def base(ctx, verbose):
"""Puzzle: manage DNA variant resources."""
# configure root logger to print to STDERR
loglevel = LEVELS.get(min(verbose, 3))
configure_stream(level=loglevel)
# launch the command line interface
logger.debug('Booting up command line interface')
ctx.obj = {}
def base(ctx, verbose, config):
"""Puzzle: manage DNA variant resources."""
# configure root logger to print to STDERR
loglevel = LEVELS.get(min(verbose, 3))
configure_stream(level=loglevel)
ctx.obj = {}
if config and os.path.exists(config):
ctx.obj = yaml.load(open(config, 'r')) or {}
ctx.obj['config_path'] = config
# launch the command line interface
logger.debug('Booting up command line interface')
import logging
from sqlalchemy import create_engine
from sqlalchemy.orm import sessionmaker
# from puzzle.factory import create_app
from puzzle.models import (Variant, DotDict, Individual)
from puzzle.models.sql import BASE
from puzzle.models.sql import Case as SqlCase
from puzzle.plugins import VcfPlugin, SqlStore
from puzzle.utils import (get_cases, get_header)
# from puzzle.settings import TestConfig
from puzzle.log import configure_stream
root_logger = configure_stream()
logger = logging.getLogger(__name__)
@pytest.fixture
def vcf():
db = VcfPlugin()
return db
@pytest.fixture(scope='function')
def puzzle_dir(request, dir_path):
"""Return a puzzle dir with a database initialized"""
db_path = os.path.join(dir_path, 'puzzle_db.sqlite3')
logger.debug("db path is: {}".format(db_path))
import pytest
import logging
from sqlalchemy import create_engine
from sqlalchemy.orm import sessionmaker
# from puzzle.factory import create_app
from puzzle.models import Variant
from puzzle.models.sql import BASE
from puzzle.plugins import VcfPlugin, SqlStore
from puzzle.utils import get_case
# from puzzle.settings import TestConfig
from puzzle.log import configure_stream
root_logger = configure_stream()
logger = logging.getLogger(__name__)
@pytest.fixture
def vcf():
db = VcfPlugin()
return db
@pytest.fixture
def variant():
"""Return a variant dictionary"""
data = dict(CHROM='1', POS='100', ID='rs01', REF='A', ALT='T', QUAL='100',
FILTER='PASS')
variant = Variant(**data)