Run black formatting on hpc-modules.py.

aertslab · Nov 21, 2022 · b69accb · b69accb
1 parent 8ad6ca9
commit b69accb
Showing 1 changed file with 50 additions and 18 deletions.
diff --git a/scripts/hpc-modules.py b/scripts/hpc-modules.py
@@ -8,7 +8,7 @@
 
 from pyscenic.utils import modules_from_adjacencies
 
-RESOURCES_FOLDER="."
+RESOURCES_FOLDER = "."
 RHO_THRESHOLDS = [0.03, 0.1, 0.3]
 MODULES_EXT = "modules.dat"
 EXP_MTX_EXT = "mtx.tsv"
@@ -23,44 +23,76 @@ def exp_mtx_fname(name):
     return os.path.join(RESOURCES_FOLDER, "{}.{}".format(name, EXP_MTX_EXT))
 
 
-def calc_modules(adjacencies, exp_mtx, name, rho_dichotomize, rho_threshold=None, mask_dropouts=None):
+def calc_modules(
+    adjacencies, exp_mtx, name, rho_dichotomize, rho_threshold=None, mask_dropouts=None
+):
     if rho_dichotomize:
-        print('{} - {} masking - rho threshold {}'.format(name, "with" if mask_dropouts else "without", rho_threshold))
-
-        out_fname = os.path.join(RESOURCES_FOLDER,
-            "{}.{}.{}".format(name, rho_threshold, MODULES_EXT) if mask_dropouts
-            else "{}.{}.no_mask.{}".format(name, rho_threshold, MODULES_EXT))
+        print(
+            "{} - {} masking - rho threshold {}".format(
+                name, "with" if mask_dropouts else "without", rho_threshold
+            )
+        )
+
+        out_fname = os.path.join(
+            RESOURCES_FOLDER,
+            "{}.{}.{}".format(name, rho_threshold, MODULES_EXT)
+            if mask_dropouts
+            else "{}.{}.no_mask.{}".format(name, rho_threshold, MODULES_EXT),
+        )
     else:
-        print('{} - all'.format(name))
+        print("{} - all".format(name))
 
-        out_fname = os.path.join(RESOURCES_FOLDER, "{}.all.{}".format(name, MODULES_EXT))
+        out_fname = os.path.join(
+            RESOURCES_FOLDER, "{}.all.{}".format(name, MODULES_EXT)
+        )
 
     if os.path.isfile(out_fname):
         return
 
-    modules = list(modules_from_adjacencies(adjacencies, exp_mtx,
-                                            rho_dichotomize=rho_dichotomize,
-                                            rho_threshold=rho_threshold,
-                                            rho_mask_dropouts=mask_dropouts))
+    modules = list(
+        modules_from_adjacencies(
+            adjacencies,
+            exp_mtx,
+            rho_dichotomize=rho_dichotomize,
+            rho_threshold=rho_threshold,
+            rho_mask_dropouts=mask_dropouts,
+        )
+    )
     print(len(modules))
 
-    with open(out_fname, 'wb') as f:
+    with open(out_fname, "wb") as f:
         pickle.dump(modules, f)
 
 
 def run():
-    for fname in glob.glob(os.path.join(RESOURCES_FOLDER, '*.{}'.format(ADJACENCIES_EXT))):
+    for fname in glob.glob(
+        os.path.join(RESOURCES_FOLDER, "*.{}".format(ADJACENCIES_EXT))
+    ):
         name = get_name(fname)
         mtx_fname = exp_mtx_fname(name)
 
         # Load datasets.
         adjacencies = pd.read_csv(fname)
-        exp_mtx = pd.read_csv(mtx_fname, sep='\t', index_col=0).T
+        exp_mtx = pd.read_csv(mtx_fname, sep="\t", index_col=0).T
 
         # Calculate modules.
         for rho_threshold in RHO_THRESHOLDS:
-            calc_modules(adjacencies, exp_mtx, name, rho_dichotomize=True, rho_threshold=rho_threshold, mask_dropouts=False)
-            calc_modules(adjacencies, exp_mtx, name, rho_dichotomize=True, rho_threshold=rho_threshold, mask_dropouts=True)
+            calc_modules(
+                adjacencies,
+                exp_mtx,
+                name,
+                rho_dichotomize=True,
+                rho_threshold=rho_threshold,
+                mask_dropouts=False,
+            )
+            calc_modules(
+                adjacencies,
+                exp_mtx,
+                name,
+                rho_dichotomize=True,
+                rho_threshold=rho_threshold,
+                mask_dropouts=True,
+            )
 
         calc_modules(adjacencies, exp_mtx, name, rho_dichotomize=False)