updated site scanning

Author: lala8

src/polygraph/models.py

@@ -288,7 +288,7 @@ def ism_score(model, seqs, batch_size, device="cpu", task=None):
         if preds.ndim == 2:
             preds = preds.mean(1, keepdims=True)
     else:
-        preds = preds[:, [task]]
+        preds = preds[:, task]
 
     # Mutate sequences
     ism = ISM(seqs)  # N x L x 4
@@ -308,7 +308,7 @@ def ism_score(model, seqs, batch_size, device="cpu", task=None):
     ism_preds = ism_preds.max(-1)
 
     # Compute base-level importance score
-    preds = np.abs(ism_preds - preds)
+    preds = np.abs(ism_preds - np.expand_dims(preds, 1))
     return preds
 
 

src/polygraph/motifs.py

@@ -50,8 +50,12 @@ def scan(seqs, meme_file, group_col="Group", pthresh=1e-3, rc=True):
         for m in match:
             out["MotifID"].append(motif.name.decode())
             out["SeqID"].append(m.source.accession.decode())
-            out["start"].append(m.start)
-            out["end"].append(m.stop)
+            if m.strand=='+':
+                out["start"].append(m.start)
+                out["end"].append(m.stop)
+            else:
+                out["end"].append(m.start)
+                out["start"].append(m.stop)
             out["strand"].append(m.strand)
 
     return pd.DataFrame(out).merge(seqs[[group_col]], left_on="SeqID", right_index=True)