def test_multigrmpy_pg_het_ins(self):
import multigrmpy
with tempfile.TemporaryDirectory() as output_dir:
args = ADict({
"input":
self.hg38_input_vcf,
"manifest":
self.hg38_manifest,
"reference":
self.hg38_reference,
"output":
output_dir,
"grmpy":
os.path.join(os.path.dirname(__file__), "module-wrapper.sh") +
" " + os.path.join(GRMPY_INSTALL, "bin", "grmpy"),
"verbose":
False,
"quiet":
True,
"logfile":
None,
"write_alignments":
False,
"infer_read_haplotypes":
False,
"graph_sequence_matching":
True,
"klib_sequence_matching":
False,
"kmer_sequence_matching":
False,
"bad_align_uniq_kmer_len":
0,
"threads":
1,
"sample_threads":
1,
"genotyping_parameters":
None,
"max_reads_per_event":
10000,
"split_type":
"lines",
"read_length":
150,
"max_ref_node_length":
1000,
"graph_type":
"alleles",
"alt_splitting":
True,
"retrieve_reference_sequence":
False,
"scratch_dir":
None,
"keep_scratch":
True,
})
output_json_path = os.path.join(output_dir, "genotypes.json.gz")
multigrmpy.run(args)
# compare genotyping results
with gzip.open(output_json_path, 'rt') as result_json:
observed = json.load(result_json)
with open(self.hg38_expected_genotypes_json,
'rt') as expected_json:
expected = json.load(expected_json)
# uncomment to keep observed json
# check if genotypes are the same
observed_lines = json.dumps(observed,
sort_keys=True,
indent=4,
separators=(',', ': '))
expected_lines = json.dumps(expected,
sort_keys=True,
indent=4,
separators=(',', ': '))
if observed_lines != expected_lines:
for line in difflib.context_diff(
expected_lines.split("\n"),
observed_lines.split("\n"),
fromfile=self.hg38_expected_genotypes_json,
tofile=output_json_path):
sys.stderr.write(line + "\n")
with open("test_gt.json", "wt") as out_file:
json.dump(observed,
out_file,
sort_keys=True,
indent=4,
separators=(',', ': '))
raise Exception(
"Genotyping results don't match! If this is expected and new behavior, "
"cp test_gt.json %s" % self.hg38_expected_genotypes_json)
# check if variants are the same
output_json_path = os.path.join(output_dir, "variants.json.gz")
with gzip.open(output_json_path, 'rt') as result_json:
observed = json.load(result_json)
# uncomment to keep observed json
with open(self.hg38_expected_variants_json, 'rt') as expected_json:
expected = json.load(expected_json)
# contains temp file locations
del observed[0]["graph"]["model_name"]
if "model_name" in expected[0]["graph"]:
del expected[0]["graph"]["model_name"]
observed_lines = json.dumps(observed,
sort_keys=True,
indent=4,
separators=(',', ': '))
expected_lines = json.dumps(expected,
sort_keys=True,
indent=4,
separators=(',', ': '))
if observed_lines != expected_lines:
for line in difflib.context_diff(
expected_lines.split("\n"),
observed_lines.split("\n"),
fromfile=self.hg38_expected_genotypes_json,
tofile=output_json_path):
sys.stderr.write(line + "\n")
with open("test_variants.json", "wt") as out_file:
json.dump(observed,
out_file,
sort_keys=True,
indent=4,
separators=(',', ': '))
raise Exception(
"Converted variants don't match! If this is expected and new behavior, "
"cp test_variants.json %s" %
self.hg38_expected_variants_json)
def test_multigrmpy(self):
import multigrmpy
with tempfile.TemporaryDirectory() as output_dir:
args = ADict({
"input":
self.input_vcf,
"manifest":
self.manifest,
"reference":
self.reference,
"output":
output_dir,
"grmpy":
os.path.join(os.path.dirname(__file__), "module-wrapper.sh") +
" " + os.path.join(GRMPY_INSTALL, "bin", "grmpy"),
"verbose":
False,
"quiet":
True,
"logfile":
None,
"infer_read_haplotypes":
False,
"write_alignments":
False,
"graph_sequence_matching":
True,
"klib_sequence_matching":
False,
"kmer_sequence_matching":
False,
"bad_align_uniq_kmer_len":
0,
"threads":
1,
"sample_threads":
1,
"genotyping_parameters":
None,
"max_reads_per_event":
10000,
"split_type":
"lines",
"read_length":
150,
"max_ref_node_length":
1000,
"graph_type":
"alleles",
"alt_splitting":
True,
"retrieve_reference_sequence":
False,
"scratch_dir":
None,
"keep_scratch":
True,
})
output_json_path = os.path.join(output_dir, "genotypes.json.gz")
multigrmpy.run(args)
with gzip.open(output_json_path, 'rt') as result_json:
observed = json.load(result_json)
for item in observed:
if item["graphinfo"]["ID"] == "test-ins":
self.assertEqual(
item["samples"]["sample1"]["gt"]["GT"], "S1/S1")
self.assertEqual(
item["samples"]["sample2"]["gt"]["GT"], "./.")
if item["graphinfo"]["ID"] == "test-del":
self.assertEqual(
item["samples"]["sample1"]["gt"]["GT"], "./.")
self.assertEqual(
item["samples"]["sample2"]["gt"]["GT"], "S1/S1")
def test_multigrmpy_expected_genotypes(self):
import multigrmpy
with tempfile.TemporaryDirectory() as output_dir:
args = ADict({
"input":
self.swaps_input_vcf,
"manifest":
self.swaps_manifest,
"reference":
self.swaps_reference,
"output":
output_dir,
"grmpy":
os.path.join(os.path.dirname(__file__), "module-wrapper.sh") +
" " + os.path.join(GRMPY_INSTALL, "bin", "grmpy"),
"verbose":
False,
"quiet":
True,
"logfile":
None,
"infer_read_haplotypes":
False,
"write_alignments":
False,
"graph_sequence_matching":
True,
"klib_sequence_matching":
False,
"kmer_sequence_matching":
False,
"bad_align_uniq_kmer_len":
0,
"threads":
1,
"sample_threads":
1,
"genotyping_parameters":
None,
"max_reads_per_event":
10000,
"split_type":
"lines",
"read_length":
150,
"max_ref_node_length":
1000,
"graph_type":
"alleles",
"alt_splitting":
True,
"retrieve_reference_sequence":
False,
"scratch_dir":
None,
"keep_scratch":
False,
})
multigrmpy.run(args)
output_json_path = os.path.join(output_dir, "genotypes.json.gz")
with gzip.open(output_json_path, 'rt') as result_json:
observed = json.load(result_json)
with open(self.swaps_expected_genotypes_json,
'rt') as expected_json:
expected = json.load(expected_json)
# event ordering is not guaranteed
observed = sorted(observed, key=lambda x: x["graphinfo"]["ID"])
expected = sorted(expected, key=lambda x: x["graphinfo"]["ID"])
match = True
for i, o in enumerate(observed):
if o["samples"]["SWAPS"]["gt"]["GT"] != expected[i]["samples"][
"SWAPS"]["gt"]["GT"]:
match = False
break
if not match:
observed_lines = json.dumps(observed,
sort_keys=True,
indent=4,
separators=(',', ': '))
expected_lines = json.dumps(expected,
sort_keys=True,
indent=4,
separators=(',', ': '))
for line in difflib.context_diff(
expected_lines.split("\n"),
observed_lines.split("\n"),
fromfile=self.swaps_expected_genotypes_json,
tofile=output_json_path):
sys.stderr.write(line + "\n")
with open("test_swaps_genotypes.json", "wt") as out_file:
json.dump(observed,
out_file,
sort_keys=True,
indent=4,
separators=(',', ': '))
raise Exception(
"Swaps test genotyping output doesn't match! If this is expected and new behavior, "
"cp test_swaps_genotypes.json %s" %
self.swaps_expected_genotypes_json)
output_vcf_path = os.path.join(output_dir, "genotypes.vcf.gz")
with gzip.open(output_vcf_path, 'rt') as result_vcf:
observed_lines = result_vcf.read().splitlines(keepends=False)
observed_lines = [
x for x in observed_lines if not x.startswith("#")
]
with open(self.swaps_expected_genotypes_vcf, 'rt') as expected_vcf:
expected_lines = expected_vcf.read().splitlines(keepends=False)
if observed_lines != expected_lines:
for line in difflib.context_diff(
expected_lines,
observed_lines,
fromfile=self.swaps_expected_genotypes_vcf,
tofile=output_vcf_path):
sys.stderr.write(line + "\n")
with open("test_swaps_genotypes.vcf", "wt") as out_file:
for x in observed_lines:
print(x, file=out_file)
raise Exception(
"Swaps VCF output doesn't match! If this is expected and new behavior, "
"cp test_swaps_genotypes.vcf %s" %
self.swaps_expected_genotypes_vcf)
output_json_path = os.path.join(output_dir, "variants.json.gz")
with gzip.open(output_json_path, 'rt') as result_json:
observed = json.load(result_json)
with open(self.swaps_expected_variants_json,
'rt') as expected_json:
expected = json.load(expected_json)
# event ordering is not guaranteed
observed = sorted(observed, key=lambda x: x["ID"])
expected = sorted(expected, key=lambda x: x["ID"])
# remove temp file information
for o in observed:
del o["graph"]["model_name"]
for e in expected:
if "model_name" in e["graph"]:
del e["graph"]["model_name"]
observed_lines = json.dumps(observed,
sort_keys=True,
indent=4,
separators=(',', ': '))
expected_lines = json.dumps(expected,
sort_keys=True,
indent=4,
separators=(',', ': '))
if observed_lines != expected_lines:
for line in difflib.context_diff(
expected_lines.split("\n"),
observed_lines.split("\n"),
fromfile=self.swaps_expected_variants_json,
tofile=output_json_path):
sys.stderr.write(line + "\n")
with open("test_swaps_variants.json", "wt") as out_file:
json.dump(observed,
out_file,
sort_keys=True,
indent=4,
separators=(',', ': '))
raise Exception(
"Swaps test converted variants don't match! If this is expected and new behavior, "
"cp test_swaps_variants.json %s" %
self.swaps_expected_variants_json)