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:...

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