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(';'))