def test_parse_protein_mutations(self):
test_info = \
"QNAME=hCoV-19_Guangdong_2020XN4373-P0039_2020_EPI_ISL_413851_2020-01-30;QSTART=274;QSTRAND=+;ANN=" \
"T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|" \
"protein_coding|1/2|c.9C>T|p.Ser3Ser|9/21291|9/21291|3/7096||," \
"T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|" \
"protein_coding|1/1|c.9C>T|p.Ser3Ser|9/540|9/540|3/179||WARNING_TRANSCRIPT_NO_STOP_CODON," \
"T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|" \
"protein_coding|1/1|c.9C>T|p.Ser3Ser|9/540|9/540|3/179||WARNING_TRANSCRIPT_NO_STOP_CODON," \
"T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|" \
"protein_coding|1/1|c.9C>T|p.Ser3Ser|9/13218|9/13218|3/4405||," \
"T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|" \
"protein_coding||c.-532C>T|||||532|WARNING_TRANSCRIPT_NO_START_CODON," \
"T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|" \
"protein_coding||c.-532C>T|||||532|WARNING_TRANSCRIPT_NO_START_CODON," \
"T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|" \
"protein_coding||c.-2446C>T|||||2446|WARNING_TRANSCRIPT_NO_START_CODON," \
"T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|" \
"protein_coding||c.-2446C>T|||||2446|WARNING_TRANSCRIPT_NO_START_CODON"
vcf_obj = vcf_parser.VcfParser()
muts = vcf_obj._extract_protein_mutations(test_info)
self.assertEqual(len(muts), 4)
self.assertEqual(muts[0], 'p.Ser3Ser')
self.assertEqual(muts[-1], 'p.Ser3Ser')
def test_load_with_snpeff_data__protein(self):
vcf_obj = vcf_parser.VcfParser()
vcf_obj.read_vcf_file(TEST_VCF_FILE2)
self.assertEqual(vcf_obj.df_vcf.shape, (500, 10))
# Test get mutations
muts = vcf_obj.get_protein_mutations(is_strict_check=False)
print(muts[:5])
# Test write to file
output_file = f'__out_{time.time()}__ut_mutations_vcf2-protein.txt'
vcf_obj.write_mutations_to_file(muts, output_file)
def test_load(self):
vcf_obj = vcf_parser.VcfParser()
vcf_obj.read_vcf_file(TEST_VCF_FILE1)
self.assertEqual(vcf_obj.df_vcf.shape, (19756, 10))
# Test get mutations
muts = vcf_obj.get_mutations()
print(muts[:5])
# Test write to file
output_file = f'__out_{time.time()}__ut_mutations_vcf1.txt'
vcf_obj.write_mutations_to_file(muts, output_file)
def get_mutations_from_file(vcf_file_name, check_protein_mutations = False, verbose = 0):
if not os.path.isfile(vcf_file_name):
raise FileNotFoundError(f"Cannot find VCF file: {vcf_file_name}")
# Parse VCF into sequence of mutations
vcf_parser_obj = vcf_parser.VcfParser()
try:
vcf_parser_obj.read_vcf_file(vcf_file_name, verbose=verbose)
if check_protein_mutations:
vcf_mutations = vcf_parser_obj.get_protein_mutations(is_strict_check=False, verbose=verbose)
else:
vcf_mutations = vcf_parser_obj.get_mutations(verbose=verbose)
assert isinstance(vcf_mutations, list)
except Exception as e:
# Re-raise exception with additional context
raise Exception(f'ERROR while parsing vcf file: {e}')
return vcf_mutations
def test_convert_protein_mutations(self):
vcf_obj = vcf_parser.VcfParser()
muts = ['p.Ser3Ser', 'p.Thr5262Ile']
new_muts = vcf_obj.convert_protein_mutations_from_3_to_1_letters(muts)
self.assertEqual(new_muts, ['S3S', 'T5262I'])
# Bad first letter ('x')
with self.assertRaisesRegex(ValueError, 'Unexpected format'):
vcf_obj.convert_protein_mutations_from_3_to_1_letters(
['x.Ser3Ser'])
# Bad acid1 (non-existing)
with self.assertRaisesRegex(ValueError, 'Cannot recognize acid1'):
vcf_obj.convert_protein_mutations_from_3_to_1_letters(
['p.Xxx3Ser'])
# Bad acid2 (non-existing)
with self.assertRaisesRegex(ValueError, 'Cannot recognize acid2'):
vcf_obj.convert_protein_mutations_from_3_to_1_letters(
['p.Ser3Xxx'])