import os
import pandas as pd
import re

data_dir = os.path.join(os.getcwd(), "data_units")

species_list = ["rat_SD", "mouse_BALB_c", "mouse_C57BL_6", "human"]

for species in species_list:
    print(f"Downloading {species} files")
    species_url_file = os.path.join(data_dir, species + ".txt")
    with open(species_url_file, "r") as f:
        i = 0
        os.makedirs(species, exist_ok=True)
        for csv_file in f.readlines():
            print(csv_file)
            filename = os.path.basename(csv_file)
            run_id = str(re.search(r"^(.*)_[Pp]aired", filename)[1])
            url = csv_file
            run_data = pd.read_csv(
                url,
                header=1,
                compression="gzip",
                on_bad_lines="warn",
                low_memory=False,
            )
            run_data = run_data[
                [
                    "sequence_alignment_aa_heavy",
                    "cdr1_aa_heavy",
                    "cdr2_aa_heavy",
                    "cdr3_aa_heavy",
                    "sequence_alignment_aa_light",
                    "cdr1_aa_light",
                    "cdr2_aa_light",
                    "cdr3_aa_light",
                ]
            ]
            run_data = run_data.dropna()
            run_data.insert(0, "data_unit", run_id)
            print(run_data.shape)
            output_path = os.path.join(species, "train_" + str(i) + ".parquet")
            run_data.to_parquet(output_path, index=False)
            i += 1