How to use _log_variants method in avocado

Best Python code snippet using avocado_python Github


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...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"""884'haplotypes: %s', name)885 for haplotype, genotypes in haplotypes:886' %s with %s', haplotype, genotypes)887def _log_variants(name, variants):888 """Write basic information about variants to"""889'variants: %s [%d]', name, len(variants))890 for v in variants:891' %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]

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...376'data %s', data_dir.get_data_dir())377'logs %s', self.logdir)378'')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 def _log_tmp_dir(self):385'Temporary dir: %s', self.tmpdir)386'')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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