diff --git a/tests/perf/srv_perf.py b/tests/perf/srv_perf.py index 94be374e..645030cb 100644 --- a/tests/perf/srv_perf.py +++ b/tests/perf/srv_perf.py @@ -88,7 +88,7 @@ def get_pdb_files_and_target_data(data_path: str) -> tuple[list[str], list, list, list, list]: - csv_data = pd.read_csv(os.path.join(data_path, "srv_target_values.csv")) + csv_data = pd.read_csv(os.path.join(data_path, "srv_target_values_curated.csv")) # before running this script change .ent to .pdb pdb_files = glob.glob(os.path.join(data_path, "pdb", "*.pdb")) pdb_files.sort() diff --git a/tutorials/data_generation_srv.ipynb b/tutorials/data_generation_srv.ipynb index a4fb3c16..f8606c7e 100644 --- a/tutorials/data_generation_srv.ipynb +++ b/tutorials/data_generation_srv.ipynb @@ -114,7 +114,7 @@ "metadata": {}, "source": [ "- Raw data are PDB files in `data_raw/srv/pdb/`, which contains atomic coordinates of the protein structure containing the variant.\n", - "- Target data, so in our case pathogenic versus benign labels, are in `data_raw/srv/srv_target_values.csv`.\n", + "- Target data, so in our case pathogenic versus benign labels, are in `data_raw/srv/srv_target_values_curated.csv`.\n", "- The final SRV processed data will be saved in `data_processed/srv/` folder, which in turns contains a folder for residue-level data and another one for atomic-level data. More details about such different levels will come a few cells below.\n" ] }, @@ -133,7 +133,7 @@ "outputs": [], "source": [ "def get_pdb_files_and_target_data(data_path):\n", - " csv_data = pd.read_csv(os.path.join(data_path, \"srv_target_values.csv\"))\n", + " csv_data = pd.read_csv(os.path.join(data_path, \"srv_target_values_curated.csv\"))\n", " pdb_files = glob.glob(os.path.join(data_path, \"pdb\", \"*.ent\"))\n", " pdb_files.sort()\n", " pdb_file_names = [os.path.basename(pdb_file) for pdb_file in pdb_files]\n",