KaneAI - World’s First E2E Software Testing Agent.Book a Demo Join TestMu Conference

How to use _log_variants method in avocado

Best Python code snippet using avocado_python

haplotype_labeler.py

Source:haplotype_labeler.py

...805  """806  candidates = list(candidates)807  truths = list(truths)808  if _DEBUG_PRINTING_IS_ENABLED:809    _log_variants('candidates', candidates)810    _log_variants('truth', truths)811  if not variant_utils.variants_are_sorted(candidates):812    raise ValueError('candidates are not sorted', candidates)813  if not variant_utils.variants_are_sorted(truths):814    raise ValueError('truths are not sorted', truths)815  def _hom_ref_enum_if_empty(list_of_variants, non_empty_enum):816    """If list_of_variants is empty, use a ONLY_HOM_REF enum for speed."""817    return non_empty_enum if list_of_variants else EnumerationType.ONLY_HOM_REF818  truth_haplotypes = deduplicate_haplotypes(819      enumerate_all_possible_haplotypes(820          truths, ref, _hom_ref_enum_if_empty(candidates,821                                              EnumerationType.TRUTH)))822  # Note, it may be worth deduplicating these haplotypes as well.823  variant_haplotypes = enumerate_all_possible_haplotypes(824      candidates, ref, _hom_ref_enum_if_empty(truths,825                                              EnumerationType.CANDIDATES))826  found = []827  for vh, vgt in variant_haplotypes:828    for th, tgt in truth_haplotypes:829      if th == vh:830        found.append(831            HaplotypeMatch(832                haplotypes=th,833                candidates=candidates,834                candidate_genotypes=vgt,835                truths=truths,836                truth_genotypes=tgt))837  if not found:838    return None839  else:840    return select_best_haplotype_match(found)841def select_best_haplotype_match(all_matches):842  """Returns the best HaplotypeMatch among all_matches.843  The best matching HaplotypeMatch is the one with the lowest match_metrics844  score.845  Args:846    all_matches: iterable[HaplotypeMatch]. An iterable of HaplotypeMatch objects847      we want to select the best match from.848  Returns:849    The best matching HaplotypeMatch object.850  """851  sorted_matches = sorted(all_matches, key=lambda x: x.match_metrics)852  best = sorted_matches[0]853  equivalents = [854      f for f in all_matches if f.match_metrics == best.match_metrics855  ]856  # redacted857  if len(equivalents) > 1:858    for i, f in enumerate(equivalents):859      extra_info = 'best' if i == 0 else i860      logging.warning('Equivalent match to best: %s [%s]', f, extra_info)861  return equivalents[0]862# -----------------------------------------------------------------------------863#864# Private utility functions865#866# -----------------------------------------------------------------------------867def _variant_genotypes(variants, missing_genotypes_default=(-1, -1)):868  """Returns the genotypes of variants as a list of tuples.869  Args:870    variants: iterable[nucleus.protos.Variant]. The variants whose genotypes we871      want to get.872    missing_genotypes_default: tuple. If a variant in variants doesn't have873      genotypes, this value is returned. The default value is (-1, -1), the874      standard representation for "missing" diploid genotypes.875  Returns:876    list[nucleus.protos.Variant] protos in the same order as variants.877  """878  return [879      tuple(v.calls[0].genotype) if v.calls else missing_genotypes_default880      for v in variants881  ]882def _log_haplotypes(name, haplotypes):883  """Write basic information about haplotypes to logging.info."""884  logging.info('haplotypes: %s', name)885  for haplotype, genotypes in haplotypes:886    logging.info('  %s with %s', haplotype, genotypes)887def _log_variants(name, variants):888  """Write basic information about variants to logging.info."""889  logging.info('variants: %s [%d]', name, len(variants))890  for v in variants:891    logging.info('  %s gt=%s', variant_utils.variant_key(v),892                 _variant_genotypes([v])[0])893def n_zeroes(l):894  """Returns the number of elements of l that are 0."""895  return sum(1 for x in l if x == 0)896def _allele_from_index(variant, allele_index):897  """Gets the reference_bases or alternative_bases for allele_index."""898  if allele_index == 0:899    return variant.reference_bases900  else:901    return variant.alternate_bases[allele_index - 1]

job.py

Source:job.py

...376        LOG_JOB.info('data     %s', data_dir.get_data_dir())377        LOG_JOB.info('logs     %s', self.logdir)378        LOG_JOB.info('')379    @staticmethod380    def _log_variants(variants):381        lines = variants.to_str(summary=1, variants=1, use_utf8=False)382        for line in lines.splitlines():383            LOG_JOB.info(line)384    def _log_tmp_dir(self):385        LOG_JOB.info('Temporary dir: %s', self.tmpdir)386        LOG_JOB.info('')387    def _log_job_debug_info(self, variants):388        """389        Log relevant debug information to the job log.390        """391        self._log_cmdline()392        self._log_avocado_version()393        self._log_avocado_config()394        self._log_avocado_datadir()395        self._log_variants(variants)396        self._log_tmp_dir()397        self._log_job_id()398    def create_test_suite(self):399        """400        Creates the test suite for this Job401        This is a public Job API as part of the documented Job phases402        """403        try:404            self.test_suite = self._make_test_suite(self.references)405            self.result.tests_total = len(self.test_suite)406        except loader.LoaderError as details:407            stacktrace.log_exc_info(sys.exc_info(), LOG_UI.getChild("debug"))408            raise exceptions.OptionValidationError(details)409        if not self.test_suite:...

Automation Testing Tutorials

Learn to execute automation testing from scratch with LambdaTest Learning Hub. Right from setting up the prerequisites to run your first automation test, to following best practices and diving deeper into advanced test scenarios. LambdaTest Learning Hubs compile a list of step-by-step guides to help you be proficient with different test automation frameworks i.e. Selenium, Cypress, TestNG etc.