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