def test_add_tag(self): rec1 = vcf.VcfRecord("1", "42", "A", "C", sample_tag_values={ "SA": { "JQ_SUMMARY_DP_RANGE": "4" }, "SB": { "JQ_SUMMARY_DP_RANGE": "7" } }) rec2 = vcf.VcfRecord("1", "42", "A", "C", sample_tag_values={ "SA": { "JQ_SUMMARY_DP_RANGE": "13" }, "SB": { "JQ_SUMMARY_DP_RANGE": "16" } }) reader = MockVcfReader(records=[rec1, rec2]) tag = zscore_caller._DepthZScoreTag(reader) tag.add_tag_values(rec1) sampleA_tag_values = rec1.sample_tag_values["SA"] self.assertEquals("-1.2649", sampleA_tag_values["JQ_SUMMARY_DP_ZSCORE"]) sampleB_tag_values = rec1.sample_tag_values["SB"] self.assertEquals("-0.6325", sampleB_tag_values["JQ_SUMMARY_DP_ZSCORE"])
def test_add_tag(self): rec1 = vcf.VcfRecord("1", "42", "A", "C", sample_tag_values={"SA":{"JQ_SUMMARY_DP_RANGE":"4"}, "SB":{"JQ_SUMMARY_DP_RANGE":"7"}}) rec2 = vcf.VcfRecord("1", "42", "A", "C", sample_tag_values={"SA":{"JQ_SUMMARY_DP_RANGE":"13"}, "SB":{"JQ_SUMMARY_DP_RANGE":"16"}}) reader = MockVcfReader(records=[rec1, rec2]) tag = zscore_caller._DepthZScoreTag(reader) tag.add_tag_values(rec1) sampleA_tag_values = rec1.sample_tag_values["SA"] self.assertEquals("-1.2649", sampleA_tag_values["JQ_SUMMARY_DP_ZSCORE"]) sampleB_tag_values = rec1.sample_tag_values["SB"] self.assertEquals("-0.6325", sampleB_tag_values["JQ_SUMMARY_DP_ZSCORE"])
def test_init_metaheaders(self): rec1 = vcf.VcfRecord("1", "42", "A", "C", sample_tag_values={"SA":{"JQ_SUMMARY_DP_RANGE":"4"}, "SB":{"JQ_SUMMARY_DP_RANGE":"7"}}) rec2 = vcf.VcfRecord("1", "42", "A", "C", sample_tag_values={"SA":{"JQ_SUMMARY_DP_RANGE":"13"}, "SB":{"JQ_SUMMARY_DP_RANGE":"16"}}) reader = MockVcfReader(records=[rec1, rec2]) tag = zscore_caller._DepthZScoreTag(reader) self.assertEquals(3, len(tag.metaheaders)) it = iter(tag.metaheaders) self.assertRegexpMatches(next(it), '##jacquard.summarize.JQ_SUMMARY_DP_ZSCORE.JQ_SUMMARY_DP_RANGE_mean=') self.assertRegexpMatches(next(it), '##jacquard.summarize.JQ_SUMMARY_DP_ZSCORE.JQ_SUMMARY_DP_RANGE_stdev=') self.assertRegexpMatches(next(it), '##FORMAT=<ID=JQ_SUMMARY_DP_ZSCORE,Number=1,Type=Float,Description="Concordance of reported depth.*">')
def test_init_metaheaders(self): rec1 = vcf.VcfRecord("1", "42", "A", "C", sample_tag_values={ "SA": { "JQ_SUMMARY_DP_RANGE": "4" }, "SB": { "JQ_SUMMARY_DP_RANGE": "7" } }) rec2 = vcf.VcfRecord("1", "42", "A", "C", sample_tag_values={ "SA": { "JQ_SUMMARY_DP_RANGE": "13" }, "SB": { "JQ_SUMMARY_DP_RANGE": "16" } }) reader = MockVcfReader(records=[rec1, rec2]) tag = zscore_caller._DepthZScoreTag(reader) self.assertEquals(3, len(tag.metaheaders)) it = iter(tag.metaheaders) self.assertRegexpMatches( next(it), '##jacquard.summarize.JQ_SUMMARY_DP_ZSCORE.JQ_SUMMARY_DP_RANGE_mean=' ) self.assertRegexpMatches( next(it), '##jacquard.summarize.JQ_SUMMARY_DP_ZSCORE.JQ_SUMMARY_DP_RANGE_stdev=' ) self.assertRegexpMatches( next(it), '##FORMAT=<ID=JQ_SUMMARY_DP_ZSCORE,Number=1,Type=Float,Description="Concordance of reported depth.*">' )