#!/usr/bin/env python3
"""Configuration options for pyllelic."""
import re
from dataclasses import dataclass
from pathlib import Path
from typing import Pattern
[docs]@dataclass
class Config:
"""pyllelic configuration dataclass with TERT promoter defaults.
Pyllelic expects .bam files to be analyzed to be in analysis_directory, under
a base_directory, with the promoter reference sequence in the base_directory.
"""
base_directory: Path = Path("/")
promoter_file: Path = base_directory / "promoter.txt"
results_directory: Path = base_directory / "results"
analysis_directory: Path = base_directory / "test"
promoter_start: int = 1293200
promoter_end: int = 1296000
chromosome: str = "5"
offset: int = 1298163
viz_backend: str = "plotly"
fname_pattern: Pattern[str] = re.compile(r"^[a-zA-Z]+_([a-zA-Z0-9]+)_.+bam$")