fix bug regarding overwrite in tools, replace MEME tomtom with tanger…

…meme
buenrostrolab · Nov 26, 2024 · f7ae125 · f7ae125
1 parent 7edd525
commit f7ae125
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Showing 3 changed files with 14 additions and 10 deletions.
diff --git a/scprinter/datasets.py b/scprinter/datasets.py
@@ -84,7 +84,7 @@ def datasets():
                 "gencode_vM30_GRCm39.gff3.gz": "sha256:6f433e2676e26569a678ce78b37e94a64ddd50a09479e433ad6f75e37dc82e48",
                 "gencode_vM30_GRCm39.fa.gz": "sha256:3b923c06a0d291fe646af6bf7beaed7492bf0f6dd5309d4f5904623cab41b0aa",
                 # Tutorial files
-                "BMMCTutorial.zip": "md5:d9027cf73b558d03276483384ddad88c",
+                "scprinter_BMMCTutorial.zip": "md5:d9027cf73b558d03276483384ddad88c",
                 # Blacklist file
                 "hg38-blacklist.v2.bed.gz": "md5:83fe6bf8187a64dee8079b80f75ba289",
                 "mm10-blacklist.v2.bed.gz": "md5:4ae47e40309533c2a71de55494cda9bc",
@@ -128,7 +128,7 @@ def datasets():
                 # Blacklist file
                 "hg38-blacklist.v2.bed.gz": "https://github.com/Boyle-Lab/Blacklist/raw/master/lists/hg38-blacklist.v2.bed.gz",
                 "mm10-blacklist.v2.bed.gz": "https://github.com/Boyle-Lab/Blacklist/raw/master/lists/mm10-blacklist.v2.bed.gz",
-                "BMMCTutorial.zip": "https://drive.google.com/uc?export=download&confirm=s5vl&id=1L-9yPkNKf-IcWgubfp2Yz2oYusEVEico",
+                "scprinter_BMMCTutorial.zip": "https://zenodo.org/records/14164466/files/scprinter_BMMCTutorial.zip",
             },
         )
     return _datasets
@@ -238,7 +238,7 @@ def BMMCTutorial():
     -------
     str: path to the BMMC Tutorial data
     """
-    files = datasets().fetch("BMMCTutorial.zip", processor=giverightstothegroup)
+    files = datasets().fetch("scprinter_BMMCTutorial.zip", processor=giverightstothegroup)
     dict1 = {}
     for f in files:
         if "bed" in f:

diff --git a/scprinter/seq/Models.py b/scprinter/seq/Models.py
@@ -1,5 +1,6 @@
 from copy import deepcopy
 
+import torch
 import wandb
 from sklearn.linear_model import LinearRegression
 from tqdm.auto import tqdm, trange
@@ -742,10 +743,12 @@ def fit(
                 scaler.scale(loss).backward()
                 moving_avg_loss += loss_footprint.item()
                 if (iteration + 1) % accumulate_grad == 0:
-                    # scaler.unscale_(
-                    #     optimizer
-                    # )  # Unscale gradients for clipping without inf/nan gradients affecting the model
-                    # torch.nn.utils.clip_grad_norm_(self.parameters(), max_norm=5.0)  # Adjust max_norm accordingly
+                    scaler.unscale_(
+                        optimizer
+                    )  # Unscale gradients for clipping without inf/nan gradients affecting the model
+                    torch.nn.utils.clip_grad_norm_(
+                        self.parameters(), max_norm=1.0
+                    )  # Adjust max_norm accordingly
 
                     scaler.step(optimizer)
                     scaler.update()

diff --git a/scprinter/tools.py b/scprinter/tools.py
@@ -2177,6 +2177,7 @@ def seq_denovo_seq2print(
     n_seqlets=1000000,
     modisco_window=1000,
     leiden_resolution=1,
+    leiden_solver="modularity",
     save_path: str | Path = None,
     overwrite=False,
     verbose=False,
@@ -2267,6 +2268,7 @@ def seq_denovo_seq2print(
             n=n_seqlets,
             w=modisco_window,
             resolution=leiden_resolution,
+            solver=leiden_solver,
             launch=launch,
         )
 
@@ -2347,6 +2349,7 @@ def modisco_helper(
     n=1000000,
     w=1000,
     resolution=1.0,
+    solver="modularity",
     verbose=False,
     launch=False,
 ):
@@ -2363,9 +2366,7 @@ def modisco_helper(
         hypo = hypo_path
     else:
         hypo = hypo[0]
-    command = (
-        f"seq2print_modisco motifs -s {ohe} -a {hypo} -n {n} -o {output} -w {w} -r {resolution}"
-    )
+    command = f"seq2print_modisco motifs -s {ohe} -a {hypo} -n {n} -o {output} -w {w} -r {resolution} --solver {solver}"
     if verbose:
         if launch:
             print(launch_template)