From 2dff4cf57ec7142da28f6eb8db730d5431566236 Mon Sep 17 00:00:00 2001
From: NMarthe <nina.marthe@ird.fr>
Date: Thu, 7 Dec 2023 13:35:33 +0100
Subject: [PATCH] corrected the inference when there is a frameshift. it
simplfied the algorithm (less conditions)
---
inference.py | 150 ++++++++++++++++++++-------------------------------
1 file changed, 58 insertions(+), 92 deletions(-)
diff --git a/inference.py b/inference.py
index 052175e..84d4d16 100644
--- a/inference.py
+++ b/inference.py
@@ -213,7 +213,7 @@ def findOtherStart(cds,segments_on_target_genome): # look for another start codo
if True not in ( (stop_pos%3==start_pos_frame) & (stop_pos>start_pos) for stop_pos in stop_pos_list) :
#print("codon start candidat trouvé dans l'arn messager,",n,"bases en amont du cds")
# calculer le décalage : si on en trouve un 2 bases en amont, ça décale le cadre de lecture !
- frame_shift=(frame_shift+n)%3 # vérifier le frame shift !!
+ frame_shift=(frame_shift+n)%3 # vérifier le frameshift !!
print("the start codon at the position",start_pos,",",n,"bases before the CDS, doesn't have a stop codon after in the same reading frame")
else:
print("the start codon at the position",start_pos,",",n,"bases before the CDS, has a stop codon after in the same reading frame")
@@ -256,7 +256,7 @@ for feature in Features.values(): # add the sequence of all features
for cds_id in cds_var.keys():
cds=Features[cds_id]
print("analysis of the variations in the CDS",cds_id,":\n")
- frame_shift=0
+ frameshift=0
for index, var in enumerate(cds_var[cds_id]): #Â for each variation in the current cds :
type_var=var[8]
if type_var!="no_var": #Â if there is a variation
@@ -279,106 +279,72 @@ for cds_id in cds_var.keys():
#findOtherStart(cds,segments_on_target_genome) #Â for now we don't look for another start codon
break
- if abs(length_alt-length_ref)%3 == 0: # size diff 3k -> no frame shift.
-
- if (posVar[0])%3==0: #size diff 3k, position 3k
- print("variation between two codons not causing a frameshift")
- if type_var=="insertion":
- print("insertion of",var[10])
- elif type_var=="deletion":
- print("deletion of",var[9])
- else:
- print("substitution of",var[9],"by",var[10])
+ old_frameshift=frameshift
+ frameshift=(frameshift+length_ref-length_alt)%3
+ if old_frameshift!=frameshift:
+ print("variation causing a frameshift")
+ #Â frameshift=0 -> reading frame recovered. may need to get a base before.
+ #Â frameshift=1 -> frameshift of 1 base to the right
+ #Â frameshift=2 -> frameshift of 2 bases to the right
+ if frameshift==0:
+ print("recovery of the original reading frame")
+ if old_frameshift==0:
+ print("loss of the original reading frame")
+ #else:
+ # print("variation not causing a frameshift")
- 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]
- stop=print_variation_change(deleted_sequence,inserted_sequence)
- if stop:
- break
- else: # size diff 3k, position !=3k
- print("variation in the middle of a codon not causing a frameshift")
- if type_var=="insertion":
- print("insertion of",var[10])
- elif type_var=="deletion":
- print("deletion of",var[9])
- else:
- print("substitution of",var[9],"by",var[10])
+ if type_var=="insertion":
+ print("insertion of",var[10])
+ elif type_var=="deletion":
+ print("deletion of",var[9])
+ else:
+ print("substitution of",var[9],"by",var[10])
- len_fragment_before=(posVar[0])%3
- len_fragment_after=(3-(len_fragment_before+length_ref))%3
+ len_fragment_before_del=(posVar[0])%3
+ len_fragment_before_ins=(posVar[1])%3
- 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]
+ if frameshift==0:
+ # print only the local change.
+ 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)
+ if stop:
+ break
- stop=print_variation_change(total_del,total_ins)
+ else:
+ # print changes from local var to next var. at the next var, we will see if the reading frame is recovered.
+ print("frameshift of",frameshift,"base(s) to the right.")
+ if index==len(cds_var[cds_id])-1: # it is the last variation. translate until the end of the cds.
+ total_total_del=cds.sequence[posVar[0]-len_fragment_before_del:]
+ total_total_ins=sequence_target[posVar[1]-len_fragment_before_ins:]
+ stop=print_variation_change(total_total_del,total_total_ins)
if stop:
break
- # possible that it prints too many variations : for ex if we have a snp on the first and the last base of a codon,
- # while printing the effect of the first snp we aso use the second one.
+ else: # not the last variation. translate until the next var.
+ nextVar=cds_var[cds_id][index+1]
+ posNextVar=[int(nextVar[12]),int(nextVar[13])]
- else: # size diff !=3k
- print("variation causing a frameshift")
- old_frameshift=frame_shift
- frame_shift=(frame_shift+length_ref-length_alt)%3
- #Â frameshift=0 -> reading frame recovered. may need to get a base before.
- #Â frameshift=1 -> frame shift of 1 base to the right
- #Â frameshift=2 -> frame shift of 2 bases to the right
-
- if type_var=="insertion":
- print("insertion of",var[10])
- elif type_var=="deletion":
- print("deletion of",var[9])
- else:
- print("substitution of",var[9],"by",var[10])
-
- len_fragment_before_del=(posVar[0])%3
- len_fragment_before_ins=(posVar[1])%3
- print(len_fragment_before_ins,len_fragment_before_del)
-
- if frame_shift==0:
- # print only the local change.
- 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]
- print("recovery of the original reading frame")
- stop=print_variation_change(total_del,total_ins)
+ if nextVar[8]=="insertion":
+ length_ref_nextvar=0
+ else:
+ length_ref_nextvar:len(nextVar[9])
+ if nextVar[8]=="deletion":
+ length_alt_nextvar=0
+ else:
+ length_alt_nextvar=len(nextVar[10])
+
+ len_fragment_before_del_nextvar=(posNextVar[0])%3
+ 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]
+ stop=print_variation_change(total_total_del,total_total_ins)
if stop:
break
-
- else:
- # print changes from local var to next var. at the next var, we will see if the reading frame is recovered.
- print("creating frame shift of",frame_shift,"base(s) to the right.")
- if old_frameshift==0:
- print("loss of the original reading frame")
- if index==len(cds_var[cds_id])-1: # it is the last variation. translate until the end of the cds.
- total_total_del=cds.sequence[posVar[0]-len_fragment_before_del:]
- total_total_ins=sequence_target[posVar[1]-len_fragment_before_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])]
-
- if nextVar[8]=="insertion":
- length_ref_nextvar=0
- else:
- length_ref_nextvar:len(nextVar[9])
- if nextVar[8]=="deletion":
- length_alt_nextvar=0
- else:
- length_alt_nextvar=len(nextVar[10])
-
- len_fragment_before_del_nextvar=(posNextVar[0])%3
- 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]
- stop=print_variation_change(total_total_del,total_total_ins)
- if stop:
- break
+ # possible that it prints too many variations : for ex if we have a snp on the first and the last base of a codon,
+ # while printing the effect of the first snp we aso use the second one.
print("\n")
--
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