import os
import pandas as pd
import re

data_dir = os.getcwd()
output_path = os.getcwd()

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


for species in species_list:
    print(f"Downloading {species} files")
    list_of_df = []
    species_url_file = os.path.join(data_dir, species + "_oas_paired.txt")
    with open(species_url_file, "r") as f:
        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])
            run_data = pd.read_csv(
                csv_file,
                header=1,
                compression="gzip",
                on_bad_lines="warn",
            )
            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()

            def calc_cdr_coordinates(row):
                for i in range(1, 4):
                    for j in ["heavy", "light"]:
                        row[f"cdr{i}_aa_{j}_start"] = row[
                            f"sequence_alignment_aa_{j}"
                        ].find(row[f"cdr{i}_aa_{j}"])
                        row[f"cdr{i}_aa_{j}_end"] = row[f"cdr{i}_aa_{j}_start"] + len(
                            row[f"cdr{i}_aa_{j}"]
                        )
                return row

            run_data = run_data.apply(calc_cdr_coordinates, axis=1)

            run_data = run_data.drop(
                columns=[
                    "cdr1_aa_heavy",
                    "cdr2_aa_heavy",
                    "cdr3_aa_heavy",
                    "cdr1_aa_light",
                    "cdr2_aa_light",
                    "cdr3_aa_light",
                ]
            )

            run_data.insert(
                0, "pair_id", run_id + "_" + run_data.reset_index().index.map(str)
            )
            list_of_df.append(run_data)
        species_df = pd.concat(list_of_df, ignore_index=True)
        print(f"{species} output summary:")
        print(species_df.head())
        print(species_df.shape)
        output_file_name = os.path.join(output_path, species + ".zip")
        print(f"Creating {output_file_name}")
        species_df.to_csv(output_file_name, index=False, compression="zip")