def test_provenances_default_values(self):
parser = cli.get_tskit_parser()
cmd = "provenances"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence])
self.assertEqual(args.tree_sequence, tree_sequence)
self.assertEqual(args.human, False)
def test_provenances_long_args(self):
parser = cli.get_tskit_parser()
cmd = "provenances"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence, "--human"])
self.assertEqual(args.tree_sequence, tree_sequence)
self.assertEqual(args.human, True)
def test_mutations_default_values(self):
parser = cli.get_tskit_parser()
cmd = "mutations"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence])
self.assertEqual(args.tree_sequence, tree_sequence)
self.assertEqual(args.precision, 6)
def test_mutations_short_args(self):
parser = cli.get_tskit_parser()
cmd = "mutations"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence, "-p", "4"])
self.assertEqual(args.tree_sequence, tree_sequence)
self.assertEqual(args.precision, 4)
def test_vcf_long_args(self):
parser = cli.get_tskit_parser()
cmd = "vcf"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence, "--ploidy", "5"])
self.assertEqual(args.tree_sequence, tree_sequence)
self.assertEqual(args.ploidy, 5)
def test_fasta_long_args(self):
parser = cli.get_tskit_parser()
cmd = "fasta"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence, "--wrap", "50"])
self.assertEqual(args.tree_sequence, tree_sequence)
self.assertEqual(args.wrap, 50)
def test_fasta_short_args(self):
parser = cli.get_tskit_parser()
cmd = "fasta"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence, "-w", "100"])
self.assertEqual(args.tree_sequence, tree_sequence)
self.assertEqual(args.wrap, 100)
def test_vcf_default_values(self):
parser = cli.get_tskit_parser()
cmd = "vcf"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence])
self.assertEqual(args.tree_sequence, tree_sequence)
self.assertEqual(args.ploidy, 1)
def test_individuals_long_args(self):
parser = cli.get_tskit_parser()
cmd = "individuals"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence, "--precision", "5"])
assert args.tree_sequence == tree_sequence
assert args.precision == 5
def test_individuals_default_values(self):
parser = cli.get_tskit_parser()
cmd = "individuals"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence])
assert args.tree_sequence == tree_sequence
assert args.precision == 6
def test_vcf_long_args(self):
parser = cli.get_tskit_parser()
cmd = "vcf"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence, "--ploidy", "5"])
assert args.tree_sequence == tree_sequence
assert args.ploidy == 5
def test_sites_long_args(self):
parser = cli.get_tskit_parser()
cmd = "sites"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence, "--precision", "5"])
self.assertEqual(args.tree_sequence, tree_sequence)
self.assertEqual(args.precision, 5)
def test_fasta_long_args(self):
parser = cli.get_tskit_parser()
cmd = "fasta"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence, "--wrap", "50"])
assert args.tree_sequence == tree_sequence
assert args.wrap == 50
def test_vcf_default_values(self):
parser = cli.get_tskit_parser()
cmd = "vcf"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence])
assert args.tree_sequence == tree_sequence
assert args.ploidy is None
def test_fasta_default_values(self):
parser = cli.get_tskit_parser()
cmd = "fasta"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence])
assert args.tree_sequence == tree_sequence
assert args.wrap == 60
def test_fasta_short_args(self):
parser = cli.get_tskit_parser()
cmd = "fasta"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence, "-w", "100"])
assert args.tree_sequence == tree_sequence
assert args.wrap == 100
def test_provenances_default_values(self):
parser = cli.get_tskit_parser()
cmd = "provenances"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence])
assert args.tree_sequence == tree_sequence
assert not args.human
def test_provenances_long_args(self):
parser = cli.get_tskit_parser()
cmd = "provenances"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence, "--human"])
assert args.tree_sequence == tree_sequence
assert args.human
def test_mutations_long_args(self):
parser = cli.get_tskit_parser()
cmd = "mutations"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence, "--precision", "9"])
assert args.tree_sequence == tree_sequence
assert args.precision == 9
def test_sites_short_args(self):
parser = cli.get_tskit_parser()
cmd = "sites"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence, "-p", "8"])
assert args.tree_sequence == tree_sequence
assert args.precision == 8
def test_fasta_default_values(self):
parser = cli.get_tskit_parser()
cmd = "fasta"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence])
self.assertEqual(args.tree_sequence, tree_sequence)
self.assertEqual(args.wrap, 60)
def test_individuals_short_args(self):
parser = cli.get_tskit_parser()
cmd = "individuals"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence, "-p", "8"])
self.assertEqual(args.tree_sequence, tree_sequence)
self.assertEqual(args.precision, 8)
def test_upgrade_default_values(self):
parser = cli.get_tskit_parser()
cmd = "upgrade"
source = "in.trees"
destination = "out.trees"
args = parser.parse_args([cmd, source, destination])
assert args.source == source
assert args.destination == destination
assert not args.remove_duplicate_positions
def test_upgrade_default_values(self):
parser = cli.get_tskit_parser()
cmd = "upgrade"
source = "in.trees"
destination = "out.trees"
args = parser.parse_args([cmd, source, destination])
self.assertEqual(args.source, source)
self.assertEqual(args.destination, destination)
self.assertEqual(args.remove_duplicate_positions, False)
def test_populations_default_values(self):
parser = cli.get_tskit_parser()
cmd = "populations"
tree_sequence = "test.trees"
args = parser.parse_args([cmd, tree_sequence])
assert args.tree_sequence == tree_sequence