from Graph_gff import Features,load_intersect
from Functions import get_segment_sequence,convert_strand
target_genome_name="genome2_chr10"
pos_seg=target_genome_name+".bed"
var_file=target_genome_name+"_variations.txt"
gfa="graph.gfa"
intersect_path='intersect.bed'
load_intersect(intersect_path)
# présent dans Fuctions.py mais relou à importer ?
def get_segments_sequence_and_paths(gfa): # creates two dict with the sequences of the graph's segments, and the paths
file_gfa=open(gfa,'r')
lines_gfa=file_gfa.readlines()
file_gfa.close()
seg_seq={}
paths={}
for line in lines_gfa:
line=line.split()
if (line[0]=="S"): # get the sequence of the segment
seg_id='s'+line[1]
seg_seq[seg_id]=line[2]
if (line[0]=="W") & (line[1]!="_MINIGRAPH_"): # get the walk of the genome
path=line[6].replace(">",";>")
path=path.replace("<",";<").split(';')
list_path=[]
for segment in path:
if segment[0:1]=='>':
list_path.append('+s'+segment[1:])
elif segment[0:1]=='<':
list_path.append('-s'+segment[1:])
paths[line[3]]=list_path
return [paths,seg_seq]
# présent dans Fuctions.py mais relou à importer ?
def get_segments_positions_on_genome(pos_seg): # creates a dict with the position of the segments on the target genome
bed=open(pos_seg,'r')
lines=bed.readlines() # read line by line ?
bed.close()
segments_on_target_genome={}
for line in lines:
line=line.split()
[seg,chrom,start,stop,strand]=[line[3][1:],line[0],line[1],line[2],line[3][0:1]]
segments_on_target_genome[seg]=[chrom,start,stop,strand]
return segments_on_target_genome
def add_feature_sequence(feature,seg_seq): # add the feature's sequence in the Feature object
feature_sequence=""
for segment in feature.segments_list:
if segment==feature.segments_list[0]:
feature_sequence+=get_segment_sequence(seg_seq,segment)[feature.pos_start-2:] # revérifier les +/- 1 pour la position, avec de vraies données
elif segment==feature.segments_list[-1]:
feature_sequence+=get_segment_sequence(seg_seq,segment)[0:feature.pos_stop] # revérifier les +/- 1 pour la position, avec de vraies données
else:
feature_sequence+=get_segment_sequence(seg_seq,segment)
feature.sequence=feature_sequence
def get_first_seg(list_seg,segments_on_target_genome): # get the first segment of the list that is in the target genome
first_seg_found=''
for segment in list_seg:
if segment[1:] in segments_on_target_genome:
first_seg_found=segment[1:]
break
return first_seg_found
def get_feature_path(paths,first_seg,last_seg):# find the feature's path in the target genome
first_strand=convert_strand(segments_on_target_genome[first_seg][3])
first_seg_stranded=first_strand+first_seg
last_strand=convert_strand(segments_on_target_genome[last_seg][3])
last_seg_stranded=last_strand+last_seg
index_first_seg=int(paths[target_genome_name].index(first_seg_stranded))
index_last_seg=int(paths[target_genome_name].index(last_seg_stranded))
first_index=min(index_first_seg,index_last_seg)
last_index=max(index_last_seg,index_first_seg)
list_segfeat_azu=paths[target_genome_name][first_index:last_index+1]
list_segfeat_azu_corrected=[convert_strand(segment_stranded[0])+segment_stranded[1:] for segment_stranded in list_segfeat_azu]
return list_segfeat_azu_corrected
def get_rna(dna_sequence):
return dna_sequence.replace("T","U")
def get_aa(rna_codon): # gives the aa coded by the rna codon
match rna_codon[0:2]:
case "UU":
if (rna_codon[2]=="U") | (rna_codon[2]=="C"):
return "Phe"
else:
return "Leu"
case "UC":
return "Ser"
case "UA":
if (rna_codon[2]=="U") | (rna_codon[2]=="C"):
return "Tyr"
else:
return "*"
case "UG":
if (rna_codon[2]=="U") | (rna_codon[2]=="C"):
return "Cys"
elif rna_codon[2]=="A":
return "*"
else:
return "Trp"
case "CU":
return "Leu"
case "CC":
return "Pro"
case "CA":
if (rna_codon[2]=="U") | (rna_codon[2]=="C"):
return "His"
else:
return "Gln"
case "CG":
return "Arg"
case "AU":
if rna_codon[2]=="G":
return "Met"
else:
return "Ile"
case "AC":
return "Thr"
case "AA":
if (rna_codon[2]=="U") | (rna_codon[2]=="C"):
return "Asn"
else:
return "Lys"
case "AG":
if (rna_codon[2]=="U") | (rna_codon[2]=="C"):
return "Ser"
else:
return "Arg"
case "GU":
return "Val"
case "GC":
return "Ala"
case "GA":
if (rna_codon[2]=="U") | (rna_codon[2]=="C"):
return "Asp"
else:
return "Glu"
case "GG":
return "Gly"
from textwrap import wrap
def cut_codon(sequence):
return wrap(sequence,3)
def traduction(sequence_arn): # translate rna
list_codons=cut_codon(sequence_arn)
prot=list()
for codon in list_codons:
if len(codon)==3:
prot.append(get_aa(codon))
else:
print("attempt to get the amino acid for an incomplete codon")
return prot
def get_sequence_on_genome(feature,segments_on_target_genome): # returns the sequence of the feature on the target genome
list_seg=Features[feature].segments_list
first_seg=get_first_seg(list_seg,segments_on_target_genome)
last_seg=get_first_seg(reversed(list_seg),segments_on_target_genome)
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-2:]
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)
return new_sequence
def get_cds_variations(var_file): # creates dict : cds_id -> list of variations from the var file
var=open(var_file,'r')
lines=var.readlines()
var.close()
# dict cds-var
cds_var={}
for line in lines:
line=line.split()
if line[1]=="CDS":
cds_id=line[0].replace('.','_').replace(':','_')
if cds_id not in cds_var.keys():
cds_var[cds_id]=list()
cds_var[cds_id].append(line)
return cds_var
import re
def findOtherStart(cds,segments_on_target_genome): # look for another start codon, before or after the original one
print("\nlooking for a new start codon:")
frame_shift=0
# chercher codon start en amont du cds, dans le mrna
seq_parent=get_sequence_on_genome(cds.parent,segments_on_target_genome)
seq_cds=get_sequence_on_genome(cds_id,segments_on_target_genome)
sequence_amont=seq_parent[0:seq_parent.rfind(seq_cds)] # get the mrna sequence before the last occurence of the cds sequence
print("sequence before the CDS in the mRNA:",sequence_amont)
if "ATG" in sequence_amont:
start_pos_list=[m.start() for m in re.finditer('(?=ATG)', sequence_amont)]
stop_pos_list=[m.start() for m in re.finditer('(?=TAG|TAA|TGA)', sequence_amont)]
print("start codons position:",start_pos_list,"stop codons position:",stop_pos_list,"before the CDS") # positions (overlapping) où on trouve un atg.
# vérifier ensuite s'il y a un stop après un atg, et sinon le cadre de lecture de l'atg (peut décaler toute la prot !)
print("checking if there is a stop codon after the start codons in the same reading frame:")
for start_pos in start_pos_list:
start_pos_frame=start_pos%3
n=len(sequence_amont)-start_pos+1
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 !!
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")
# chercher codon start en aval, dans le cds
if "ATG" in seq_cds:
start_pos_list=[m.start() for m in re.finditer('(?=ATG)', seq_cds)]
print("start codon candidate found later in the CDS, at the base",start_pos_list[0]) # print seulement le premier
print("\n")
return frame_shift
def print_variation_change(deleted_sequence,inserted_sequence): # print the consequence of the variation represented by the insertion and deletion
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("consequence :",",".join(deleted_aa),"changes into",",".join(inserted_aa))
else:
print("consequence : synonymous variation in",",".join(deleted_aa))
elif len(inserted_aa)!=0:
print("consequence : insertion of",",".join(inserted_aa))
else:
print("consequence : deletion of",",".join(deleted_aa))
if ("*" in inserted_aa):
print("stop codon apparition in the cds of the target genome")
stop=True
return stop
[paths,seg_seq]=get_segments_sequence_and_paths(gfa)
segments_on_target_genome=get_segments_positions_on_genome(pos_seg)
cds_var=get_cds_variations(var_file)
for feature in Features.values(): # add the sequence of all features
add_feature_sequence(feature,seg_seq)
# analysing the variations for all the cds :
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
for index, var in enumerate(cds_var[cds_id]): # for each variation in the current cds :
type_var=var[8]
if type_var!="no_var": # if there is a variation
posVar=[int(var[12]),int(var[13])]
sequence_target=get_sequence_on_genome(cds_id,segments_on_target_genome)
if type_var=="insertion":
length_ref=0
else:
length_ref=len(var[9])
if type_var=="deletion":
length_alt=0
else:
length_alt=len(var[10])
print("variation",index, ":")
if posVar[0]<=3:
print("variation of the start codon, mRNA most likely wont be translated")
#findOtherStart(cds,segments_on_target_genome) # 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])
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])
len_fragment_before=(posVar[0])%3
len_fragment_after=(3-(len_fragment_before+length_ref))%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]
stop=print_variation_change(total_del,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: # size diff !=3k
print("frameshift variation")
old_frameshift=frame_shift
frame_shift=(frame_shift+length_ref-length_alt)%3
# frameshift=0 -> reading frame recovered. may need to get a base before.
# frameshift=1 -> frame shift of 1 base to the right
# 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
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]
stop=print_variation_change(total_del,total_ins)
print("recovery of the original reading frame")
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
print("\n")