supprimé du vieux code inutilisé

inference.py

@@ -274,6 +274,7 @@ def findOtherStart(cds,segments_on_target_genome):
         start_pos_list=[m.start() for m in re.finditer('(?=ATG)', seq_cds)]
         print("codon start candidat trouvé plus loin dans le cds, à la base",start_pos_list[0]) # print seulement le premier
     print("\n")
+    return frame_shift
 
 
 version="new"
@@ -375,98 +376,3 @@ for cds_id in cds_var.keys():
 
             print("\n")
 
-
-if version=="old":
-    for cds_id in cds_var.keys(): # for a gene that has cds, concatenate all cds to make a prot. then detail var by cds.
-        cds=Features[cds_id]
-        print("analysing variations in cds",cds_id)
-        add_feature_sequence(cds,seg_seq)
-        cds_prot=traduction(get_rna(cds.sequence))
-
-        list_seg=Features[cds_id].segments_list
-        first_seg=get_first_seg(list_seg)
-        last_seg=get_first_seg(reversed(list_seg))
-        path_on_target=get_feature_path(paths,first_seg,last_seg)
-
-        new_sequence=""
-        for segment in path_on_target:
-            if segment==cds.segments_list[0]:
-                new_sequence+=get_segment_sequence(seg_seq,segment)[cds.pos_start-1:]
-            elif segment==cds.segments_list[-1]:
-                new_sequence+=get_segment_sequence(seg_seq,segment)[0:cds.pos_stop]
-            else:
-                new_sequence+=get_segment_sequence(seg_seq,segment)
-
-        new_prot=traduction(get_rna(new_sequence))
-        print("original prot = ", cds_prot)
-        print("new prot = ", new_prot) # print new version with new start and stop codons of deleted. (before and after the gene sequence)
-
-
-        if new_prot[0]!="Met":
-            print("no Met at the start of the new version of the protein -> start codon loss")
-            if "Met" in new_prot:
-                print("Met found at position", (new_prot.index("Met")+1),"-> possible later start codon") # print cette version de la prot
-
-            print("look for start codon before. if none, print 'no start codon, likely gene not active'")
-            # récupérer n pb avant, les traduire, chercher la dernière Met (list[::-1].index("Met")), donner cette version de la prot
-
-        sequence_before=get_sequence_before(path_on_target[0],seg_seq,100,paths,cds)
-        print(sequence_before)
-
-
-        first_stop_index=new_prot.index("*") if "*" in new_prot else "None"
-        if "*" not in new_prot:
-            print("no stop codon")
-            # récupérer n pb après, les traduire, chercher le premier *, donner cette version de la prot.
-        elif first_stop_index+1!=len(new_prot):
-            print("early stop codon at position",(first_stop_index+1),"instead of",len(new_prot))
-        else:
-            print("stop codon found at expected position")
-
-        sequence_after=get_sequence_after(path_on_target[-1],seg_seq,100,paths,cds)
-        print(sequence_after)
-
-
-
-        for var in cds_var[cds_id]:
-            #print("\n",var)
-            size_var=int(var[11])
-            type_var=var[8]
-            pos_var=int(var[12])-1
-
-
-            if type_var=="insertions":
-                sequence_var=var[10]
-                if size_var%3==0:
-                    print("pas de décalage du cadre de lecture")
-                    trad_seq_ins=traduction(get_rna(sequence_var))
-
-                    if pos_var%3==0:
-                        print("insertion entre deux codons")
-                        if "*" in trad_seq_ins:
-                            print("apparition d'un codon stop")
-                            print(f'ancienne sequence : {", ".join(cds_prot)}')
-                            print(f'nouvelle sequence : {", ".join(cds_prot[0:(pos_var//3)-1])}, *')
-                        else:
-                            print(f'ancienne sequence : {", ".join(cds_prot)}')
-                            print(f'{type_var} de {size_var//3} acides amines {", ".join(trad_seq_ins)} à la position {pos_var//3}')
-                    else:
-                        print("insertion au milieu d'un codon, changement de certains acides amines")
-
-            elif type_var=="deletions":
-                sequence_var=line[9]
-                if size_var%3==0:
-                    print("pas de décalage du cadre de lecture")
-                    trad_seq_ins=traduction(get_rna(sequence_var))
-
-                    if pos_var%3==0:
-                        print("deletion de codons entiers")
-                        if "*" in trad_seq_ins:
-                            print("disparition d'un codon stop")
-                        else:
-                            print(f'ancienne sequence : {", ".join(cds_prot)}')
-                            print(f'{type_var} de {size_var//3} acides amines {", ".join(trad_seq_ins)} à la position {pos_var//3}')
-                    else:
-                        print("deletion au milieu d'un codon, changement de certains acides amines")
-
-