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"""The datatypes this package will use."""
from dataclasses import dataclass
from typing import Sequence, Optional
@dataclass
class DotGenoFields:
"""Custom .geno file format values"""
name: str,
mat: str,
pat: str,
het: str,
type_: Optional[str] = None
unk: Optional[str] = None
@dataclass(frozen=True)
class FieldsIdentity:
"""Data type for identity of the fields."""
marker: str
chromosome: str
genetic_distance: str # cM
physical_distance: str # Mb
samples: Sequence[str]
@dataclass(frozen=True)
class LineDetails:
"""Data type for processed line details"""
line_content: Sequence[Union[str, None]]
geno_symbols: Sequence[str]
line_header: Optional[str] = None
@dataclass(frozen=True)
class LineError:
"""An error object for a line."""
marker: str
field: str
value: Union[str, None]
message: str
@dataclass(frozen=True)
class FileStats:
"""Custom file statistics."""
data_lines: int
total_lines: int
geno_symbols: Sequence[str]
blank_lines: int = 0
comment_lines: int = 0
dot_geno_lines: int = 0
dot_geno_fields: Optional[DotGenoFields] = None
samples: Sequence[str] = field(default_factory=tuple)
samples_list: Sequence[str] = field(default_factory=tuple)
markers_list: Sequence[str] = field(default_factory=tuple)
errors: Sequence[LineError] = field(default_factory=tuple)
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