def test_claim_ignoresNonVcfExtensions(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = ["##foo", "##MuTect=123", "#chrom", record1]
reader1 = MockFileReader("fileA.txt", content1)
file_readers = [reader1]
caller = mutect.Mutect()
unrecognized_readers, vcf_readers = caller.claim(file_readers)
self.assertEquals(1, len(unrecognized_readers))
self.assertEquals([reader1], unrecognized_readers)
self.assertEquals(0, len(vcf_readers))
def test_claim_metaheaderRecognizesMutectV2x(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = [
"##foo", "##MuTect=2.1", "##FORMAT=<ID=FA,...>", "#chrom", record1
]
reader1 = MockFileReader("fileA.vcf", content1)
file_readers = [reader1]
caller = mutect.Mutect()
unrecognized_readers, vcf_readers = caller.claim(file_readers)
self.assertEquals(0, len(unrecognized_readers))
self.assertEquals(1, len(vcf_readers))
def test_claim_vcfExtensionCaseInsensitive(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = [
"##foo", "##MuTect=123", "##FORMAT=<ID=AF,...>", "#chrom", record1
]
reader1 = MockFileReader("fileA.VcF", content1)
file_readers = [reader1]
caller = mutect.Mutect()
unrecognized_readers, vcf_readers = caller.claim(file_readers)
self.assertEquals(0, len(unrecognized_readers))
self.assertEquals(1, len(vcf_readers))
def test_claim_metaheaderRecognizesMutectV4x(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = [
"##foo",
'##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 ...">',
"##FORMAT=<ID=AF,...>", "#chrom", record1
]
reader1 = MockFileReader("fileB.vcf", content1)
file_readers = [reader1]
caller = mutect.Mutect()
unrecognized_readers, vcf_readers = caller.claim(file_readers)
self.assertEquals(0, len(unrecognized_readers))
self.assertEquals(1, len(vcf_readers))
def test_claim(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = ["##foo", "##source=strelka", "#chrom", record1]
content2 = [
"##foo", "##MuTect=123", "##FORMAT=<ID=AF,...>", "#chrom", record1
]
reader1 = MockFileReader("fileA.vcf", content1)
reader2 = MockFileReader("fileB.vcf", content2)
file_readers = [reader1, reader2]
caller = mutect.Mutect()
unrecognized_readers, vcf_readers = caller.claim(file_readers)
self.assertEquals(1, len(unrecognized_readers))
self.assertEquals([reader1], unrecognized_readers)
self.assertEquals(1, len(vcf_readers))
self.assertIsInstance(vcf_readers[0], mutect._MutectVcfReader)
self.assertEquals(reader2.file_name,
vcf_readers[0]._vcf_reader.file_name)
def setUp(self):
super(MutectTestCase, self).setUp()
self.caller = mutect.Mutect()
def __init__(self, args=None):
self._callers = [
varscan.Varscan(args),
strelka.Strelka(),
mutect.Mutect()
]