def test_filter_contigs(self):
ivcf = get_test_data_path("filter_contigs.vcf")
(fd, fn) = tempfile.mkstemp(suffix=".vcf")
with captured_output() as (_, stderr):
filter_contigs(ivcf, fn)
found = 0
exp_chroms = ["chr1", "chr2"]
rdr = pysam.VariantFile(fn)
try:
for record in rdr:
self.assertTrue(record.chrom in exp_chroms)
found += 1
finally:
rdr.close()
self.assertEqual(found, 2)
cleanup_files(fn)
(fd, fn) = tempfile.mkstemp(suffix=".vcf.gz")
with captured_output() as (_, stderr):
filter_contigs(ivcf, fn)
found = 0
rdr = pysam.VariantFile(fn)
try:
for record in rdr:
self.assertTrue(record.chrom in exp_chroms)
found += 1
finally:
rdr.close()
self.assertEqual(found, 2)
cleanup_files(fn)
def test_filter_nonstandard_variants(self):
ivcf = get_test_data_path("test_nonstandard_variants.vcf")
(fd, fn) = tempfile.mkstemp(suffix=".vcf.gz")
try:
with captured_output() as (_, stderr):
filter_nonstandard_variants(ivcf, fn)
vcf = pysam.VariantFile(fn)
record = next(vcf)
self.assertTrue(record.chrom == "chr1")
record = next(vcf)
self.assertTrue(record.chrom == "chr3")
with self.assertRaises(StopIteration):
record = next(vcf)
vcf.close()
serr = stderr.getvalue()
self.assertTrue("Drops non-ACTG loci from a VCF." in serr)
self.assertTrue("Removing chr2:1:A,R" in serr)
self.assertTrue("Creating tabix index..." in serr)
self.assertTrue("Processed 3 records - Removed 1; Wrote 2" in serr)
finally:
cleanup_files(fn)
def test_filter_somatic_score_defaults(self):
ivcf = get_test_data_path("test_somatic_score.vcf")
(fd, fn) = tempfile.mkstemp(suffix=".vcf.gz")
try:
total = 0
tagged = 0
with captured_output() as (_, stderr):
filter_somatic_score(ivcf, fn)
vcf = pysam.VariantFile(fn)
for record in vcf:
total += 1
self.assertTrue(record.pos != 1)
if "ssc40" in record.filter:
tagged += 1
self.assertTrue(record.samples["TUMOR"]["SSC"] == 25)
vcf.close()
self.assertEqual(total, 3)
self.assertEqual(tagged, 1)
serr = stderr.getvalue()
self.assertTrue(
"Filters SomaticSniper VCF files based on Somatic Score." in
serr)
self.assertTrue("Filter tag: ssc40" in serr)
self.assertTrue("Creating tabix index..." in serr)
self.assertTrue(
"Processed 4 records - Removed 1; Tagged 1; Wrote 3" in serr)
finally:
cleanup_files(fn)
def test_cli(self):
ifa = get_test_data_path("test_oxog_ref.fa")
imaf = get_test_data_path("test_oxog_annotated.maf")
(fd, fn) = tempfile.mkstemp(suffix=".vcf.gz")
try:
with captured_output() as (_, stderr):
main(["dtoxog-maf-to-vcf", imaf, ifa, fn])
vout = pysam.VariantFile(fn)
for record in vout:
self.assertEqual(record.chrom, "chr1")
self.assertEqual(record.pos, 10)
self.assertEqual(record.alleles, (
"A",
"T",
))
self.assertEqual(record.filter.keys(), ["oxog"])
vout.close()
serr = stderr.getvalue()
self.assertTrue(
"[gdc_filtration_tools.dtoxog_maf_to_vcf] - Creating tabix index..."
in serr)
self.assertTrue(
"[gdc_filtration_tools.dtoxog_maf_to_vcf] - Processed 2 records - Wrote 1"
in serr)
self.assertTrue("[gdc_filtration_tools.main] - Finished!" in serr)
finally:
cleanup_files([fn, fn + ".tbi"])
def test_cli(self):
ivcf = get_test_data_path("test.vcf")
(fd, fn) = tempfile.mkstemp()
try:
found = []
expected = ["chr1:1", "chr2:1"]
with captured_output() as (_, stderr):
main(args=["create-oxog-intervals", ivcf, fn])
with open(fn, "rt") as fh:
for line in fh:
found.append(line.rstrip("\r\n"))
self.assertEqual(len(found), 2)
self.assertEqual(found, expected)
serr = stderr.getvalue()
self.assertTrue(
"Extracts interval-file for Broad OxoG metrics from VCF." in serr
)
self.assertTrue("Processed 2 records" in serr)
serr = [i for i in serr.split("\n") if i.rstrip("\r\n")]
self.assertTrue("gdc_filtration_tools.create_oxog_intervals" in serr[0])
self.assertTrue("gdc_filtration_tools.main" in serr[-1])
finally:
cleanup_files(fn)
def test_cli(self):
ivcf = get_test_data_path("test_somatic_score.vcf")
(fd, fn) = tempfile.mkstemp(suffix=".vcf.gz")
try:
total = 0
tagged = 0
with captured_output() as (_, stderr):
main(args=["filter-somatic-score", ivcf, fn])
vcf = pysam.VariantFile(fn)
for record in vcf:
total += 1
self.assertTrue(record.pos != 1)
if "ssc40" in record.filter:
tagged += 1
self.assertTrue(record.samples["TUMOR"]["SSC"] == 25)
vcf.close()
self.assertEqual(total, 3)
self.assertEqual(tagged, 1)
serr = stderr.getvalue()
self.assertTrue(
"Filters SomaticSniper VCF files based on Somatic Score." in
serr)
self.assertTrue("Filter tag: ssc40" in serr)
self.assertTrue("Creating tabix index..." in serr)
self.assertTrue(
"Processed 4 records - Removed 1; Tagged 1; Wrote 3" in serr)
serr = [i for i in serr.split("\n") if i.rstrip("\r\n")]
self.assertTrue(
"gdc_filtration_tools.filter_somatic_score" in serr[0])
self.assertTrue("gdc_filtration_tools.main" in serr[-1])
finally:
cleanup_files(fn)
def test_cli(self):
imets = get_test_data_path("test_oxog_metrics.txt")
vcf_file = get_test_data_path("test_input_for_dtoxog.vcf")
fa_file = get_test_data_path("test_oxog_ref.fa")
(fd, fn) = tempfile.mkstemp()
try:
with captured_output() as (_, stderr):
main(args=[
"create-dtoxog-maf", vcf_file, fn, fa_file, imets, "32.0"
])
with open(fn, "rt") as fh:
self.assertEqual(fh.readline(), "#version 2.4.1\n")
header = fh.readline().rstrip("\r\n").split("\t")
self.assertEqual(header, MAF_COLUMNS)
count = 0
for line in fh:
dat = dict(zip(header,
line.rstrip("\r\n").split("\t")))
self.assertEqual(dat,
TestCreatedToxoGMaf.exp_maf[count])
count += 1
self.assertEqual(count, 3)
serr = stderr.getvalue()
self.assertTrue("Converts a SNP VCF to dToxoG MAF format." in serr)
self.assertTrue("Processed 3 records" in serr)
serr = [i for i in serr.split("\n") if i.rstrip("\r\n")]
self.assertTrue(
"gdc_filtration_tools.create_dtoxog_maf" in serr[0])
self.assertTrue("gdc_filtration_tools.main" in serr[-1])
finally:
cleanup_files(fn)
def test_cli(self):
ivcf = get_test_data_path("sanger_pindel_test.vcf")
(fd, fn) = tempfile.mkstemp(suffix=".vcf.gz")
try:
with captured_output() as (_, stderr):
main(["format-sanger-pindel-vcf", ivcf, fn])
vcf = pysam.VariantFile(fn)
self.assertEqual(list(vcf.header.samples), ["NORMAL", "TUMOR"])
rec = next(vcf)
self.assertEqual(rec.pos, 10)
self.assertEqual(rec.samples["TUMOR"]["GT"], (0, 1))
self.assertEqual(rec.samples["NORMAL"]["GT"], (0, 0))
rec = next(vcf)
self.assertEqual(rec.pos, 20)
self.assertEqual(rec.samples["TUMOR"]["GT"], (0, 1))
self.assertEqual(rec.samples["NORMAL"]["GT"], (0, 0))
with self.assertRaises(StopIteration):
rec = next(vcf)
vcf.close()
serr = stderr.getvalue()
self.assertTrue(
"[gdc_filtration_tools.format_sanger_pindel_vcf] - Creating tabix index..."
in serr
)
self.assertTrue(
"[gdc_filtration_tools.format_sanger_pindel_vcf] - Processed 2 records."
in serr
)
self.assertTrue("gdc_filtration_tools.main" in serr)
finally:
cleanup_files(fn)
def test_cli(self):
ivcf = get_test_data_path("test_nonstandard_variants.vcf")
(fd, fn) = tempfile.mkstemp(suffix=".vcf.gz")
try:
with captured_output() as (_, stderr):
main(args=["filter-nonstandard-variants", ivcf, fn])
vcf = pysam.VariantFile(fn)
record = next(vcf)
self.assertTrue(record.chrom == "chr1")
record = next(vcf)
self.assertTrue(record.chrom == "chr3")
with self.assertRaises(StopIteration):
record = next(vcf)
vcf.close()
serr = stderr.getvalue()
self.assertTrue("Drops non-ACTG loci from a VCF." in serr)
self.assertTrue("Removing chr2:1:A,R" in serr)
self.assertTrue("Creating tabix index..." in serr)
self.assertTrue("Processed 3 records - Removed 1; Wrote 2" in serr)
serr = [i for i in serr.split("\n") if i.rstrip("\r\n")]
self.assertTrue(
"gdc_filtration_tools.filter_nonstandard_variants" in serr[0])
self.assertTrue("gdc_filtration_tools.main" in serr[-1])
finally:
cleanup_files(fn)
def test_cli(self):
oxo_vcf = get_test_data_path(
"test_input_for_add_oxog_filters_from_maf.vcf.gz")
vcf_file = get_test_data_path("test_input_for_add_oxog_filters.vcf")
(fd, fn) = tempfile.mkstemp(suffix=".vcf.gz")
try:
with captured_output() as (_, stderr):
main(args=["add-oxog-filters", vcf_file, oxo_vcf, fn])
vcf = pysam.VariantFile(fn)
self.assertEqual(vcf.header.filters.keys(), ["PASS", "oxog"])
for record in vcf:
if (record.contig == "chr1" and record.pos == 10
and record.alleles == (
"A",
"T",
)):
self.assertEqual(record.filter.keys(), ["oxog"])
else:
self.assertEqual(record.filter.keys(), ["PASS"])
vcf.close()
serr = stderr.getvalue()
self.assertTrue(
"[gdc_filtration_tools.add_oxog_filters] - Creating tabix index"
in serr)
self.assertTrue(
"[gdc_filtration_tools.add_oxog_filters] - Processed 4 records - Tagged 1; Wrote 4"
in serr)
self.assertTrue("[gdc_filtration_tools.main] - Finished!" in serr)
finally:
cleanup_files(fn)
def test_parse_options(self):
'''
test_parse_options: $ANDROID_PRODUCT_OUT or -c must be provided
'''
with captured_output() as (_, err):
with self.assertRaises(SystemExit) as cm:
parse_options([])
exception = cm.exception
err_msg = err.getvalue()
self.assertIn(
'Environment variable $ANDROID_PRODUCT_OUT or parameter "-c" should be provided.',
err_msg)
self.assertEquals(2, exception.code)
def test_import_global_variable_invalid(self):
"""
This is a valid way to import, but you cannot import "importlib"
and other such libraries. Only ones from the whitelist
"""
with captured_output() as (out, err):
with self.assertRaises(CompilationException) as context:
self.si.execute_code_str("""
from test_contracts.good import balances
print('Hacked', balances) # Should not print this!
""")
self.assertEqual(out.getvalue().strip(), '')
def test_cli(self):
ivcf = get_test_data_path("test.vcf")
(fd, fn) = tempfile.mkstemp(suffix=".vcf.gz")
obj = FakeOpts(ivcf, fn)
params = obj.to_cli_list()
with captured_output() as (_, stderr):
main(args=params)
vcf = pysam.VariantFile(fn)
hdr = vcf.header.copy()
vcf.close()
cleanup_files(fn)
self.validate_header(obj, hdr)
serr = [i for i in stderr.getvalue().split("\n") if i.rstrip("\r\n")]
self.assertTrue("gdc_filtration_tools.format_gdc_vcf" in serr[0])
self.assertTrue("gdc_filtration_tools.main" in serr[-1])
def do_test_snapshot(self, ci_generator, version_input, version_output):
version_input_full_path = full_path_from_relative_path(version_input)
version_output_full_path = full_path_from_relative_path(version_output)
with captured_output() as (out, err):
with mock.patch(f'{self.class_path}.get_unity_versions_path'
) as mocked_get_unity_versions_path:
mocked_get_unity_versions_path.return_value = version_input_full_path
ci_generator.output()
output = out.getvalue().strip()
if os.environ.get('UPDATE_SNAPSHOTS'): # no cover
with open(version_output_full_path, 'w') as f: # no cover
f.write(output) # no cover
with open(version_output_full_path) as f:
self.maxDiff = None
self.assertEqual(output, f.read())
def test_position_filter_dkfz(self):
ivcf = get_test_data_path("test_dfkz.vcf")
(fd, fn) = tempfile.mkstemp(suffix=".vcf.gz")
try:
total = 0
with captured_output() as (_, stderr):
position_filter_dkfz(ivcf, fn)
vcf = pysam.VariantFile(fn)
for record in vcf:
total += 1
self.assertEqual(record.chrom, "chr2")
vcf.close()
self.assertEqual(total, 1)
serr = stderr.getvalue()
self.assertTrue("Position Filter for DKFZ." in serr)
self.assertTrue("Creating tabix index..." in serr)
self.assertTrue("Processed 2 records - Removed 1; Wrote 1" in serr)
finally:
cleanup_files(fn)
def test_extract_oxoq_from_sqlite(self):
rec = OxoqRecord("10000", "200", "100", "30.23")
exp = 30.23
(fd, fn) = tempfile.mkstemp()
# Generate test db
with sqlite3.connect(fn) as conn:
# make schema
build_test_schema(conn)
cur = conn.cursor()
rec.insert(cur)
with captured_output() as (stdout, _):
extract_oxoq_from_sqlite(fn,
input_state="gatk_applybqsr_readgroups")
cleanup_files(fn)
sout = float(stdout.getvalue().rstrip("\r\n"))
self.assertEqual(sout, 30.23)
def test_create_oxog_intervals(self):
ivcf = get_test_data_path("test.vcf")
(fd, fn) = tempfile.mkstemp()
try:
found = []
expected = ["chr1:1", "chr2:1"]
with captured_output() as (_, stderr):
create_oxog_intervals(ivcf, fn)
with open(fn, "rt") as fh:
for line in fh:
found.append(line.rstrip("\r\n"))
self.assertEqual(len(found), 2)
self.assertEqual(found, expected)
serr = stderr.getvalue()
self.assertTrue(
"Extracts interval-file for Broad OxoG metrics from VCF." in serr
)
self.assertTrue("Processed 2 records" in serr)
finally:
cleanup_files(fn)
def test_create_dtoxog_maf(self):
imets = get_test_data_path("test_oxog_metrics.txt")
vcf_file = get_test_data_path("test_input_for_dtoxog.vcf")
fa_file = get_test_data_path("test_oxog_ref.fa")
(fd, fn) = tempfile.mkstemp()
try:
with captured_output() as (_, stderr):
create_dtoxog_maf(vcf_file, fn, fa_file, imets, 32.0)
with open(fn, "rt") as fh:
self.assertEqual(fh.readline(), "#version 2.4.1\n")
header = fh.readline().rstrip("\r\n").split("\t")
self.assertEqual(header, MAF_COLUMNS)
count = 0
for line in fh:
dat = dict(zip(header,
line.rstrip("\r\n").split("\t")))
self.assertEqual(dat,
TestCreatedToxoGMaf.exp_maf[count])
count += 1
serr = stderr.getvalue().split("\n")
self.assertTrue("Processed 3 records" in serr[2])
finally:
cleanup_files(fn)
def test_cli(self):
ivcf = get_test_data_path("test_dfkz.vcf")
(fd, fn) = tempfile.mkstemp(suffix=".vcf.gz")
try:
total = 0
with captured_output() as (_, stderr):
main(args=["position-filter-dkfz", ivcf, fn])
vcf = pysam.VariantFile(fn)
for record in vcf:
total += 1
self.assertEqual(record.chrom, "chr2")
vcf.close()
self.assertEqual(total, 1)
serr = stderr.getvalue()
self.assertTrue("Position Filter for DKFZ." in serr)
self.assertTrue("Creating tabix index..." in serr)
self.assertTrue("Processed 2 records - Removed 1; Wrote 1" in serr)
serr = [i for i in serr.split("\n") if i.rstrip("\r\n")]
self.assertTrue(
"gdc_filtration_tools.position_filter_dkfz" in serr[0])
self.assertTrue("gdc_filtration_tools.main" in serr[-1])
finally:
cleanup_files(fn)
def test_add_oxog_filters(self):
oxo_vcf = get_test_data_path(
"test_input_for_add_oxog_filters_from_maf.vcf.gz")
vcf_file = get_test_data_path("test_input_for_add_oxog_filters.vcf")
(fd, fn) = tempfile.mkstemp(suffix=".vcf")
try:
with captured_output() as (_, stderr):
add_oxog_filters(vcf_file, oxo_vcf, fn)
vcf = pysam.VariantFile(fn)
self.assertEqual(vcf.header.filters.keys(), ["PASS", "oxog"])
for record in vcf:
if (record.contig == "chr1" and record.pos == 10
and record.alleles == (
"A",
"T",
)):
self.assertEqual(record.filter.keys(), ["oxog"])
else:
self.assertEqual(record.filter.keys(), ["PASS"])
vcf.close()
serr = stderr.getvalue()
self.assertTrue("Processed 4 records - Tagged 1; Wrote 4" in serr)
finally:
cleanup_files(fn)
def test_format_pindel_vcf(self):
ivcf = get_test_data_path("pindel_test.vcf")
(fd, fn) = tempfile.mkstemp(suffix=".vcf.gz")
try:
with captured_output() as (_, stderr):
format_pindel_vcf(ivcf, fn)
vcf = pysam.VariantFile(fn)
self.assertEqual(list(vcf.header.samples), ["NORMAL", "TUMOR"])
rec = next(vcf)
self.assertEqual(rec.info.get("TYPEOFSV"), "INS")
with self.assertRaises(ValueError):
rec.info.get("SVTYPE")
self.assertFalse(rec.info.get("forcedHet"))
self.assertEqual(rec.samples["TUMOR"]["GT"], (0, 1))
rec = next(vcf)
self.assertEqual(rec.info.get("TYPEOFSV"), "INS")
self.assertTrue(rec.info.get("forcedHet"))
self.assertEqual(rec.samples["TUMOR"]["GT"], (0, 1))
with self.assertRaises(StopIteration):
rec = next(vcf)
vcf.close()
serr = stderr.getvalue()
self.assertTrue(
"[gdc_filtration_tools.format_pindel_vcf] - Creating tabix index..."
in serr
)
self.assertTrue(
"[gdc_filtration_tools.format_pindel_vcf] - Processed 2 records."
in serr
)
finally:
cleanup_files(fn)
