def test_relation_to_type_material():
"""Test the -M/--type-material option works as expected."""
# Empty args should default to 'all'
args = ['bacteria']
parser = argument_parser()
ns = parser.parse_args(args)
assert ns.type_material == 'any'
args = ['-M', 'type', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args)
assert ns.type_material == 'type'
args = ['-M', 'type,synonym', 'fungi']
parser = argument_parser()
ns = parser.parse_args(args)
assert ns.type_material == 'type,synonym'
args = ['--type-material', 'reference', 'fungi']
parser = argument_parser()
ns = parser.parse_args(args)
assert ns.type_material == 'reference'
args = ['-M', 'all', 'fungi']
parser = argument_parser()
ns = parser.parse_args(args)
assert ns.type_material == 'all'
def test_relation_to_type_material(): """Test the -M/--type-material option works as expected.""" # Empty args should default to 'all' args = ['bacteria'] parser = argument_parser() ns = parser.parse_args(args) assert ns.type_material == 'any' args = ['-M', 'type', 'bacteria'] parser = argument_parser() ns = parser.parse_args(args) assert ns.type_material == 'type' args = ['-M', 'type,synonym', 'fungi'] parser = argument_parser() ns = parser.parse_args(args) assert ns.type_material == 'type,synonym' args = ['--type-material', 'reference', 'fungi'] parser = argument_parser() ns = parser.parse_args(args) assert ns.type_material == 'reference' args = ['-M', 'all', 'fungi'] parser = argument_parser() ns = parser.parse_args(args) assert ns.type_material == 'all'
def test_assembly_accessions():
"""Test the -A/--assembly-accessions option works as ecpected."""
args = ['-A', 'GCF_000203835.1', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.assembly_accessions == 'GCF_000203835.1'
args = ['--assembly-accessions', 'GCF_000203835.1,GCF_000444875.1', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.assembly_accessions == 'GCF_000203835.1,GCF_000444875.1'
args = ['--assembly-accessions', 'some/path/here.txt', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.assembly_accessions == 'some/path/here.txt'
def test_formats():
"""Test the -F/--format option works as expected."""
args = ['-F', 'genbank', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.file_format == 'genbank'
args = ['--format', 'fasta', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.file_format == 'fasta'
args = ['--format', 'genbank,fasta', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.file_format == 'genbank,fasta'
def test_assembly_levels():
"""Test the -l/--assembly-level option works as expected."""
args = ['-l', 'complete', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.assembly_level == 'complete'
args = ['--assembly-level', 'chromosome', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.assembly_level == 'chromosome'
args = ['--assembly-level', 'complete,chromosome', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.assembly_level == 'complete,chromosome'
def test_assembly_accessions():
"""Test the -A/--assembly-accessions option works as ecpected."""
args = ['-A', 'GCF_000203835.1', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.assembly_accessions == 'GCF_000203835.1'
args = ['--assembly-accessions', 'GCF_000203835.1,GCF_000444875.1', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.assembly_accessions == 'GCF_000203835.1,GCF_000444875.1'
args = ['--assembly-accessions', 'some/path/here.txt', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.assembly_accessions == 'some/path/here.txt'
def test_formats():
"""Test the -F/--format option works as expected."""
args = ['-F', 'genbank', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.file_format == 'genbank'
args = ['--format', 'fasta', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.file_format == 'fasta'
args = ['--format', 'genbank,fasta', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.file_format == 'genbank,fasta'
def test_assembly_levels():
"""Test the -l/--assembly-level option works as expected."""
args = ['-l', 'complete', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.assembly_level == 'complete'
args = ['--assembly-level', 'chromosome', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.assembly_level == 'chromosome'
args = ['--assembly-level', 'complete,chromosome', 'bacteria']
parser = argument_parser()
ns = parser.parse_args(args=args)
assert ns.assembly_level == 'complete,chromosome'