revisions to work with self-median monoploid genome

module1_2/inputData/project-legumes8/Genomes.txt

 #genomeID	genomeName	ancestor	numChr
-64965	Vitis	1	19
-64962	Prunus	1	8
-64734	Quillaja	2	14
-64742	Cercis	3	7
-64767	Sindora	4	12
-64768	Senna	5	13
-64963	Phaseolus	6	11
-64964	Medicago	6	8
+64965	Vitis	6	19
+64962	Prunus	6	8
+64734	Quillaja	5	14
+64742	Cercis	4	7
+64767	Sindora	3	12
+64768	Senna	2	13
+64963	Phaseolus	1	11
+64964	Medicago	1	8

module1_2/src/GeneFamily.py

@@ -154,16 +154,21 @@ class GeneFamily:
                 [leaf1.replace("-", ","), leaf2.replace("-", ","), self.find_other_leaves(leaf1, leaf2, all_leaves)])
             newick_tree = newick_tree.replace(newick_tree[last_left: first_right + 1], leaf_pair)
 
-            print("The order of ancestors: ")
-            print(median_structure[-1])
-            #  print(newick_tree)
+            
+            #print(median_structure)
+            #print(newick_tree)
+
 
             first_right = newick_tree.find(")")
             last_left = newick_tree.rfind("(", 0, first_right)
 
             # print("FR "+str(first_right))
             # print("LL "+str(last_left))
-
+          
+        print("Confirm ancestors:")            
+        for median in median_structure: print(median)
+        print()
+        
         try:
             neighbours = newick_tree[last_left + 1: first_right].replace(" ", "")
             leaf1, leaf2 = neighbours.split(",")
@@ -200,9 +205,12 @@ class GeneFamily:
         leaves_to_remove = leaves1 + leaves2
 
         other_leaves = [leaf[0] for leaf in all_leaves if leaf[0] not in leaves_to_remove]
-
-        # print(leaves_to_remove)
-        # print(other_leaves)
+        #print("all leaves")
+        #print(all_leaves)
+        #print("leaves to remove")
+        #print(leaves_to_remove)
+        #print("other leaves")
+        #print(other_leaves)
 
         result = ','.join(other_leaves)