ajouté la détection des codons stop

inference.py

@@ -266,8 +266,10 @@ def findOtherStart(cds,segments_on_target_genome):
 
 # ajouter la vérification qu'on introduit/delete pas un codon stop
 def print_variation_change(deleted_sequence,inserted_sequence):
+    stop=False
     deleted_aa=traduction(get_rna(deleted_sequence))
     inserted_aa=traduction(get_rna(inserted_sequence))
+
     if (len(deleted_aa)!=0) & (len(inserted_aa)!=0):
         if deleted_aa!=inserted_aa:
             print("conséquence : changement de",",".join(deleted_aa),"en",",".join(inserted_aa))
@@ -277,6 +279,10 @@ def print_variation_change(deleted_sequence,inserted_sequence):
         print("conséquence : insertion de",",".join(inserted_aa))
     else:
         print("conséquence : deletion de",",".join(deleted_aa))
+    if ("*" in inserted_aa):
+        print("apparition d'un codon stop dans le cds du génome cible")
+        stop=True
+    return stop
 
 
 version="new"
@@ -286,7 +292,7 @@ for feature in Features.values():
 
 for cds_id in cds_var.keys():
     cds=Features[cds_id]
-    print("analyse des variations dans le cds",cds_id)
+    print("analyse des variations dans le cds",cds_id,"\n")
     frame_shift=0
     #for var in cds_var[cds_id]:
     for index, var in enumerate(cds_var[cds_id]):
@@ -320,7 +326,9 @@ for cds_id in cds_var.keys():
                     len_fragment_after=(3-length_ref)%3
                     deleted_sequence=cds.sequence[posVar[0]:posVar[0]+length_ref+len_fragment_after]
                     inserted_sequence=sequence_target[posVar[1]:posVar[1]+length_alt+len_fragment_after]
-                    print_variation_change(deleted_sequence,inserted_sequence)
+                    stop=print_variation_change(deleted_sequence,inserted_sequence)
+                    if stop:
+                        break
 
                 else: # taille diff 3k, position !=3k
                     print("variation au milieu d'un codon sans décalage du cadre de lecture")
@@ -337,7 +345,9 @@ for cds_id in cds_var.keys():
                     total_ins=sequence_target[posVar[1]-len_fragment_before:posVar[1]+length_alt+len_fragment_after]
                     total_del=cds.sequence[posVar[0]-len_fragment_before:posVar[0]+length_ref+len_fragment_after]
 
-                    print_variation_change(total_del,total_ins)
+                    stop=print_variation_change(total_del,total_ins)
+                    if stop:
+                        break
                 # possibilité que j'ai print en compte une variation de trop, si on a un snp sur la premiere et la derniere base d'un codon : 
                 # pour le traitement de la première j'ai également considéré la dernière ! 
 
@@ -366,8 +376,10 @@ for cds_id in cds_var.keys():
                     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]
-                    print_variation_change(total_del,total_ins)
+                    stop=print_variation_change(total_del,total_ins)
                     print("rétablissement du cadre de lecture originel")
+                    if stop:
+                        break
 
                 else:
                     # print changes from local to next var
@@ -377,7 +389,9 @@ for cds_id in cds_var.keys():
                     if index==len(cds_var[cds_id])-1: # on est sur la dernière variation. traduire jusqu'à la fin du cds
                         total_total_del=cds.sequence[posVar[0]-len_fragment_before_del:]
                         total_total_ins=sequence_target[posVar[1]-len_fragment_before_ins:]
-                        print_variation_change(total_total_del,total_total_ins)
+                        stop=print_variation_change(total_total_del,total_total_ins)
+                        if stop:
+                            break
                     else: 
                         nextVar=cds_var[cds_id][index+1]
                         posNextVar=[int(nextVar[12]),int(nextVar[13])]
@@ -395,7 +409,9 @@ for cds_id in cds_var.keys():
                         len_fragment_before_ins_nextvar=(posNextVar[1])%3
                         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]
-                        print_variation_change(total_total_del,total_total_ins)
+                        stop=print_variation_change(total_total_del,total_total_ins)
+                        if stop:
+                            break
 
 
 
@@ -405,7 +421,7 @@ for cds_id in cds_var.keys():
 
 
             if posVar[0]<=3: # pour l'instant on cherche pas d'autre start.
-                print("codon start touché donc gène non fonctionnel")
+                print("codon start touché, gène non fonctionnel")
                 #findOtherStart(cds,segments_on_target_genome)
                 break