import pandas import pyarrow.parquet import pickle # Gabe requested that the splits defined in ThermoMPNN of the MegaScale dataset be the default splits # ThermoMPNN/datsets.py # class MegaScaleDataset # def __init__(csg, split): # fname = self.cfg.data_loc.megascale_csv # df = pd.read_csv(fname, usecols=["ddG_ML", "mut_type", "WT_name", "aa_seq", "dG_ML"]) # # # remove unreliable data and more complicated mutations # df = df.loc[df.ddG_ML != '-', :].reset_index(drop=True) # df = df.loc[ # ~df.mut_type.str.contains("ins") & # ~df.mut_type.str.contains("del") & # ~df.mut_type.str.contains(":"), :].reset_index(drop=True) # # splits = # # if self.split != 'all' and (cfg.reduce != 'prot' or self.split != 'train'): # self.wt_names = splits[split] # # # # local.yaml # data_loc: # megascale_csv: "/Processed_K50_dG_datasets/Tsuboyama2023_Dataset2_Dataset3_20230416.csv" with open("data/ThermoMPNN/dataset_splits/mega_splits.pkl", "rb") as f: mega_splits = pickle.load(f) splits = [] for split_name, split_ids in mega_splits.items(): splits.append( pandas.DataFrame({ 'split_name': split_name, 'id': split_ids})) splits = pandas.concat(splits) splits.reset_index(drop=True, inplace=True) pyarrow.parquet.write_table( pyarrow.Table.from_pandas(splits), where = "intermediate/ThermoMPNN_splits.parquet") parquet_file = pyarrow.parquet.ParquetFile('intermediate/ThermoMPNN_splits.parquet') parquet_file.metadata # # created_by: parquet-cpp-arrow version 17.0.0 # num_columns: 2 # num_rows: 2020 # num_row_groups: 1 # format_version: 2.6 # serialized_size: 1881