def main(argv=None):
if argv is None:
argv = sys.argv[1:]
args = parser.parse_args(argv)
assert not (args.debug and args.quiet), \
'make up your mind: debug OR normal OR quiet'
if args.debug:
set_debug()
if args.quiet:
set_warning()
if args.log:
appendlog(args.log)
if args.excepthook:
sys.excepthook = traceit
args.func(args)
import unittest
from kvarq.log import set_debug
set_debug()
import os.path
import sys
sys.path.insert(0, os.path.dirname(__file__))
from bacillus_anthracis import bacillus_anthracis
from yersinia_pestis import yersinia_pestis
from coxiella_burnetii import coxiella_burnetii
def create_coverages(tests, snps):
coverages = dict([(test, False) for test in tests])
for test in tests:
if test.genotype.identifier in snps:
coverages[test] = True
return coverages
class GenesCanSNPer(unittest.TestCase):
def test_bacillus_anthracis(self):
# patch tests
for test in bacillus_anthracis.tests:
test.template.validate = lambda x: x
# child / parent nodes must not be included
coverages = create_coverages(bacillus_anthracis.tests, 'A/B.Br.001;B.Br.003'.split(';'))
