update: remove relative path references in data directory configurations across multiple analysis scripts

Author: amorehead

notebooks/astex_method_interaction_analysis_plotting_slurm.py

@@ -65,7 +65,6 @@
 )
 
 ad_set_dir = os.path.join(
-    "..",
     "data",
     "astex_diverse_set",
 )
@@ -256,9 +255,9 @@ def signal_handler(signum, frame):
         "dataset": dataset,
         "relax_protein": relax_protein,
         "pocket_only_baseline": pocket_only_baseline,
-        "input_data_dir": os.path.join("..", "data", f"{dataset}_set"),
-        "posebusters_ccd_ids_filepath": os.path.join("..", "data", "posebusters_pdb_ccd_ids.txt"),
-        "dockgen_test_ids_filepath": os.path.join("..", "data", "dockgen_set", "split_test.txt"),
+        "input_data_dir": os.path.join("data", f"{dataset}_set"),
+        "posebusters_ccd_ids_filepath": os.path.join("data", "posebusters_pdb_ccd_ids.txt"),
+        "dockgen_test_ids_filepath": os.path.join("data", "dockgen_set", "split_test.txt"),
     }
 )
 
@@ -289,12 +288,10 @@ def signal_handler(signum, frame):
                 cfg.method = method
                 cfg.repeat_index = repeat_index
                 cfg.input_csv_path = str(
-                    ".."
-                    / Path(resolve_method_input_csv_path(method, dataset, pocket_only_baseline))
+                    Path(resolve_method_input_csv_path(method, dataset, pocket_only_baseline))
                 )
                 cfg.output_dir = str(
-                    ".."
-                    / Path(
+                    Path(
                         resolve_method_output_dir(
                             method,
                             dataset,

notebooks/casp15_method_interaction_analysis_plotting_slurm.py

@@ -61,7 +61,6 @@
 )
 
 casp15_set_dir = os.path.join(
-    "..",
     "data",
     "casp15_set",
     "targets",
@@ -264,7 +263,6 @@ def signal_handler(signum, frame):
 
         if not os.path.exists(f"{method}_{dataset}_interaction_dataframes_{repeat_index}.h5"):
             method_casp15_set_dir = os.path.join(
-                "..",
                 "data",
                 "test_cases",
                 "casp15",

notebooks/dockgen_method_interaction_analysis_plotting_slurm.py

@@ -65,7 +65,6 @@
 )
 
 dg_set_dir = os.path.join(
-    "..",
     "data",
     "dockgen_set",
 )
@@ -203,7 +202,7 @@ def signal_handler(signum, frame):
 # %%
 if not os.path.exists("dockgen_interaction_dataframes.h5"):
     dockgen_test_ids_filepath = os.path.join(
-        "..", "data", "dockgen_set", "split_test.txt"
+        "data", "dockgen_set", "split_test.txt"
     )  # NOTE: change as needed
     assert os.path.exists(
         dockgen_test_ids_filepath
@@ -269,9 +268,9 @@ def signal_handler(signum, frame):
         "dataset": dataset,
         "relax_protein": relax_protein,
         "pocket_only_baseline": pocket_only_baseline,
-        "input_data_dir": os.path.join("..", "data", f"{dataset}_set"),
-        "posebusters_ccd_ids_filepath": os.path.join("..", "data", "posebusters_pdb_ccd_ids.txt"),
-        "dockgen_test_ids_filepath": os.path.join("..", "data", "dockgen_set", "split_test.txt"),
+        "input_data_dir": os.path.join("data", f"{dataset}_set"),
+        "posebusters_ccd_ids_filepath": os.path.join("data", "posebusters_pdb_ccd_ids.txt"),
+        "dockgen_test_ids_filepath": os.path.join("data", "dockgen_set", "split_test.txt"),
     }
 )
 
@@ -302,12 +301,10 @@ def signal_handler(signum, frame):
                 cfg.method = method
                 cfg.repeat_index = repeat_index
                 cfg.input_csv_path = str(
-                    ".."
-                    / Path(resolve_method_input_csv_path(method, dataset, pocket_only_baseline))
+                    Path(resolve_method_input_csv_path(method, dataset, pocket_only_baseline))
                 )
                 cfg.output_dir = str(
-                    ".."
-                    / Path(
+                    Path(
                         resolve_method_output_dir(
                             method,
                             dataset,

notebooks/posebusters_method_interaction_analysis_plotting_slurm.py

@@ -66,7 +66,6 @@
 method_max_training_cutoff_date = "2021-09-30"
 
 pb_set_dir = os.path.join(
-    "..",
     "data",
     "posebusters_benchmark_set",
 )
@@ -222,7 +221,6 @@ def signal_handler(signum, frame):
 # %%
 if not os.path.exists("posebusters_benchmark_interaction_dataframes.h5"):
     posebusters_ccd_ids_filepath = os.path.join(
-        "..",
         "data",
         "posebusters_pdb_ccd_ids.txt",
     )
@@ -287,9 +285,9 @@ def signal_handler(signum, frame):
         "dataset": dataset,
         "relax_protein": relax_protein,
         "pocket_only_baseline": pocket_only_baseline,
-        "input_data_dir": os.path.join("..", "data", f"{dataset}_set"),
-        "posebusters_ccd_ids_filepath": os.path.join("..", "data", "posebusters_pdb_ccd_ids.txt"),
-        "dockgen_test_ids_filepath": os.path.join("..", "data", "dockgen_set", "split_test.txt"),
+        "input_data_dir": os.path.join("data", f"{dataset}_set"),
+        "posebusters_ccd_ids_filepath": os.path.join("data", "posebusters_pdb_ccd_ids.txt"),
+        "dockgen_test_ids_filepath": os.path.join("data", "dockgen_set", "split_test.txt"),
     }
 )
 
@@ -320,12 +318,10 @@ def signal_handler(signum, frame):
                 cfg.method = method
                 cfg.repeat_index = repeat_index
                 cfg.input_csv_path = str(
-                    ".."
-                    / Path(resolve_method_input_csv_path(method, dataset, pocket_only_baseline))
+                    Path(resolve_method_input_csv_path(method, dataset, pocket_only_baseline))
                 )
                 cfg.output_dir = str(
-                    ".."
-                    / Path(
+                    Path(
                         resolve_method_output_dir(
                             method,
                             dataset,