deleted the prints for debug

inference.py

@@ -57,9 +57,6 @@ def add_feature_sequence(feature,seg_seq): # add the feature's sequence in the F
             feature_sequence=get_segment_sequence(seg_seq,segment)[feature.pos_start-2:feature.pos_stop-1]
         if segment==feature.segments_list[0]:
             feature_sequence+=get_segment_sequence(seg_seq,segment)[feature.pos_start-2:] # revérifier les +/- 1 pour la position, avec de vraies données
-            if feature.type=="CDS":
-                print(get_segment_sequence(seg_seq,segment), feature.pos_start)
-                print(feature.segments_list)
         elif segment==feature.segments_list[-1]:
             feature_sequence+=get_segment_sequence(seg_seq,segment)[0:feature.pos_stop-1] # revérifier les +/- 1 pour la position, avec de vraies données
         else:
@@ -260,11 +257,9 @@ segments_on_target_genome=get_segments_positions_on_genome(pos_seg)
 mrna_var=get_mrna_var(var_file)
 for feature in Features.values(): # add the sequence of all features
     add_feature_sequence(feature,seg_seq)
-    if feature.type=="CDS":
-        print(feature.id,feature.sequence)
 
 
-analysis=False
+analysis=True
 if analysis==True:
     # analysing the variations for all the mrna :
     for mrna_id in mrna_var.keys():
@@ -326,13 +321,11 @@ if analysis==True:
 
                     if frameshift==0:
                         # print only the local change.
-                        print(cds.sequence,sequence_target)
                         len_fragment_after_del=(3-(len_fragment_before_del+length_ref))%3
                         len_fragment_after_ins=(3-(len_fragment_before_ins+length_alt))%3
                         total_ins=sequence_target[posVar[1]-len_fragment_before_ins:posVar[1]+length_alt+len_fragment_after_ins]
                         total_del=cds.sequence[posVar[0]-len_fragment_before_del:posVar[0]+length_ref+len_fragment_after_del]
                         stop=print_variation_change(total_del,total_ins)
-                        print("a",total_del,total_ins)
                         if stop:
                             break
 
@@ -347,13 +340,11 @@ if analysis==True:
                             # en fait non. il faut récupérer les séquences sur les seq des cds (sans l'intron dcp), prendre la taille sur ça et supprimer sur ça
                             del_leftover_len=len(total_total_del)%3
                             ins_leftover_len=len(total_total_ins)%3
-                            print("b",ins_leftover_len,total_total_ins)
                             if del_leftover_len!=0:
                                 total_total_del=total_total_del[0:-del_leftover_len]
                             if ins_leftover_len!=0:
                                 total_total_ins=total_total_ins[0:-ins_leftover_len]
                             stop=print_variation_change(total_total_del,total_total_ins)
-                            print("b",total_total_del,total_total_ins)
                             if stop:
                                 break
                         else: # not the last variation. translate until the next var. 
@@ -374,7 +365,6 @@ if analysis==True:
                             total_total_del=cds.sequence[posVar[0]-len_fragment_before_del:posNextVar[0]-len_fragment_before_del_nextvar]
                             total_total_ins=sequence_target[posVar[1]-len_fragment_before_ins:posNextVar[1]-len_fragment_before_ins_nextvar]
                             stop=print_variation_change(total_total_del,total_total_ins)
-                            print("c",total_total_del,total_total_ins)
                             if stop:
                                 break