Source code for rocco.constants

r"""
ROCCO: Constants
====================

Default effective genome sizes, chromosome size files, chromosome-specific budget/gamma parameters
for supported assemblies: `hg38`, `hg19`, `mm10`, `mm39`, and `dm6`.

Universally optimal parameters/default values cannot be established for all datasets. When possible, users may find improved results by tuning the parameters to their specific data. See `existing assembly-specific files <https://github.com/nolan-h-hamilton/ROCCO/tree/main/rocco>`_ for default parameter files you may use as a template.

Use the `--params` CLI argument to specify a custom parameter file. 


Variables
---------
GENOME_DICT : dict
    Dictionary of genome assemblies with effective genome size, chromosome sizes file, and parameters file.
    Keys are assembly names, values are dictionaries with keys 'effective_genome_size', 'sizes_file', and 'params'.
    Default assemblies: `hg38`, `hg19`, `mm10`, `mm39`, and `dm6`.

"""

import os
import warnings



def get_file_path(filename):
    file_path = os.path.join(os.path.dirname(__file__), filename)
    if not os.path.exists(file_path):
        warnings.warn(f"File not found: {file_path}")
    return file_path


GENOME_DICT = {
    'hg38': {'effective_genome_size': int(2.7e9), 'sizes_file': get_file_path('hg38.sizes'), 'params': get_file_path('hg_params.csv')},
    'hg19': {'effective_genome_size': int(2.7e9), 'sizes_file': get_file_path('hg19.sizes'), 'params': get_file_path('hg_params.csv')},
    'mm10': {'effective_genome_size': int(1.87e9), 'sizes_file': get_file_path('mm10.sizes'), 'params': get_file_path('mm_params.csv')},
    'mm39': {'effective_genome_size': int(1.87e9), 'sizes_file': get_file_path('mm39.sizes'), 'params': get_file_path('mm_params.csv')},
    'dm6': {'effective_genome_size': int(1.45e8), 'sizes_file': get_file_path('dm6.sizes'), 'params': get_file_path('dm_params.csv')}}