[FIX] ensure orthologGroup at the MRCA of all genes

this was not always the case, i.e. if only at a later stage on
the species tree traversal, two subhog were put together although
they came from the same sub clade of the taxonomy.

Author: alpae

FastOMA/_hog_class.py

@@ -337,10 +337,17 @@ def _sorter_key(sh):
         elif len(element_list) > 1:
             #hog_elemnt = ET.Element('orthologGroup', attrib={"id": str(self._hogid)})
             hog_elemnt = ET.Element('orthologGroup', attrib={"id": str(self._hogid)}, )
-            num_species_tax_hog = len(set([i.split("||")[1] for i in self._members]))  #  'tr|H2MU14|H2MU14_ORYLA||ORYLA||1056022282'
-            completeness_score = round(num_species_tax_hog/self._tax_now.size, 4)
+            species_of_members = set([i.split("||")[1] for i in self._members])  #  'tr|H2MU14|H2MU14_ORYLA||ORYLA||1056022282'
+            num_species_tax_hog = len(species_of_members)
+            mrca = self.taxlevel.get_common_ancestor(
+                *[self.taxlevel.search_nodes(name=x)[0] for x in species_of_members])
+            if mrca != self.taxlevel:
+                logger.info(f"mrca ({mrca.name}) != self.taxlevel ({self.taxlevel.name})")
+                logger.info(f"<{hog_elemnt.tag} {hog_elemnt.attrib}>")
+
+            completeness_score = round(num_species_tax_hog/mrca.size, 4)
             property_element = ET.SubElement(hog_elemnt, "score", attrib={"id": "CompletenessScore", "value": str(completeness_score)})
-            property_element = ET.SubElement(hog_elemnt, "property", attrib={"name": "TaxRange", "value": str(self._tax_now.name)})
+            property_element = ET.SubElement(hog_elemnt, "property", attrib={"name": "TaxRange", "value": str(mrca.name)})
 
             for element in element_list:
                 hog_elemnt.append(element)