def test_claim_allSnpOrIndelOkay(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = ["##foo", "##source=strelka", "#chrom", record1]
reader1 = MockFileReader("fileA.indels.vcf", content1)
reader2 = MockFileReader("fileB.indels.vcf", content1)
file_readers = [reader1, reader2]
caller = strelka.Strelka()
unrecognized_readers, vcf_readers = caller.claim(file_readers)
self.assertEquals(0, len(unrecognized_readers))
self.assertEquals(2, len(vcf_readers))
def test_claim_ignores_non_vcf_files(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = ["##foo", "##source=strelka", "#chrom", record1]
reader1 = MockFileReader("fileA.txt", content1)
file_readers = [reader1]
caller = strelka.Strelka()
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_mismatchingSnpIndelFiles(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = ["##foo", "##source=strelka", "#chrom", record1]
reader1 = MockFileReader("fileA.snvs.vcf", content1)
reader2 = MockFileReader("fileA.indels.vcf", content1)
reader3 = MockFileReader("fileB.indels.vcf", content1)
file_readers = [reader1, reader2, reader3]
caller = strelka.Strelka()
self.assertRaisesRegexp(
utils.JQException,
r"Some Strelka VCFs were missing either a snvs or indels file. Review inputs/command options and try again.",
caller.claim, file_readers)
actual_log_errors = test.utils.mock_logger.messages["ERROR"]
expected_log_errors = ["Strelka VCF [fileB.indels] has no snvs file."]
self.assertEquals(expected_log_errors, actual_log_errors)
def test_claim(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = ["##foo", "##source=strelka", "#chrom", record1]
content2 = ["##foo", "##MuTect", "#chrom", record1]
reader1 = MockFileReader("fileA.vcf", content1)
reader2 = MockFileReader("fileB.vcf", content2)
file_readers = [reader1, reader2]
caller = strelka.Strelka()
unrecognized_readers, vcf_readers = caller.claim(file_readers)
self.assertEquals(1, len(unrecognized_readers))
self.assertEquals([reader2], unrecognized_readers)
self.assertEquals(1, len(vcf_readers))
self.assertIsInstance(vcf_readers[0], strelka._StrelkaVcfReader)
self.assertEquals(reader1.file_name,
vcf_readers[0]._vcf_reader.file_name)
def setUp(self):
super(StrelkaTestCase, self).setUp()
self.caller = strelka.Strelka()
strelka.logger = test.utils.mock_logger
def __init__(self, args=None):
self._callers = [
varscan.Varscan(args),
strelka.Strelka(),
mutect.Mutect()
]