| 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.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 + ".csv") | |
| print(f"Creating {output_file_name}") | |
| species_df.to_csv(output_file_name, index=False) | |