move filter_blocks outside print_to_file

jcvi/compara/base.py

@@ -50,6 +50,10 @@ def make_ranges(self, order, clip=10):
         return ranges, block_pairs
 
     def filter_blocks(self, accepted: Dict[Tuple[str, str], str]):
+        """
+        Filter the blocks based on the accepted pairs. This is used to update
+        the anchors so that they match the info in the LAST file.
+        """
         new_blocks = []
         nremoved = 0
         ncorrected = 0
@@ -76,12 +80,14 @@ def filter_blocks(self, accepted: Dict[Tuple[str, str], str]):
         if nblocks_removed:
             logger.debug("Removed %d empty blocks", nblocks_removed)
         logger.debug("Corrected scores for %d anchors", ncorrected)
-        return new_blocks
+        self.blocks = new_blocks
 
-    def print_to_file(self, filename="stdout", accepted=None):
+    def print_to_file(self, filename="stdout"):
+        """
+        Print the anchors to a file, optionally filtering them based on the
+        accepted pairs.
+        """
         fw = must_open(filename, "w")
-        if accepted:
-            self.blocks = self.filter_blocks(accepted)
         for block in self.blocks:
             print("###", file=fw)
             for line in block:

jcvi/compara/synteny.py

@@ -1871,7 +1871,9 @@ def liftover(args):
 
     logger.debug("%d new pairs found (dist=%d).", lifted, dist)
     newanchorfile = anchor_file.rsplit(".", 1)[0] + ".lifted.anchors"
-    ac.print_to_file(filename=newanchorfile, accepted=accepted)
+    if accepted:
+        ac.filter_blocks(accepted)
+    ac.print_to_file(filename=newanchorfile)
     summary([newanchorfile])
 
     return newanchorfile