added prints

primers_generation_V2.py

@@ -20,8 +20,8 @@ use the dna_storage_primer_tools script from
 """
 
 #TODO
-param_file_name = "param_dnarxiv_bigBlocks"
-#param_file_name = "param_dnarxiv_V2"
+#param_file_name = "param_dnarxiv_bigBlocks"
+param_file_name = "param_dnarxiv_V2"
 
 
 def generate_compatible_primers(primer_number: int, output_primers_path=None):
@@ -88,7 +88,7 @@ def filter_primers_with_oligos(oligo_path, input_primers_path=None, output_filte
     checked_primers_dict = dict((name, primer) for name, primer in primers_dict.items() if sequence_control.sequence_check(primer)) # check for potential constraints in primers
 
     #random.shuffle(checked_primers_list)
-
+    print(str(len(checked_primers_dict))+" primers remaining")
     # save the non hybrided primers
     dfr.save_dict_to_fasta(checked_primers_dict, output_filtered_primers_path)
         
@@ -154,6 +154,9 @@ def get_pair_with_lowest_temp_diff(compatible_primers_list):
             best_primer_couple = primer_a, primer_b
             lowest_temp_diff = pair_temp_diff
 
+    if best_primer_couple == ("", ""):
+        print("get_pair_with_lowest_temp_diff: no compatible primer couple found")
+
     return best_primer_couple
 
 
@@ -186,14 +189,20 @@ def get_pair_with_closest_temp(compatible_primers_list, other_primers_dict):
                 best_primer_couple = primer_a, primer_b
                 lowest_temp_diff = pair_temp_diff
 
+
+    if best_primer_couple == ("", ""):
+        print("get_pair_with_closest_temp: no compatible primer couple found")
+        print(compatible_primers_list)
+
     return best_primer_couple
 
 
-def get_best_compatible_pair(source_primers_dict = None, other_primers_dict = None) -> list:
+def get_best_compatible_pair(source_primers_dict = None, other_primers_dict = None, only_compatible_temp = False) -> list:
     """
     select a list of primers (2 primers for each assembly)
     output primers needs to not hybridize with each other
     can add a dict of other primers that the result has to be compatible with
+    param:only_compatible_temp if you don't need to check hybridation & GC with the others primers
     """
 
     primer_generator_dir = currentdir+"/dna-storage-primer-tools"
@@ -205,11 +214,17 @@ def get_best_compatible_pair(source_primers_dict = None, other_primers_dict = No
 
     compatible_primers_list = [] # list of intercompatible primers groups found
 
-    primers_keys = [] # list of primers names that do not hybridize with any of the other primers
+    primers_keys = [] # list of primers names that do not hybridize with any of the other previous primers
+    # primers_keys = [primer_name for primer_name in source_primers_dict.keys if primer_name not in other_primers_dict.keys()]
+
+
     for primer_name, primer_seq in source_primers_dict.items():
-        if test_hybridation_and_GC(primer_seq, list(other_primers_dict.values()), 4):
+        if test_hybridation_and_GC(primer_seq, list(other_primers_dict.values()), 5) or only_compatible_temp:
             primers_keys.append(primer_name)
 
+    if not primers_keys:
+        print("no compatible primer couple without hybridation found")
+
     # get all group of primers with no inter hybridization
     for index_primer, primer_name in enumerate(primers_keys):
         primer_sequence = source_primers_dict[primer_name]
@@ -226,6 +241,8 @@ def get_best_compatible_pair(source_primers_dict = None, other_primers_dict = No
         if len(compatible_primers_dict) >= 2: # keep groups of at least 2 primers
             compatible_primers_list.append(compatible_primers_dict)
 
+    print("compatibles lists lengths : ")
+    print([len(k.keys()) for k in compatible_primers_list])
     if other_primers_dict == {}:
         # get the pair with the closest temperature
         best_primer_couple = get_pair_with_lowest_temp_diff(compatible_primers_list)
@@ -234,6 +251,7 @@ def get_best_compatible_pair(source_primers_dict = None, other_primers_dict = No
         # get the pair with the closest temperature to the other selected primers
         best_primer_couple = get_pair_with_closest_temp(compatible_primers_list, other_primers_dict)
 
+    print(best_primer_couple)
     selected_primers_dict = {best_primer_couple[0]:source_primers_dict[best_primer_couple[0]], best_primer_couple[1]:source_primers_dict[best_primer_couple[1]]}
 
     return selected_primers_dict