def test_SomaticTagSS_metaheaders(self):
vcf_reader = MockVcfReader(
metaheaders=["##foo", "##MuTect=123", '##FORMAT=<ID=FA,...>'])
mutect_vcf_reader = mutect._MutectVcfReader(vcf_reader)
metaheaders = mutect_vcf_reader.metaheaders
self.assertIn(mutect._SomaticTagSS().metaheader, metaheaders)
def test_vcf_records_newTagsPresent(self):
record1 = vcf.VcfRecord(chrom="chr1",
pos="21",
ref="A",
alt="G",
sample_tag_values={"sampleA": {"DP": "45"},
"sampleB": {"DP": "67"}})
record2 = vcf.VcfRecord(chrom="chr1",
pos="22",
ref="A",
alt="G",
sample_tag_values={"sampleA": {"FA": "0.54"},
"sampleB": {"FA": "0.76"}})
vcf_reader = MockVcfReader(records=[record1, record2])
mutect_vcf_reader = mutect._MutectVcfReader(vcf_reader)
vcf_records = [record for record in mutect_vcf_reader.vcf_records()]
self.assertEquals(2, len(vcf_records))
self.assertIn("DP", vcf_records[0].format_tags)
self.assertIn(mutect.JQ_MUTECT_TAG + "DP", vcf_records[0].format_tags)
self.assertIn(mutect.JQ_MUTECT_TAG + "HC_SOM", vcf_records[0].format_tags)
self.assertIn(mutect.JQ_MUTECT_TAG + "CALLER_REPORTED", vcf_records[0].format_tags)
self.assertIn(mutect.JQ_MUTECT_TAG + "CALLER_PASSED", vcf_records[0].format_tags)
self.assertIn("FA", vcf_records[1].format_tags)
self.assertIn(mutect.JQ_MUTECT_TAG + "AF", vcf_records[1].format_tags)
self.assertIn(mutect.JQ_MUTECT_TAG + "HC_SOM", vcf_records[1].format_tags)
self.assertIn(mutect.JQ_MUTECT_TAG + "CALLER_REPORTED", vcf_records[1].format_tags)
self.assertIn(mutect.JQ_MUTECT_TAG + "CALLER_PASSED", vcf_records[1].format_tags)
def test_open_and_close(self):
vcf_reader = MockVcfReader(metaheaders=["##foo", "##MuTect=123"])
mutect_vcf_reader = mutect._MutectVcfReader(vcf_reader)
mutect_vcf_reader.open()
mutect_vcf_reader.close()
self.assertTrue(mutect_vcf_reader.open)
self.assertTrue(mutect_vcf_reader.close)
def test_open_and_close(self):
vcf_reader = MockVcfReader(
metaheaders=["##foo", "##MuTect=123", '##FORMAT=<ID=FA,...>'])
mutect_vcf_reader = mutect._MutectVcfReader(vcf_reader)
mutect_vcf_reader.open()
mutect_vcf_reader.close()
self.assertTrue(mutect_vcf_reader.open)
self.assertTrue(mutect_vcf_reader.close)
def test_SomaticTagFilterMutectCalls_metaheaders(self):
vcf_reader = MockVcfReader(metaheaders=[
"##foo", "##MuTect=123", '##FORMAT=<ID=FA,...>',
"##source=FilterMutectCalls"
])
mutect_vcf_reader = mutect._MutectVcfReader(vcf_reader)
metaheaders = mutect_vcf_reader.metaheaders
self.assertIn(mutect._SomaticTagFilterMutectCalls().metaheader,
metaheaders)
def test_column_header_mangleSampleNameMutect2IgnoresHelpFlag(self):
column_header = self.entab("#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|25714|25715")
meta_header = '##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample 25715 --normal-sample 25714 --help false",Date="recent">'
vcf_reader = MockVcfReader(metaheaders=[meta_header],
column_header=column_header)
mutect_vcf_reader = mutect._MutectVcfReader(vcf_reader)
expected_column_header = self.entab("#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|NORMAL|TUMOR")
self.assertEquals(expected_column_header, mutect_vcf_reader.column_header)
def test_column_header_mangleSampleNameMutect1(self):
column_header = self.entab("#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|25714|25715")
meta_header = '##MuTect="123 tumor_sample_name=25715 normal_sample_name=25714"'
vcf_reader = MockVcfReader(metaheaders=[meta_header],
column_header=column_header)
mutect_vcf_reader = mutect._MutectVcfReader(vcf_reader)
expected_column_header = self.entab("#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|NORMAL|TUMOR")
self.assertEquals(expected_column_header, mutect_vcf_reader.column_header)
def test_metaheaders(self):
vcf_reader = MockVcfReader(metaheaders=["##foo", "##MuTect=123"])
mutect_vcf_reader = mutect._MutectVcfReader(vcf_reader)
metaheaders = mutect_vcf_reader.metaheaders
self.assertIn(mutect._AlleleFreqTag().metaheader, metaheaders)
self.assertIn(mutect._DepthTag().metaheader, metaheaders)
self.assertIn(mutect._SomaticTag().metaheader, metaheaders)
self.assertIn("##foo", metaheaders)
self.assertIn("##MuTect=123", metaheaders)
self.assertIn("##jacquard.translate.caller=MuTect", metaheaders)
def test_common_metaheaders(self):
vcf_reader = MockVcfReader(
metaheaders=["##foo", "##MuTect=123", '##FORMAT=<ID=FA,...>'])
mutect_vcf_reader = mutect._MutectVcfReader(vcf_reader)
metaheaders = mutect_vcf_reader.metaheaders
self.assertIn(
mutect._AlleleFreqTag(vcf_reader.metaheaders).metaheader,
metaheaders)
self.assertIn(mutect._DepthTag().metaheader, metaheaders)
self.assertIn("##foo", metaheaders)
self.assertIn("##MuTect=123", metaheaders)
self.assertIn("##jacquard.translate.caller=MuTect", metaheaders)
def test_vcf_records_newTagsPresent(self):
record1 = vcf.VcfRecord(chrom="chr1",
pos="21",
ref="A",
alt="G",
sample_tag_values={
"sampleA": {
"DP": "45"
},
"sampleB": {
"DP": "67"
}
})
record2 = vcf.VcfRecord(chrom="chr1",
pos="22",
ref="A",
alt="G",
sample_tag_values={
"sampleA": {
"FA": "0.54"
},
"sampleB": {
"FA": "0.76"
}
})
vcf_reader = MockVcfReader(metaheaders=['##FORMAT=<ID=FA,...>'],
records=[record1, record2])
mutect_vcf_reader = mutect._MutectVcfReader(vcf_reader)
vcf_records = [record for record in mutect_vcf_reader.vcf_records()]
self.assertEquals(2, len(vcf_records))
self.assertIn("DP", vcf_records[0].format_tags)
self.assertIn(mutect.JQ_MUTECT_TAG + "DP", vcf_records[0].format_tags)
self.assertIn(mutect.JQ_MUTECT_TAG + "HC_SOM",
vcf_records[0].format_tags)
self.assertIn(mutect.JQ_MUTECT_TAG + "CALLER_REPORTED",
vcf_records[0].format_tags)
self.assertIn(mutect.JQ_MUTECT_TAG + "CALLER_PASSED",
vcf_records[0].format_tags)
self.assertIn("FA", vcf_records[1].format_tags)
self.assertIn(mutect.JQ_MUTECT_TAG + "AF", vcf_records[1].format_tags)
self.assertIn(mutect.JQ_MUTECT_TAG + "HC_SOM",
vcf_records[1].format_tags)
self.assertIn(mutect.JQ_MUTECT_TAG + "CALLER_REPORTED",
vcf_records[1].format_tags)
self.assertIn(mutect.JQ_MUTECT_TAG + "CALLER_PASSED",
vcf_records[1].format_tags)
def test_column_header_mangleSampleNameMutect2UsesSampleMetalinesIfAvailable(self):
column_header = self.entab("#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|25714|25715")
meta_header = '''
##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample A --normal-sample B",Date="recent">'
##foo=42
##SAMPLE=<ID=NORMAL,SampleName=25714,File=foo.bam>
##SAMPLE=<ID=TUMOR,SampleName=25715,File=bar.bam>
##baz=42
'''
vcf_reader = MockVcfReader(metaheaders=meta_header.strip().split('\n'),
column_header=column_header)
mutect_vcf_reader = mutect._MutectVcfReader(vcf_reader)
expected_column_header = self.entab("#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|NORMAL|TUMOR")
self.assertEquals(expected_column_header, mutect_vcf_reader.column_header)
def test_column_header_mangleSampleNameMutect2IgnoresHelpFlag(self):
column_header = self.entab(
"#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|25714|25715")
metaheaders = [
'##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample 25715 --normal-sample 25714 --help false",Date="recent">',
'##FORMAT=<ID=FA,...>',
]
vcf_reader = MockVcfReader(metaheaders=metaheaders,
column_header=column_header)
mutect_vcf_reader = mutect._MutectVcfReader(vcf_reader)
expected_column_header = self.entab(
"#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|NORMAL|TUMOR")
self.assertEquals(expected_column_header,
mutect_vcf_reader.column_header)
def test_column_header_mangleSampleNameMutect1(self):
column_header = self.entab(
"#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|25714|25715")
metaheaders = [
'##MuTect="123 tumor_sample_name=25715 normal_sample_name=25714"',
'##FORMAT=<ID=FA,...>',
]
vcf_reader = MockVcfReader(metaheaders=metaheaders,
column_header=column_header)
mutect_vcf_reader = mutect._MutectVcfReader(vcf_reader)
expected_column_header = self.entab(
"#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|NORMAL|TUMOR")
self.assertEquals(expected_column_header,
mutect_vcf_reader.column_header)
def test_column_header_mangleSampleNameMutect2UsesSampleMetalinesIfAvailable(
self):
column_header = self.entab(
"#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|25714|25715")
meta_header = '''
##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample A --normal-sample B",Date="recent">'
##FORMAT=<ID=FA,...>
##foo=42
##SAMPLE=<ID=NORMAL,SampleName=25714,File=foo.bam>
##SAMPLE=<ID=TUMOR,SampleName=25715,File=bar.bam>
##baz=42
'''
vcf_reader = MockVcfReader(metaheaders=meta_header.strip().split('\n'),
column_header=column_header)
mutect_vcf_reader = mutect._MutectVcfReader(vcf_reader)
expected_column_header = self.entab(
"#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|NORMAL|TUMOR")
self.assertEquals(expected_column_header,
mutect_vcf_reader.column_header)