| 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 | |