def metadata(path, email, update):
"""Download assembly_summary.txt and BioSample metadata."""
logbook.set_datetime_format("local")
handler = logbook.TimedRotatingFileHandler(os.path.join(
path, ".logs", "metadata.log"),
backup_count=10)
handler.push_application()
genbank = Genbank(path)
metadata = genbank.metadata(email=email, update=update)
genbank.species_metadata(metadata)
def cli(ctx, path):
"""Assess the integrity of your genomes through automated analysis of
species-based statistics and metadata.
"""
if ctx.invoked_subcommand is None:
logbook.set_datetime_format("local")
handler = logbook.TimedRotatingFileHandler(os.path.join(
path, ".logs", "qc.log"),
backup_count=10)
handler.push_application()
genbank = Genbank(path)
genbank.qc()
def genbank():
resources = Path("test/resources").absolute()
tmp = Path(tempfile.mkdtemp())
for resource in resources.iterdir():
target = tmp / resource.name
shutil.copytree(resource, target)
yield Genbank(tmp)
shutil.rmtree(tmp)
def cli(ctx, path):
# TODO: Option for basic info about PATH
"""
Assess the integrity of your genomes through automated analysis of
species-based statistics and metadata.
"""
genbank = Genbank(path)
_ctx = namedtuple('ctx', ['genbank', 'assembly_summary'])
ctx.obj = _ctx(genbank=genbank, assembly_summary=genbank.assembly_summary)
logbook.set_datetime_format("local")
log_dir = os.path.join(path, ".logs")
log_file = os.path.join(log_dir, "qc.log")
if not os.path.isdir(log_dir):
os.mkdir(log_dir)
handler = logbook.TimedRotatingFileHandler(log_file, backup_count=10)
handler.push_application()
if ctx.invoked_subcommand is None:
genbank.qc()
def genbank():
resources = 'test/resources'
genbank = tempfile.mkdtemp()
for resource in os.listdir(resources):
source = os.path.join(resources, resource)
target = os.path.join(genbank, resource)
shutil.copytree(source, target)
yield Genbank(genbank)
shutil.rmtree(genbank)
def info(path):
"""Print basic info about existing GenBank database.
"""
genbank = Genbank(path)
info = genbank.info()
click.echo(info)
def genbank_bare():
temp_dir = tempfile.mkdtemp()
yield Genbank(temp_dir)
shutil.rmtree(temp_dir)