def __init__(self, file, ref):
"""
:param file: The path to the database file to work with.
:param ref: The name that will be given to the reference strain in the database.
"""
self.__database = DatabaseCLA(file, ref)
self.__file = file
create_logger()
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(force, prompt, mlst, database, species):
"""Create a claMLST 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_mlst(' '.join(species), prompt, mlst)
if url is None:
logging.info('No choice selected')
return
logging.info('Downloading mlst...')
with tempfile.TemporaryDirectory() as tmp_dir, \
pymlst.open_cla(os.path.abspath(database)) as mlst_db:
web.get_mlst_files(url, tmp_dir)
mlst_db.create(open(tmp_dir + '/profiles.csv', 'rt'), [
open(tmp_dir + '/locus/' + locus, 'r')
for locus in os.listdir(tmp_dir + '/locus')
])
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))