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"""Parsers for generating some files in genenetwork"""
import os
from typing import Any, Dict, List, Tuple
def parse_genofile(file_path: str) -> Tuple[List[str],
List[Dict[str, Any]]]:
"""Parse a genotype file with a given format"""
if not os.path.exists(file_path):
raise FileNotFoundError
__map = {
'b': -1,
'd': 1,
'h': 0,
'u': None,
}
genotypes, samples = [], []
with open(file_path, "r", encoding="utf-8") as _genofile:
for line in _genofile:
line = line.strip()
if line.startswith(("#", "@")):
continue
cells = line.split()
if line.startswith("Chr"):
samples = cells[4:]
samples = [sample.lower() for sample in samples]
continue
values = [__map.get(value.lower(), None) for value in cells[4:]]
genotype = {
"chr": cells[0],
"locus": cells[1],
"cm": cells[2],
"mb": cells[3],
"values": values,
"dicvalues": dict(zip(samples, values)),
}
genotypes.append(genotype)
return samples, genotypes
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