import pathlib

repo_root = pathlib.Path(__file__).resolve().parent

# important subdirectories
data_dir = repo_root / 'data'
park_info_file = data_dir / 'park_info_samples.tsv'

# differential expression directories/files
de_base_dir = repo_root / '4_de_analysis'
de_data_dir = de_base_dir / 'data'
de_input_dir = de_base_dir / 'de_input'
de_output_dir = de_base_dir / 'de_output'
raw_de_data_dir = de_data_dir / 'raw'
processed_counts_file = de_data_dir / 'tcga_processed_counts.tsv.gz'
de_sample_info = de_data_dir / 'tcga_expression_sample_identifiers.tsv'

# distance analysis directories/files
distance_base_dir = repo_root / '5_distance_analysis'
distance_data_dir = distance_base_dir / 'data'
distance_loss_info = distance_data_dir / 'park_loss_num_hits.pkl'
distance_gain_info = distance_data_dir / 'park_gain_num_hits.pkl'

# location of mpmp repo, some analyses depend on this
mpmp_location = pathlib.Path('~/research/mpmp/')

# location of vogelstein genes
vogelstein_base_url = "https://github.com/greenelab/pancancer/raw"
vogelstein_commit = "<KEY>"
