modifié la gestion des positions des variations

inference.py

@@ -289,8 +289,7 @@ for cds_id in cds_var.keys():
     for var in cds_var[cds_id]:
         type_var=var[8]
         if type_var!="no_var": # if there is a variation
-            posVar_on_ref=int(var[12])
-            posVar_on_alt=int(var[13])
+            posVar=[int(var[12]),int(var[13])]
             sequence_target=get_sequence_on_genome(cds_id,segments_on_target_genome)
 
             if type_var=="insertion":
@@ -306,7 +305,7 @@ for cds_id in cds_var.keys():
 
             if abs(length_alt-length_ref)%3 == 0: # taille diff 3k -> pas de frame shift.
 
-                if (posVar_on_ref)%3==0: # taille diff 3k, position 3k
+                if (posVar[1])%3==0: # taille diff 3k, position 3k
                     print("variation entre deux codons sans décalage du cadre de lecture")
                     if type_var=="insertion":
                         print(type_var,"de",var[10])
@@ -317,8 +316,8 @@ for cds_id in cds_var.keys():
 
 
                     len_fragment_after=(3-length_ref)%3
-                    deleted_aa=traduction(get_rna(cds.sequence[posVar_on_ref:posVar_on_ref+length_ref+len_fragment_after]))
-                    inserted_aa=traduction(get_rna(sequence_target[posVar_on_alt:posVar_on_alt+length_alt+len_fragment_after]))
+                    deleted_aa=traduction(get_rna(cds.sequence[posVar[1]:posVar[1]+length_ref+len_fragment_after]))
+                    inserted_aa=traduction(get_rna(sequence_target[posVar[2]:posVar[2]+length_alt+len_fragment_after]))
 
                     if (length_ref!=0) & (length_alt!=0):
                         if deleted_aa!=inserted_aa:
@@ -340,11 +339,11 @@ for cds_id in cds_var.keys():
                     else:
                         print(type_var,"de",var[9],"par",var[10])
 
-                    len_fragment_before=(posVar_on_ref)%3
+                    len_fragment_before=(posVar[1])%3
                     len_fragment_after=(3-(len_fragment_before+length_ref))%3
 
-                    total_ins=sequence_target[posVar_on_alt-len_fragment_before:posVar_on_alt+length_alt+len_fragment_after]
-                    total_del=cds.sequence[posVar_on_ref-len_fragment_before:posVar_on_ref+length_ref+len_fragment_after]
+                    total_ins=sequence_target[posVar[2]-len_fragment_before:posVar[2]+length_alt+len_fragment_after]
+                    total_del=cds.sequence[posVar[1]-len_fragment_before:posVar[1]+length_ref+len_fragment_after]
 
                     deleted_aa=traduction(get_rna(total_del))
                     inserted_aa=traduction(get_rna(total_ins))
@@ -381,7 +380,7 @@ for cds_id in cds_var.keys():
 
 
 
-            if posVar_on_ref<3: # pour l'instant on cherche pas d'autre start.
+            if posVar[1]<3: # pour l'instant on cherche pas d'autre start.
                 print("codon start touché donc gène non fonctionnel")
                 #findOtherStart(cds,segments_on_target_genome)
                 break