Пример #1
0
    def compare_test_vcf(self, raw_orig_vcf, raw_test_vcf):
        raw_orig_vcf = os.path.abspath(raw_orig_vcf)
        raw_test_vcf = os.path.abspath(raw_test_vcf)
        orig_vars    = list(pysam.VariantFile(raw_orig_vcf))
        tmp_dirname  = util.strip_extensions(raw_test_vcf, ['gz','vcf']) + "-vcomp-" + util.randstr()

        with util.TempDir(dirname=tmp_dirname):
            orig_vcf = util.bgz_tabix(raw_orig_vcf, self.conf)
            test_vcf = util.remove_halfcalls(raw_test_vcf)
            test_vcf = util.bgz_tabix(test_vcf, self.conf)
            caller_name = util.strip_extensions(test_vcf, ['gz','vcf'])
            bed = util.vars_to_bed(orig_vars)
            var_results = defaultdict(dict)
            var_quals = self.collect_var_quals({caller_name: test_vcf}, bed, orig_vcf)
            bamstats = defaultdict(dict)

            for normalizer_name, normalizer in self.normalizers.iteritems():
                logging.info("--> Running normalizer " + normalizer_name)
                normed_orig_vcf   = normalizer(orig_vcf, self.conf)
                normed_caller_vcf = normalizer(test_vcf, self.conf)

                for comparator_name, comparator in self.comparators.iteritems():
                    logging.info("--> Running comparator " + comparator_name + " (normalizer " + normalizer_name + ")")
                    all_results = comparator(normed_orig_vcf, normed_caller_vcf, None, self.conf)
                    single_results = split_results(all_results, bed)
                    for region, result in zip(util.read_regions(bed), single_results):
                        match_vars = util.find_matching_var(orig_vcf, region)
                        if not match_vars:
                            raise ValueError('Unable to find original variant from region ' + str(region))
                        result = compare_single_var(result,
                                                    region,
                                                    normed_orig_vcf,
                                                    normed_caller_vcf,
                                                    comparator,
                                                    "/".join(str(i) for i in match_vars[0].samples[0]['GT']),
                                                    self.conf)
                        key = var_key(match_vars)
                        if caller_name not in var_results[key]:
                            var_results[key][caller_name] = defaultdict(dict)
                        var_results[key][caller_name][normalizer_name][comparator_name] = result
                        bamstats[key] = {}

        # Iterate over all results and write to standard output. We do this here instead of within the loops above
        # because it keeps results organized by variant, which makes them easier to look at
        self.reporter.write_output(var_results, var_quals, bamstats)
Пример #2
0
    def test_rm_halfcalls(self):
        input_vcf = os.path.join(TestUtils.DATA_PATH, TestUtils.HALFCALL_VCF)
        try:
            no_halfcalls = util.remove_halfcalls(input_vcf)
            calls = {}
            with open(no_halfcalls) as fh:
                for line in fh:
                    if line[0] == "#":
                        continue
                    toks = line.split()
                    calls[toks[1]] = toks[9]

                self.assertTrue(len(calls) == 3)
                for pos, gt in calls.iteritems():
                    self.assertTrue("." not in gt.split(":")[0])

        except Exception as ex:
            print str(ex)

        finally:
            os.remove(no_halfcalls)