more comments

primers_generation.py

@@ -74,29 +74,34 @@ def select_primers(primers_list: list, number_assembly: int) -> list:
     primers needs to not hybridize with each other
     """
     selected_primers_list = []
-    
+       
     
     def test_hybridation(primer: str, selected_primers_list: list, max_hybridisation_value=4) -> bool:
         """
         test the hybridisation of the primer with a list of other primers
         """
-        primer_rc = dfr.reverse_complement(primer)
+        primer_rc = dfr.reverse_complement(primer) # get the reverse complement of the primer
+        
         for selected_primer in selected_primers_list:
+            
             for i in range(len(primer)-max_hybridisation_value):
+                # test if any part of the primer is contained in another primer from the list (= hybridisation)
                 if primer[i:i+max_hybridisation_value+1] in selected_primer:
                     return False
+                # test also for the reverse complement
                 if primer_rc[i:i+max_hybridisation_value+1] in selected_primer:
                     return False
-        
+        # return true if no hybridisation at all
         return True
     
     
     def compare_GC(primer_A: str, primer_B: str) -> bool:   
         """
         primers have a special temperature in PCR depending on %GC, a couple (start;stop) needs to have a close tmp, so the same %GC is better
+        return true if the %GC is the same for the 2 primers
         """
-        start_GC = (primer_A.count("C") + primer_A.count("G"))/(primer_A.count("A")+primer_A.count("T"))
-        stop_GC = (primer_B.count("C") + primer_B.count("G"))/(primer_B.count("A")+primer_B.count("T"))
+        start_GC = (primer_A.count("C") + primer_A.count("G"))/(primer_A.count("A")+primer_A.count("T")) # get the %GC of the first primer
+        stop_GC = (primer_B.count("C") + primer_B.count("G"))/(primer_B.count("A")+primer_B.count("T")) # get the %GC of the second primer
         return start_GC == stop_GC
     
     
@@ -110,19 +115,20 @@ def select_primers(primers_list: list, number_assembly: int) -> list:
                     # the primer must not hybridise with any previous selected primers
                     if test_hybridation(potential_stop_primer, selected_primers_list, 4):
                         
-                        selected_primers_list += [potential_start_primer, potential_stop_primer] # add the couple
+                        selected_primers_list += [potential_start_primer, potential_stop_primer] # add the couple to the list
                         print(str(len(selected_primers_list)//2)+"/"+str(number_assembly))   
                         
-                        # all required primers have been selected
+                        # if all required primers have been selected
                         if len(selected_primers_list) == number_assembly*2:
                             #print(selected_primers_list)
-                            return selected_primers_list
+                            return selected_primers_list # end the script with the result
                         
+                        # the corresponding stop primer has been found
                         break # return to start primers search
     
     # not enough couple of primers found
     print("error in fragment design : not enough correct primers couple found, found",str(len(selected_primers_list)),"but wanted",str(number_assembly*2))
-    print("can be solved by using a longer random sequence in primers_generation")
+    print("can be solved by using a longer random sequence in primers_generation to have a longer primer list ")
     
     return selected_primers_list