Fix Parent Count

VERSION

@@ -1 +1 @@
-0.1.3
+0.1.4

gambitdb/SplitSpecies.py

@@ -85,9 +85,10 @@ def split_high_diameter_species(self):
             if subspecies is not None and not subspecies.empty:
                 # 2+ viable clusters — subspeciate
                 species = pd.concat([species, subspecies], ignore_index=False, sort=False)
-                species.loc[
-                    species["name"] == single_species[1]["name"], "diameter"
-                ] = 0.0
+                parent_name = single_species[1]["name"]
+                parent_count = int((genome_metadata["species"] == parent_name).sum())
+                species.loc[species["name"] == parent_name, "diameter"] = 0.0
+                species.loc[species["name"] == parent_name, "ngenomes"] = parent_count
             elif subspecies is not None and subspecies.empty:
                 # Singleton outliers removed, 1 cluster remains — keep species with recalculated diameter
                 species.loc[
@@ -102,6 +103,8 @@ def split_high_diameter_species(self):
                     genome_metadata["species_taxid"] == single_species[0]
                 ]
                 self.accessions_removed.extend(genome_accessions.index.tolist())
+                genome_metadata.drop(genome_accessions.index, inplace=True)
+                species = species[species["name"] != single_species[1]["name"]]
 
         return species, genome_metadata, self.accessions_removed
 
@@ -183,11 +186,11 @@ def split_single_high_diameter_species_into_subspecies(
                 "All clusters are singletons for species %s, removing entirely",
                 single_species[1]["name"]
             )
-            self.save_small_clusters_accessions_removed(small_clusters, single_species)
+            self.save_small_clusters_accessions_removed(small_clusters, single_species, genome_metadata)
             return None, genome_metadata, single_species
 
         # Always record singleton accessions as removed
-        self.save_small_clusters_accessions_removed(small_clusters, single_species)
+        self.save_small_clusters_accessions_removed(small_clusters, single_species, genome_metadata)
 
         if num_clusters == 1:
             # Single viable cluster remains after removing singletons.
@@ -317,22 +320,14 @@ def create_subspecies_from_clusters(
 
         return subspecies, genome_metadata, single_species
 
-    def save_small_clusters_accessions_removed(self, small_clusters, single_species):
+    def save_small_clusters_accessions_removed(self, small_clusters, single_species, genome_metadata):
         """
-        Saves the accessions of small clusters to a file.
-        Args:
-          small_clusters (DataFrame): A DataFrame containing the small clusters.
-          single_species (DataFrame): A DataFrame containing the single species.
-        Returns:
-          None
-        Side Effects:
-          Updates the accessions_removed attribute.
-        Examples:
-          >>> save_small_clusters_accessions_removed(small_clusters, single_species)
+        Records singleton/small-cluster accessions as removed and drops them from genome_metadata
+        so downstream counts reflect the post-removal state.
         """
-        # save the accessions of the small clusters to a file
         small_clusters_accessions = small_clusters["assembly_accession"].tolist()
         self.accessions_removed = self.accessions_removed + small_clusters_accessions
+        genome_metadata.drop(small_clusters_accessions, inplace=True)
 
         self.logger.debug(
             "Remove small clusters: "

gambitdb/tests/SplitSpecies_test.py

@@ -91,6 +91,14 @@ def test_split_species(self):
         self.assertEqual(s.shape[0], 5)
         self.assertEqual(g.shape[0], 13)
         self.assertEqual(len(accessions_removed), 0)
+        # Parent species 'Yellow black' was subspeciated; its genomes are
+        # reassigned to the subspecies rows, so parent ngenomes must be 0.
+        parent_row = s[s['name'] == 'Yellow black']
+        self.assertEqual(len(parent_row), 1)
+        self.assertEqual(int(parent_row['ngenomes'].iloc[0]), 0)
+        self.assertEqual(float(parent_row['diameter'].iloc[0]), 0.0)
+        # No genomes in genome_metadata should still be labeled with the parent name.
+        self.assertEqual((g['species'] == 'Yellow black').sum(), 0)
 
     def test_two_genome_high_diameter_species_removed(self):
         """
@@ -107,12 +115,15 @@ def test_two_genome_high_diameter_species_removed(self):
                           1, 'average', False)
         s, g, accessions_removed = ss.split_high_diameter_species()
         # Yellow black (2 genomes, diameter 0.9) should be removed entirely
-        # Remaining: Yellow white + Yellow genus = 2 species rows, diameter set to 0.0 for Yellow black
+        # Remaining: Yellow white + Yellow genus = 2 species rows
         self.assertNotIn('Yellow black subspecies', ' '.join(s['name'].tolist()))
-        # GCA_1 and GCA_2 should be in accessions_removed
+        self.assertNotIn('Yellow black', s['name'].tolist())
+        # Both genomes should be removed from genome_metadata and recorded in accessions_removed
         self.assertIn('GCA_1', accessions_removed)
         self.assertIn('GCA_2', accessions_removed)
         self.assertEqual(len(accessions_removed), 2)
+        self.assertNotIn('GCA_1', g.index)
+        self.assertNotIn('GCA_2', g.index)
 
     def test_singleton_outliers_removed_species_kept(self):
         """
@@ -145,6 +156,11 @@ def test_singleton_outliers_removed_species_kept(self):
         self.assertEqual(int(red_black['ngenomes'].iloc[0]), 3)
         # No subspecies should have been created
         self.assertNotIn('subspecies', ' '.join(s['name'].tolist()))
+        # Singleton outliers GCA_4 and GCA_5 should have been physically dropped
+        # from genome_metadata (8 original rows - 2 removed = 6).
+        self.assertEqual(g.shape[0], 6)
+        self.assertNotIn('GCA_4', g.index)
+        self.assertNotIn('GCA_5', g.index)
 
     def test_all_singletons_species_removed(self):
         """
@@ -193,6 +209,11 @@ def test_all_singletons_species_removed(self):
             self.assertIn('GCA_1', accessions_removed)
             self.assertIn('GCA_2', accessions_removed)
             self.assertIn('GCA_3', accessions_removed)
+            # Species row should be dropped entirely; genomes dropped from metadata
+            self.assertNotIn('All apart', s['name'].tolist())
+            self.assertNotIn('GCA_1', g.index)
+            self.assertNotIn('GCA_2', g.index)
+            self.assertNotIn('GCA_3', g.index)
         finally:
             os.unlink(pw_path)
 

gambitdb/tests/data/gambitdb/pw-dists.csv

@@ -0,0 +1,5 @@
+,s2_overlap_s1,s3_partial_overlap_s1,s4_no_overlap,sample1
+s2_overlap_s1,0.0000,0.0000,0.0000,0.0000
+s3_partial_overlap_s1,0.0000,0.0000,0.0000,0.0000
+s4_no_overlap,0.0000,0.0000,0.0000,0.0000
+sample1,0.0000,0.0000,0.0000,0.0000