def test_add_tag_values_OnlyCountHCSOMTags(self): tag = summarize_caller._SomaticTag() sample_tag_values = {"SA": {"JQ_foo": "1", "JQ_foo_HC_SOM": "1", "JQ_bar_HC_SOM": "1"}} record = VcfRecord("CHROM", "POS", "REF", "ALT", sample_tag_values=sample_tag_values) tag.add_tag_values(record) self.assertEquals("2", record.sample_tag_values["SA"][SomaticTagTestCase._TAG_ID])
def test_add_tag_values_missingTag(self): tag = summarize_caller._SomaticTag() sample_tag_values = {"SA": {"JQ_foo": "1",}} record = VcfRecord("CHROM", "POS", "REF", "ALT", sample_tag_values=sample_tag_values) tag.add_tag_values(record) self.assertEquals(".", record.sample_tag_values["SA"][SomaticTagTestCase._TAG_ID])
def test_metaheader(self): split_meta_header = summarize_caller._SomaticTag().metaheader.split("\n") self.assertEqual('##FORMAT=<ID={0}SOM_COUNT,Number=1,Type=Integer,' \ 'Description="Count of recognized variant callers ' \ 'that reported confident somatic call for this '\ 'sample-locus.">'\ .format(summarize_caller.JQ_SUMMARY_TAG), split_meta_header[0])
def test_add_tag_values_inconsistentMultAlt(self): tag = summarize_caller._SomaticTag() sample_tag_values = {"SA": {"JQ_foo_HC_SOM": "0,0.1", "JQ_bar_HC_SOM": "0.2"}} record = VcfRecord("CHROM", "POS", "REF", "ALT", sample_tag_values=sample_tag_values) self.assertRaisesRegexp(JQException, r"Error summarizing values \[.*\] at record \[.*\]", tag.add_tag_values, record)