corrigé la gestion des position des variations

inference.py

 from Graph_gff import Features,load_intersect
 from Functions import get_segment_sequence,convert_strand
 
-target_genome_name="genome2_chr10"
+target_genome_name="genome5_chr10"
 
 intersect_path='intersect.bed'
 load_intersect(intersect_path)
 
-pos_seg="genome2_chr10.bed"
+pos_seg="genome5_chr10.bed"
 
-var=open("genome2_chr10_variations.txt",'r')
+var=open("genome5_chr10_variations.txt",'r')
 
 gfa="graph.gfa"
 def get_segments_sequence_and_paths(gfa):
@@ -305,7 +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[1])%3==0: # taille diff 3k, position 3k
+                if (posVar[0])%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])
@@ -316,8 +316,8 @@ for cds_id in cds_var.keys():
 
 
                     len_fragment_after=(3-length_ref)%3
-                    deleted_aa=traduction(get_rna(cds.sequence[posVar[1]:posVar[1]+length_ref+len_fragment_after]))
-                    inserted_aa=traduction(get_rna(sequence_target[posVar[2]:posVar[2]+length_alt+len_fragment_after]))
+                    deleted_aa=traduction(get_rna(cds.sequence[posVar[0]:posVar[0]+length_ref+len_fragment_after]))
+                    inserted_aa=traduction(get_rna(sequence_target[posVar[1]:posVar[1]+length_alt+len_fragment_after]))
 
                     if (length_ref!=0) & (length_alt!=0):
                         if deleted_aa!=inserted_aa:
@@ -339,11 +339,11 @@ for cds_id in cds_var.keys():
                     else:
                         print(type_var,"de",var[9],"par",var[10])
 
-                    len_fragment_before=(posVar[1])%3
+                    len_fragment_before=(posVar[0])%3
                     len_fragment_after=(3-(len_fragment_before+length_ref))%3
 
-                    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]
+                    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]
 
                     deleted_aa=traduction(get_rna(total_del))
                     inserted_aa=traduction(get_rna(total_ins))
@@ -379,11 +379,10 @@ for cds_id in cds_var.keys():
                 print(frame_shift)
 
 
-
-            if posVar[1]<3: # pour l'instant on cherche pas d'autre start.
+            if posVar[0]<=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
+                #break