move subfunctions, fix print

primers_generation.py

@@ -28,7 +28,7 @@ def generate_compatible_primers(sequence_between: str) -> list:
     
     primer_generator_dir = currentdir+"/primer_generator"
     primers_gen_script = primer_generator_dir+"/bin/primers_gen" # path to the script
-    random_sequence_path = primer_generator_dir+"/data/random_seq_100k.fasta" # some very long random sequences to create the primers from, this sequence respects the biological constraints
+    random_sequence_path = primer_generator_dir+"/data/random_seq_1M.fasta" # some very long random sequences to create the primers from, this sequence respects the biological constraints
     primers_param_path = primer_generator_dir+"/data/param_dnarxiv.txt" # file containing the parameters for the primer_generator scripts
     output_primers_path = primer_generator_dir+"/temp/primers.fasta" # output path for generated primers
     
@@ -53,7 +53,8 @@ def generate_compatible_primers(sequence_between: str) -> list:
     filter_primers_command = primers_filter_script+' '+sequence_between_path+' '+output_primers_path+' '+primers_param_path \
                                     +' '+output_compatible_primers_path+' '+output_hyb+' '+output_dic+' '+output_pos
     subprocess.call('/bin/bash -c "$PRIMERFILTER"', shell=True, env={'PRIMERFILTER': filter_primers_command})
-    
+    print() # needed cause the printer go at the start of the last printed line
+
     primers_list = list(dfr.read_fasta(output_compatible_primers_path).values())
     
     checked_primers_list = [primer for primer in primers_list if sequence_control.sequence_check(primer)] # check for potential constraints in primers
@@ -68,6 +69,35 @@ def generate_compatible_primers(sequence_between: str) -> list:
     return checked_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) # 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")) # 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
+
+
 def select_primers(primers_list: list, number_assembly: int) -> list:
     """
     select a list of primers (2 primers for each assembly)
@@ -75,36 +105,6 @@ def select_primers(primers_list: list, number_assembly: int) -> list:
     """
     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) # 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")) # 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
-    
-    
     for index_primer, potential_start_primer in enumerate(primers_list):
         # the primer must not hybridise with any previous selected primers
         if test_hybridation(potential_start_primer, selected_primers_list, 4):