MyHeritage DNA raw genotype importer.
parse_myheritage(path: str | Path) -> tuple[ArrayGenotypeCall, ...]
Parse common MyHeritage CSV/TSV rows into normalized genotype calls.
Source code in geno_lewm/deploy/import_/myheritage.py
| def parse_myheritage(path: str | Path) -> tuple[ArrayGenotypeCall, ...]:
"""Parse common MyHeritage CSV/TSV rows into normalized genotype calls."""
calls: list[ArrayGenotypeCall] = []
for line_no, line in read_text_lines(path):
fields = _split_row(line)
if _is_header(fields):
continue
if len(fields) != 4:
raise VcfParseError(
"MyHeritage row must contain rsid, chromosome, position, result",
details={"line": line_no, "field_count": len(fields)},
)
rsid, chrom, pos, genotype = fields
calls.append(
ArrayGenotypeCall(
provider=_PROVIDER,
rsid=rsid,
chrom=chrom,
pos=parse_pos(pos, provider=_PROVIDER, line_no=line_no),
genotype=genotype,
line_no=line_no,
)
)
return tuple(calls)
|
convert_myheritage_to_vcf(input_path: str | Path, output_path: str | Path, reference_alleles: ReferenceAlleles, *, sample_id: str = 'sample') -> VcfConversionSummary
Convert MyHeritage raw genotype CSV/TSV to a local VCF file.
Source code in geno_lewm/deploy/import_/myheritage.py
| def convert_myheritage_to_vcf(
input_path: str | Path,
output_path: str | Path,
reference_alleles: ReferenceAlleles,
*,
sample_id: str = "sample",
) -> VcfConversionSummary:
"""Convert MyHeritage raw genotype CSV/TSV to a local VCF file."""
return convert_array_calls_to_vcf(
parse_myheritage(input_path),
output_path,
reference_alleles,
sample_id=sample_id,
)
|