module/config.py

from pathlib import Path
import yaml
import random

import numpy as np
import torch


root = Path(__file__).parent.parent
data = root / 'data'
models = root / 'models'
notebooks = root / 'notebooks'
scripts = root / 'scripts'
output = root / 'output'
docs = root / 'docs'

# Data specific paths
data_raw = data / 'raw'
data_processed = data / 'processed'
data_final = data / 'final'

# Location of tools
libs = root / 'libs'
samtools = libs / 'samtools'
bedtools = libs / 'bedtools'
dnabert = root / 'DNABERT'

# Locations of specific files
bpe_tokenizer = data_final / 'tokenizer' / 'maize_bpe_full.tokenizer.json'

# Loading settings
settings = yaml.full_load((root / 'config.yaml').open('r'))

# Setting random seeds across the whole project
random_seed = settings['random_seed']
random.seed(random_seed)
np.random.seed(random_seed)
torch.manual_seed(random_seed)


def reload_settings():
    global settings
    settings = yaml.full_load((root / 'config.yaml').open('r'))
tissues = [
    'tassel', 
    'base', 
    'anther', 
    'middle', 
    'ear', 
    'shoot', 
    'tip', 
    'root' 
]