def cli(genome, database, **kwargs):
"""Add a strain GENOME to the wgMLST DATABASE."""
try:
with pymlst.open_wg(os.path.abspath(database)) as mlst:
mlst.add_strain(genome, **utils.clean_kwargs(kwargs))
except exceptions.PyMLSTError as err:
raise click.ClickException(str(err))
def cli(database, **kwargs):
"""Extract an strains list from a wgMLST DATABASE."""
tab_kwargs,out_kwargs = utils.get_output(utils.clean_kwargs(kwargs))
try:
with pymlst.open_wg(os.path.abspath(database)) as mlst:
mlst.extract(StrainExtractor(**tab_kwargs), **out_kwargs)
except exceptions.PyMLSTError as err:
raise click.ClickException(str(err))
def cli(database, **kwargs):
"""Compute Multiple Sequence Alignment from a wgMLST DATABASE."""
seq_kwargs, out_kwargs = utils.get_output(utils.clean_kwargs(kwargs))
try:
with pymlst.open_wg(os.path.abspath(database)) as mlst:
mlst.extract(MsaExtractor(**seq_kwargs), **out_kwargs)
except exceptions.PyMLSTError as err:
raise click.ClickException(str(err))
def cli(database, force, **kwargs):
"""Create a wgMLST DATABASE from a template COREGENE."""
try:
if os.path.exists(database):
if force:
open(database, "w").close()
else:
raise exceptions.PyMLSTError(
"Database alreadly exists, use --force to override it")
with pymlst.open_wg(os.path.abspath(database)) as mlst:
mlst.create(**utils.clean_kwargs(kwargs))
except exceptions.DuplicatedGeneSequence as err:
raise click.UsageError('{}, use -c or -r options to manage it'.format(
str(err)))
except exceptions.PyMLSTError as err:
raise click.UsageError(str(err))