sort by descending weight

src/jcvi/projects/sugarcane.py

@@ -208,20 +208,29 @@ def make(cls, name: str, chromosomes: List[Chromosome]) -> "Genome":
     def _sort_key(self, x: Chromosome):
         return x.subgenome, x.chrom
 
-    def pair_chromosomes(
-        self, inplace=False
-    ) -> Tuple[List[List[Chromosome]], List[Chromosome]]:
+    def pair_with_weights(self) -> List[List[str]]:
         """
-        Pair chromosomes by similarity.
+        Pair chromosomes by similarity, results are sorted in descending similarity.
         """
         G = nx.Graph()
+        scores = {}
         self.chromosomes.sort(key=self._sort_key)
         for _, chromosomes in groupby(self.chromosomes, key=self._sort_key):
             for a, b in combinations(chromosomes, 2):
                 weight = a.num_matching_genes(b) + 1  # +1 so we don't have zero weight
                 G.add_edge(a.uuid, b.uuid, weight=weight)
+                scores[tuple(sorted((a.uuid, b.uuid)))] = weight
         # Find the maximum matching
         matching = nx.max_weight_matching(G)
+        return sorted(matching, key=lambda x: scores[tuple(sorted(x))], reverse=True)
+
+    def pair_chromosomes(
+        self, inplace=False
+    ) -> Tuple[List[List[Chromosome]], List[Chromosome]]:
+        """
+        Pair chromosomes by similarity.
+        """
+        matching = self.pair_with_weights()
         # Partition the chromosomes into paired and singleton
         paired = set()
         pairs = []