def test_no_variants_returns_ref_chroms(self, mock_var_file,
mock_load_fasta):
recs = []
mock_var_file.return_value.fetch.return_value = iter(recs)
mock_load_fasta.return_value = self.chroms
converter = Vcf_to_prg("", "", "")
self.assertEqual("AGCAGCCCCGGG", converter._get_string())
def test_one_variant_chroms_with_no_vars_in_same_order(
self, mock_var_file, mock_load_fasta):
recs = [_MockVcfRecord(2, "G", ["CAAA", "CA"], chrom="ref3")]
mock_var_file.return_value.fetch.return_value = iter(recs)
mock_load_fasta.return_value = self.chroms
converter = Vcf_to_prg("", "", "")
self.assertEqual("AGCAGCCCCG5G6CAAA6CA6G", converter._get_string())
def test_filter_pass_record_kept(self, mock_var_file, mock_load_fasta):
recs = [_MockVcfRecord(2, "A", "G",
chrom="JAC")] # Default filter: PASS
mock_var_file.return_value.fetch.return_value = iter(recs)
mock_load_fasta.return_value = self.chroms
converter = Vcf_to_prg("", "", "")
self.assertEqual(converter._get_string(), "A5A6G6C")
def test_adjacent_snps_kept(self, mock_var_file, mock_load_fasta):
recs = [
_MockVcfRecord(1, "C", ["G"], chrom="ref2"),
_MockVcfRecord(2, "C", ["A"], chrom="ref2"),
]
mock_var_file.return_value.fetch.return_value = iter(recs)
mock_load_fasta.return_value = self.chroms
converter = Vcf_to_prg("", "", "")
self.assertEqual("AGCAGC5C6G67C8A8CGGG", converter._get_string())
def test_two_snps_same_chrom(self, mock_var_file, mock_load_fasta):
recs = [
_MockVcfRecord(1, "A", "G", chrom="ref1"),
_MockVcfRecord(3, "C", ["T", "G"], chrom="ref1"),
]
mock_var_file.return_value.fetch.return_value = iter(recs)
mock_load_fasta.return_value = self.chroms
converter = Vcf_to_prg("", "", "")
self.assertEqual("5A6G6G7C8T8G8AGCCCCGGG", converter._get_string())
def test_snp_inside_del(self, mock_var_file, mock_load_fasta):
recs = [
_MockVcfRecord(2, "T", ["G"], chrom="ref1"),
_MockVcfRecord(2, "T", ["C"], chrom="ref1"),
]
mock_var_file.return_value.fetch.return_value = iter(recs)
mock_load_fasta.return_value = self.chroms
converter = Vcf_to_prg("", "", "")
self.assertEqual("T5T6G6TTCCC", converter._get_string())
def test_snps_at_same_position(self, mock_var_file, mock_load_fasta):
recs = [
_MockVcfRecord(1, "TTTT", ["T"], chrom="ref1"),
_MockVcfRecord(2, "T", ["C"], chrom="ref1"),
]
mock_var_file.return_value.fetch.return_value = iter(recs)
mock_load_fasta.return_value = self.chroms
converter = Vcf_to_prg("", "", "")
self.assertEqual("5TTTT6T6CCC", converter._get_string())
def test_one_ins_and_one_del_diff_chroms(self, mock_var_file,
mock_load_fasta):
recs = [
_MockVcfRecord(3, "C", ["CGG"], chrom="ref1"),
_MockVcfRecord(1, "CCC", ["C"], chrom="ref2"),
]
mock_var_file.return_value.fetch.return_value = iter(recs)
mock_load_fasta.return_value = self.chroms
converter = Vcf_to_prg("", "", "")
self.assertEqual("AG5C6CGG6AGC7CCC8C8GGG", converter._get_string())
def build_from_vcfs(report, action, build_paths, args):
"""Calls utility that converts a vcf and fasta reference into a linear prg."""
if args.no_vcf_clustering:
_skip_cluster_vcf_records(report, "skip_vcf_record_clustering",
build_paths)
else:
# We also do this if only a single one is provided, to deal with overlapping records.
cluster_vcf_records(report, "vcf_record_clustering", build_paths)
built_vcf = build_paths.built_vcf
log.info(f"Running {action} on {built_vcf}")
converter = Vcf_to_prg(built_vcf,
build_paths.ref,
build_paths.prg,
mode="normal")
converter._write_bytes()
num_recs_in_vcf = _count_vcf_record_lines(built_vcf)
assert num_recs_in_vcf == converter.num_sites, log.error(
f"Mismatch between number of vcf records in {built_vcf}"
f"({num_recs_in_vcf} and number of variant sites in"
f"PRG string ({converter.num_sites}.\n"
f"Please report this to developers.")
def test_nonACGT_fails_to_convert(self, mock_var_file, mock_load_fasta):
mock_var_file.return_value.fetch.return_value = iter([])
mock_load_fasta.return_value = {}
converter = Vcf_to_prg("", "", "")
with self.assertRaises(ValueError):
converter._to_bytes("N")
def test_filter_nonpass_record_skipped(self, mock_var_file,
mock_load_fasta):
recs = [_MockVcfRecord(2, "A", "G", filter={"LOW_QUAL": ""})]
mock_var_file.return_value.fetch.return_value = iter(recs)
mock_load_fasta.return_value = self.chroms
converter = Vcf_to_prg("", "", "")
def test_integer_representation(self, mock_var_file, mock_load_fasta):
mock_var_file.return_value.fetch.return_value = iter(self.recs)
mock_load_fasta.return_value = self.chroms
converter = Vcf_to_prg("", "", "")
self.assertEqual([5, 1, 6, 3, 6, 2, 1, 2, 7, 1, 8, 1, 1, 1, 8, 1],
converter._get_ints())
def test_legacy_representation(self, mock_var_file, mock_load_fasta):
mock_var_file.return_value.fetch.return_value = iter(self.recs)
mock_load_fasta.return_value = self.chroms
converter = Vcf_to_prg("", "", "", mode="legacy")
self.assertEqual("5A6G5CAC7A8AAA7A", converter._get_string())
def _run(self, mode="normal", check=False):
converter = Vcf_to_prg(str(self.vcf_file),
str(self.ref_file),
self.outfile_prefix,
mode=mode)
converter._write_string()
