def test_claim_vcfAnd6InvalidFilterFiles(self):
#pylint: disable=too-many-locals
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = [self.entab("chrom|pos|ref|alt"), record1]
content2 = ["##foo", "##source=VarScan2", "#chrom", record1]
reader1 = MockFileReader("patientA.snp.Somatic.hc.fpfilter.pass",
content1)
reader2 = MockFileReader("patientA.snp.vcf", content2)
reader3 = MockFileReader("patientB.snp.Somatic.hc.fpfilter.pass",
content1)
reader4 = MockFileReader("patientB.snp.vcf", content2)
reader5 = MockFileReader("patientC.snp.Somatic.hc.fpfilter.pass",
content1)
reader6 = MockFileReader("patientC.snp.vcf", content2)
reader7 = MockFileReader("patientD.snp.Somatic.hc.fpfilter.pass",
content1)
reader8 = MockFileReader("patientD.snp.vcf", content2)
reader9 = MockFileReader("patientE.snp.Somatic.hc.fpfilter.pass",
content1)
reader10 = MockFileReader("patientE.snp.vcf", content2)
reader11 = MockFileReader("patientF.snp.Somatic.hc.fpfilter.pass",
content1)
reader12 = MockFileReader("patientF.snp.vcf", content2)
file_readers = [
reader1, reader2, reader3, reader4, reader5, reader6, reader7,
reader8, reader9, reader10, reader11, reader12
]
caller = varscan.Varscan()
self.assertRaisesRegexp(
utils.JQException,
r"The \[6\] input files \[.*\(1 file\(s\) omitted\)\] match high-confidence file names, but the file header is invalid or missing. Review inputs and try again.",
caller.claim, file_readers)
def test_claim_vcfAndFilterFileNameGiven(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = [self.entab("chrom|position|ref|var"), record1]
content2 = ["##foo", "##source=VarScan2", "#chrom", record1]
reader1 = MockFileReader("patientA.indel.Somatic.foo.bar", content1)
reader2 = MockFileReader("patientA.indel.vcf", content2)
reader3 = MockFileReader("patientA.snp.Somatic.foo.bar", content1)
reader4 = MockFileReader("patientA.snp.vcf", content2)
reader5 = MockFileReader("patientA.readme", ["foo"])
file_readers = [reader1, reader2, reader3, reader4, reader5]
caller = varscan.Varscan()
caller.hc_file_pattern = re.compile("foo.bar$")
unrecognized_readers, vcf_readers = caller.claim(file_readers)
self.assertEquals(1, len(unrecognized_readers))
self.assertEquals([reader5], unrecognized_readers)
self.assertEquals(2, len(vcf_readers))
self.assertIsInstance(vcf_readers[0], varscan._VarscanVcfReader)
self.assertEquals(reader2.file_name,
vcf_readers[0]._vcf_reader.file_name)
self.assertEquals(reader1.file_name,
vcf_readers[0]._som_hc_file_reader.file_name)
self.assertIsInstance(vcf_readers[1], varscan._VarscanVcfReader)
self.assertEquals(reader4.file_name,
vcf_readers[1]._vcf_reader.file_name)
self.assertEquals(reader3.file_name,
vcf_readers[1]._som_hc_file_reader.file_name)
def test_claim_allSnpOrIndelOkay(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = ["##foo", "##source=VarScan2", "#chrom", record1]
reader1 = MockFileReader("fileA.indel.vcf", content1)
reader2 = MockFileReader("fileB.indel.vcf", content1)
file_readers = [reader1, reader2]
caller = varscan.Varscan()
unrecognized_readers, vcf_readers = caller.claim(file_readers)
self.assertEquals(0, len(unrecognized_readers))
self.assertEquals(2, len(vcf_readers))
def test_claim_ignoresUnpairedNonVcfFiles(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = ["##foo", "##source=VarScan2", "#chrom", record1]
reader1 = MockFileReader("fileA.txt", content1)
file_readers = [reader1]
caller = varscan.Varscan()
unrecognized_readers, vcf_readers = caller.claim(file_readers)
self.assertEquals(1, len(unrecognized_readers))
self.assertEquals([reader1], unrecognized_readers)
self.assertEquals(0, len(vcf_readers))
def test_claim_filterRegexDoesNotMatch(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = ["##foo", "##source=VarScan2", "#chrom", record1]
reader1 = MockFileReader("patientA.vcf", content1)
file_readers = [reader1]
caller = varscan.Varscan()
caller.hc_file_pattern = re.compile("foo.bar$")
self.assertRaisesRegexp(
utils.UsageError,
r"The VarScan high-confidence filename regex \[foo\.bar\$\] didn't match any files in the input directory. The beginning of the high-confidence filename must exactly match a VCF filename up to the .vcf extension. Review inputs/command options and try again.",
caller.claim, file_readers)
def test_claim_VCFHasNoMatchingHc(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = [self.entab("chrom|position"), record1]
content2 = ["##foo", "##source=VarScan2", "#chrom", record1]
reader1 = MockFileReader("patientA.vcf", content2)
reader2 = MockFileReader("patientB.vcf", content2)
reader3 = MockFileReader("patientB.snp.Somatic.hc.fpfilter.pass",
content1)
file_readers = [reader1, reader2, reader3]
caller = varscan.Varscan()
self.assertRaisesRegexp(
utils.UsageError,
r"The VarScan VCF file \[patientA.vcf\] has no matching high-confidence file.",
caller.claim, file_readers)
def test_claim_mismatchingSnpIndelFiles(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = ["##foo", "##source=VarScan2", "#chrom", record1]
reader1 = MockFileReader("fileA.snp.vcf", content1)
reader2 = MockFileReader("fileA.indel.vcf", content1)
reader3 = MockFileReader("fileB.indel.vcf", content1)
file_readers = [reader1, reader2, reader3]
caller = varscan.Varscan()
self.assertRaisesRegexp(
utils.JQException,
r"Some Varscan VCFs were missing either a snp or indel file. Review inputs/command options and try again.",
caller.claim, file_readers)
actual_log_errors = test.utils.mock_logger.messages["ERROR"]
expected_log_errors = ["VarScan VCF [fileB.indel] has no snp file."]
self.assertEquals(expected_log_errors, actual_log_errors)
def test_claim_varscanVcfOnly(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = ["##foo", "##source=VarScan2", "#chrom", record1]
reader1 = MockFileReader("fileA.snp.vcf", content1)
reader2 = MockFileReader("fileB.snp.vcf", content1)
file_readers = [reader1, reader2]
caller = varscan.Varscan()
unrecognized_readers, vcf_readers = caller.claim(file_readers)
self.assertEquals(0, len(unrecognized_readers))
self.assertEquals([], unrecognized_readers)
self.assertEquals(2, len(vcf_readers))
self.assertIsInstance(vcf_readers[0], varscan._VarscanVcfReader)
self.assertEquals(reader1.file_name,
vcf_readers[0]._vcf_reader.file_name)
def test_claim_vcfAndInvalidFilterFile(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = [self.entab("chrom|pos|ref|alt"), record1]
content2 = ["##foo", "##source=VarScan2", "#chrom", record1]
reader1 = MockFileReader("patientA.indel.Somatic.hc.fpfilter.pass",
content1)
reader2 = MockFileReader("patientA.indel.vcf", content2)
reader3 = MockFileReader("patientA.snp.Somatic.hc.fpfilter.pass",
content1)
reader4 = MockFileReader("patientA.snp.vcf", content2)
reader5 = MockFileReader("patientA.readme", ["foo"])
file_readers = [reader1, reader2, reader3, reader4, reader5]
caller = varscan.Varscan()
self.assertRaisesRegexp(
utils.JQException,
r"The \[2\] input files \[.*\] match high-confidence file names, but the file header is invalid or missing. Review inputs and try again.",
caller.claim, file_readers)
def test_claim_multiplePatients(self):
record1 = "chr1\t.\t.\t.\t.\t.\t.\t.\t."
content1 = ["##foo", "##source=VarScan2", "#chrom", record1]
content2 = ["chrom\tposition", "1\t23"]
reader1 = MockFileReader("p2.fileA.vcf", content1)
reader2 = MockFileReader("p2.fileA.Somatic.hc.fpfilter.pass", content2)
reader3 = MockFileReader("p3.fileA.Somatic.hc.fpfilter.pass", content2)
reader4 = MockFileReader("p3.fileA.vcf", content1)
file_readers = [reader1, reader2, reader3, reader4]
caller = varscan.Varscan()
dummy, vcf_readers = caller.claim(file_readers)
self.assertEquals(2, len(vcf_readers))
self.assertIsInstance(vcf_readers[0], varscan._VarscanVcfReader)
self.assertEquals("p2.fileA.vcf", vcf_readers[0]._vcf_reader.file_name)
self.assertIn("_HCTag", self._get_tag_class_names(vcf_readers[0]))
self.assertIn("_HCTag", self._get_tag_class_names(vcf_readers[1]))
self.assertEquals(reader1.file_name,
vcf_readers[0]._vcf_reader.file_name)
def __init__(self, args=None):
self._callers = [
varscan.Varscan(args),
strelka.Strelka(),
mutect.Mutect()
]
def test_validate_filter_file_invalidFile(self):
file_reader = MockFileReader("p1.hc.fpfilter.pass",
["chrom\tpos\tref"])
caller = varscan.Varscan()
valid_reader = caller._validate_filter_file(file_reader)
self.assertEquals(None, valid_reader)
def test_validate_filter_file_validFile(self):
file_reader = MockFileReader("p1.hc.fpfilter.pass",
["chrom\tposition"])
caller = varscan.Varscan()
valid_reader = caller._validate_filter_file(file_reader)
self.assertEquals("p1.hc.fpfilter.pass", valid_reader.file_name)
def setUp(self):
super(VarscanTestCase, self).setUp()
self.caller = varscan.Varscan()
varscan.logger = test.utils.mock_logger
