = 'foo'
cfg = parse_args(['--outdir', outdir, 'replicon'])
self.assertEqual(cfg.outdir, os.path.abspath(outdir))
def test_distance_threshold(self):
cfg = parse_args(['replicon'])
self.assertEqual(cfg.distance_threshold, 4000)
dt = 50
cfg = parse_args(['--distance-thresh', str(dt), 'replicon'])
self.assertEqual(cfg.distance_threshold, dt)
def test_union_integrase(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.union_integrases)
cfg = parse_args(['--union-integrases', 'replicon'])
self.assertTrue(cfg.union_integrases)
def test_union_integrase(self):
cfg = parse_args(['replicon'])
self.assertFalse(cfg.union_integrases)
cfg = parse_args(['--union-integrases', 'replicon'])
self.assertTrue(cfg.union_integrases)
def test_prodigal(self):
cfg = parse_args(['replicon'])
prodigal = 'foo'
self.assertEqual(cfg.prodigal, distutils.spawn.find_executable('prodigal'))
cfg = parse_args(['--prodigal', prodigal, 'replicon'])
self.assertEqual(cfg.prodigal, prodigal)