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(fastqs, database, **kwargs):
"""Add a strain from FASTQS(.gz) reads to the wgMLST DATABASE."""
try:
with pymlst.open_wg(os.path.abspath(database)) as mlst:
mlst.add_reads(fastqs, **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(force, prompt, database, species):
"""Create a wgMLST DATABASE from an online resource.
The research can be filtered by adding a SPECIES name."""
utils.create_logger()
try:
if os.path.exists(database):
if force:
open(database, "w").close()
else:
raise exceptions.PyMLSTError(
"Database alreadly exists, use --force to override it")
url = web.retrieve_cgmlst(' '.join(species), prompt)
if url is None:
logging.info('No choice selected')
return
logging.info('Downloading the core genome...')
with tempfile.NamedTemporaryFile('w+', delete=False) as tmp:
skipped = web.get_cgmlst_file(url, tmp)
tmp.close()
if len(skipped) > 0:
logging.info('Skipped the following malformed file(s): %s',
', '.join(skipped))
with pymlst.open_wg(os.path.abspath(database)) as mlst:
mlst.create(tmp.name)
except requests.exceptions.HTTPError:
raise click.ClickException('Could not retrieve online data')
except requests.exceptions.ConnectionError:
raise click.ClickException(
'Could not access to the server, please verify your internet connection'
)
except requests.exceptions.Timeout:
raise click.ClickException('The server took too long to respond')
except web.StructureError:
raise click.ClickException(
'It seems like the structure of the website/API changed '
'since this application was developed.')
except exceptions.PyMLSTError as err:
raise click.ClickException(str(err))
def cli(database, strains, genes_or_strains, **kwargs):
"""Remove STRAINS or GENES from a wgMLST DATABASE."""
utils.create_logger()
try:
with pymlst.open_wg(os.path.abspath(database)) as mlst:
if strains:
logging.info("We will remove one or more strain(s)")
mlst.remove_strain(genes_or_strains, **utils.clean_kwargs(kwargs))
else :
logging.info("We will remove one or more gene(s)")
mlst.remove_gene(genes_or_strains, **utils.clean_kwargs(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))
def wg():
with pymlst.open_wg() as wg_mlst:
yield wg_mlst