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update: remove relative path references in data directory configurations across multiple analysis scripts
1 parent 7680781 commit 515394d

4 files changed

Lines changed: 16 additions & 28 deletions

notebooks/astex_method_interaction_analysis_plotting_slurm.py

Lines changed: 5 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -65,7 +65,6 @@
6565
)
6666

6767
ad_set_dir = os.path.join(
68-
"..",
6968
"data",
7069
"astex_diverse_set",
7170
)
@@ -256,9 +255,9 @@ def signal_handler(signum, frame):
256255
"dataset": dataset,
257256
"relax_protein": relax_protein,
258257
"pocket_only_baseline": pocket_only_baseline,
259-
"input_data_dir": os.path.join("..", "data", f"{dataset}_set"),
260-
"posebusters_ccd_ids_filepath": os.path.join("..", "data", "posebusters_pdb_ccd_ids.txt"),
261-
"dockgen_test_ids_filepath": os.path.join("..", "data", "dockgen_set", "split_test.txt"),
258+
"input_data_dir": os.path.join("data", f"{dataset}_set"),
259+
"posebusters_ccd_ids_filepath": os.path.join("data", "posebusters_pdb_ccd_ids.txt"),
260+
"dockgen_test_ids_filepath": os.path.join("data", "dockgen_set", "split_test.txt"),
262261
}
263262
)
264263

@@ -289,12 +288,10 @@ def signal_handler(signum, frame):
289288
cfg.method = method
290289
cfg.repeat_index = repeat_index
291290
cfg.input_csv_path = str(
292-
".."
293-
/ Path(resolve_method_input_csv_path(method, dataset, pocket_only_baseline))
291+
Path(resolve_method_input_csv_path(method, dataset, pocket_only_baseline))
294292
)
295293
cfg.output_dir = str(
296-
".."
297-
/ Path(
294+
Path(
298295
resolve_method_output_dir(
299296
method,
300297
dataset,

notebooks/casp15_method_interaction_analysis_plotting_slurm.py

Lines changed: 0 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -61,7 +61,6 @@
6161
)
6262

6363
casp15_set_dir = os.path.join(
64-
"..",
6564
"data",
6665
"casp15_set",
6766
"targets",
@@ -264,7 +263,6 @@ def signal_handler(signum, frame):
264263

265264
if not os.path.exists(f"{method}_{dataset}_interaction_dataframes_{repeat_index}.h5"):
266265
method_casp15_set_dir = os.path.join(
267-
"..",
268266
"data",
269267
"test_cases",
270268
"casp15",

notebooks/dockgen_method_interaction_analysis_plotting_slurm.py

Lines changed: 6 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -65,7 +65,6 @@
6565
)
6666

6767
dg_set_dir = os.path.join(
68-
"..",
6968
"data",
7069
"dockgen_set",
7170
)
@@ -203,7 +202,7 @@ def signal_handler(signum, frame):
203202
# %%
204203
if not os.path.exists("dockgen_interaction_dataframes.h5"):
205204
dockgen_test_ids_filepath = os.path.join(
206-
"..", "data", "dockgen_set", "split_test.txt"
205+
"data", "dockgen_set", "split_test.txt"
207206
) # NOTE: change as needed
208207
assert os.path.exists(
209208
dockgen_test_ids_filepath
@@ -269,9 +268,9 @@ def signal_handler(signum, frame):
269268
"dataset": dataset,
270269
"relax_protein": relax_protein,
271270
"pocket_only_baseline": pocket_only_baseline,
272-
"input_data_dir": os.path.join("..", "data", f"{dataset}_set"),
273-
"posebusters_ccd_ids_filepath": os.path.join("..", "data", "posebusters_pdb_ccd_ids.txt"),
274-
"dockgen_test_ids_filepath": os.path.join("..", "data", "dockgen_set", "split_test.txt"),
271+
"input_data_dir": os.path.join("data", f"{dataset}_set"),
272+
"posebusters_ccd_ids_filepath": os.path.join("data", "posebusters_pdb_ccd_ids.txt"),
273+
"dockgen_test_ids_filepath": os.path.join("data", "dockgen_set", "split_test.txt"),
275274
}
276275
)
277276

@@ -302,12 +301,10 @@ def signal_handler(signum, frame):
302301
cfg.method = method
303302
cfg.repeat_index = repeat_index
304303
cfg.input_csv_path = str(
305-
".."
306-
/ Path(resolve_method_input_csv_path(method, dataset, pocket_only_baseline))
304+
Path(resolve_method_input_csv_path(method, dataset, pocket_only_baseline))
307305
)
308306
cfg.output_dir = str(
309-
".."
310-
/ Path(
307+
Path(
311308
resolve_method_output_dir(
312309
method,
313310
dataset,

notebooks/posebusters_method_interaction_analysis_plotting_slurm.py

Lines changed: 5 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -66,7 +66,6 @@
6666
method_max_training_cutoff_date = "2021-09-30"
6767

6868
pb_set_dir = os.path.join(
69-
"..",
7069
"data",
7170
"posebusters_benchmark_set",
7271
)
@@ -222,7 +221,6 @@ def signal_handler(signum, frame):
222221
# %%
223222
if not os.path.exists("posebusters_benchmark_interaction_dataframes.h5"):
224223
posebusters_ccd_ids_filepath = os.path.join(
225-
"..",
226224
"data",
227225
"posebusters_pdb_ccd_ids.txt",
228226
)
@@ -287,9 +285,9 @@ def signal_handler(signum, frame):
287285
"dataset": dataset,
288286
"relax_protein": relax_protein,
289287
"pocket_only_baseline": pocket_only_baseline,
290-
"input_data_dir": os.path.join("..", "data", f"{dataset}_set"),
291-
"posebusters_ccd_ids_filepath": os.path.join("..", "data", "posebusters_pdb_ccd_ids.txt"),
292-
"dockgen_test_ids_filepath": os.path.join("..", "data", "dockgen_set", "split_test.txt"),
288+
"input_data_dir": os.path.join("data", f"{dataset}_set"),
289+
"posebusters_ccd_ids_filepath": os.path.join("data", "posebusters_pdb_ccd_ids.txt"),
290+
"dockgen_test_ids_filepath": os.path.join("data", "dockgen_set", "split_test.txt"),
293291
}
294292
)
295293

@@ -320,12 +318,10 @@ def signal_handler(signum, frame):
320318
cfg.method = method
321319
cfg.repeat_index = repeat_index
322320
cfg.input_csv_path = str(
323-
".."
324-
/ Path(resolve_method_input_csv_path(method, dataset, pocket_only_baseline))
321+
Path(resolve_method_input_csv_path(method, dataset, pocket_only_baseline))
325322
)
326323
cfg.output_dir = str(
327-
".."
328-
/ Path(
324+
Path(
329325
resolve_method_output_dir(
330326
method,
331327
dataset,

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