| from typing import Optional | |
| from pydantic import BaseSettings, Field | |
| import os | |
| class EnvBeagle(BaseSettings): | |
| vcf: str = Field(description='Path to the target vcf file') | |
| samples: Optional[str] = Field(default=None, | |
| description='Path to VCF with other samples for conform checks, not required if ' | |
| 'target VCF contains data for at least 20 individuals') | |
| conform: str = Field(description='Path to conform .jar file') | |
| beagle: str = Field(description='Path to beagle .jar file') | |
| ref: str = Field(description='Path to folder with reference genome:' | |
| ' .vcf.gz files are expected to start with "chr1."..."chr22.", "chrX."') | |
| maps: str = Field(description='Path to folder with PLINK format genetic maps, files are expected to start with' | |
| '"plink.chr1.", ..."plink.chr22.", "plink.chrX."') | |
| gb: int = Field(description='Number of gigabytes for running beagle') | |
| class Config: | |
| env_file = os.path.dirname(os.path.abspath(__file__))+"/.env_paths" | |
| IMPUTATION_SETTINGS = EnvBeagle() | |