constants.py

from pathlib import Path

# FOLDERS
DATA_FOLDER = Path('.data')
VCF_BY_POPULATION_FOLDER = 'vcf_by_population'
FREQ_BY_POPULATION_FOLDER = 'freq_by_population'
SNPS_DATA_FOLDER = 'SNPs_data'
SAMPLES_FOLDER = DATA_FOLDER/'samples'
SNPS_DATA_FILE_NAME = 'snps_data_all.csv'
RESULT_FREQ_FILE_NAME = 'result.freq'
GENOTYPE_DATA_FOLDER = 'genotype_data'
MERGED_GENOTYPE_FILE = 'all_phase3'
MERGED_VCF_FILE_NAME = f'{MERGED_GENOTYPE_FILE}.vcf'
SNP_LIST_FILE_NAME = 'snps.tsv'
DEFAULT_OUT_FOLDER = 'output'
DEFAULT_OUT_FILE_NAME = 'allele_frequency'
DEFAULT_SNPS_LIST_PATH = 'snps.tsv'

# PATHS
VCF_BY_POPULATION_PATH = DATA_FOLDER/VCF_BY_POPULATION_FOLDER
FREQ_BY_POPULATION_PATH = DATA_FOLDER/FREQ_BY_POPULATION_FOLDER
SNPS_DATA_PATH = DATA_FOLDER/SNPS_DATA_FOLDER
GENOTYPE_DATA_PATH = DATA_FOLDER/GENOTYPE_DATA_FOLDER
MERGED_VCF_OUTPUT_PATH = GENOTYPE_DATA_PATH/MERGED_VCF_FILE_NAME

# DOCKER IMAGES
IMAGE_WORKDIR = Path('/usr/src/app/')
IMAGE_SHARE_FOLDER_PATH = IMAGE_WORKDIR/'share_folder'
VCF_TOOLS_IMAGE_NAME = 'avelior/vcftools'
PLINK2_IMAGE_NAME = 'avelior/plink2'
HG38DB_IMAGE_NAME = 'avelior/hg38db'

# VCF
PSAM_PATH = 'https://www.dropbox.com/s/yozrzsdrwqej63q/phase3_corrected.psam?dl=1'
PVAR_PATH = 'https://www.dropbox.com/s/op9osq6luy3pjg8/all_phase3.pvar.zst?dl=1'
PGEN_PATH = 'https://www.dropbox.com/s/afvvf1e15gqzsqo/all_phase3.pgen.zst?dl=1'