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Commit 2bbe863d authored by NMarthe's avatar NMarthe
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amélioré la gestion des substitutions quand le nombre de segments est différent

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Functions.py
+ 16
− 7
View file @ 2bbe863d
......@@ -2,6 +2,10 @@ from Graph_gff import Segments, Features, get_feature_start_on_segment, get_feat
global segments_on_target_genome
segments_on_target_genome={}
global target_genome_name
target_genome_name="CM020642.1_Azucena_chromosome10"
target_genome_name="genome2_chr10"
# get the start position of the features on the linear genome, using their coordinates on the graph and the coordinantes of the segments on the genome
def get_feature_start_on_genome(start_seg,feat_id):
seg_start_pos=segments_on_target_genome[start_seg][1]
......@@ -247,11 +251,11 @@ def get_feature_path(paths,first_seg,last_seg):
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["CM020642.1_Azucena_chromosome10"].index(first_seg_stranded))
index_last_seg=int(paths["CM020642.1_Azucena_chromosome10"].index(last_seg_stranded))
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["CM020642.1_Azucena_chromosome10"][first_index:last_index+1]
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
......@@ -318,7 +322,7 @@ def reset_var(variation):
variation.ref=''
variation.alt=''
def get_old_new_pos_substitution(feat_start,variation,list_segfeat_azu,feat,j):
def get_old_new_pos_substitution(feat_start,variation,list_segfeat_azu,feat):
pos_old=str(int(Segments[variation.start_var].start)-int(feat_start)+1)
start_feat=get_feature_start_on_genome(list_segfeat_azu[0][1:],feat)
start_var=int(segments_on_target_genome[variation.start_on_target][1])
......@@ -368,11 +372,16 @@ def init_new_var(variation,type,list_segfeat_nb,list_segfeat_azu,i,j,seg_seq,fea
variation.ref=seg_seq[list_segfeat_nb[i][1:]]
variation.alt="-"
def continue_var(variation,seg_seq,list_segfeat_nb,list_segfeat_azu,i,j):
def continue_var(variation,seg_seq,list_segfeat_nb,list_segfeat_azu,i,j,genome_to_continue):
if variation.type=="substitution":
variation.ref+=seg_seq[list_segfeat_nb[i][1:]]
variation.alt+=seg_seq[list_segfeat_azu[j][1:]]
if genome_to_continue==0: # genome_to_continue allows to choose if the substitution continues for the original or the target genome, or both.
variation.ref+=seg_seq[list_segfeat_nb[i][1:]]
variation.alt+=seg_seq[list_segfeat_azu[j][1:]]
elif genome_to_continue==1: # deletion
variation.ref+=seg_seq[list_segfeat_nb[i][1:]]
elif genome_to_continue==2: # insertion
variation.alt+=seg_seq[list_segfeat_azu[j][1:]]
elif variation.type=="insertion":
variation.alt+=seg_seq[list_segfeat_azu[j][1:]]
elif variation.type=="deletion":
......
Functions_output.py
+ 41
− 17
View file @ 2bbe863d
......@@ -55,14 +55,14 @@ def genome_gff(pos_seg, gff, out, gfa):
print("generation of the genome's gff ")
# create variables and open files
[once,detail,var,stats]=[False,False,True,False]
[once,detail,var,stats]=[True,True,True,False]
if var:
[paths,seg_seq]=get_segments_sequence_and_paths(gfa)
file_out_var = open("variations_chr10.txt", 'w')
file_out_var = open("test_data/variations.txt", 'w')
global output_variations
output_variations=[0,"",file_out_var]
if detail:
file_out_detail = open("azucena_detail_chr10.gff", 'w')
file_out_detail = open("test_data/genome2_detail.gff", 'w')
global output_detail_gff
output_detail_gff=[0,"",file_out_detail]
if once:
......@@ -160,34 +160,55 @@ def print_variations(first_seg,last_seg,feat,paths,seg_seq):
# if both segments are absent in the other genome, its a substitution
variation.last_seg_in_target=list_segfeat_azu[j][1:]
if (variation.type=='insertion') | (variation.type=='deletion'): # print the current variation before treating the substitution
print_current_var(variation,feat_start,list_segfeat_azu,feat,i,j)
print_current_var(variation,feat_start,list_segfeat_azu,feat,i)
print(list_segfeat_nb[i],list_segfeat_azu[j],variation.type,"\n")
reset_var(variation)
var_count+=1
if variation.type=='substitution':
continue_var(variation,seg_seq,list_segfeat_nb,list_segfeat_azu,i,j)
continue_var(variation,seg_seq,list_segfeat_nb,list_segfeat_azu,i,j,0)
else: # initiate substitution
init_new_var(variation,"substitution",list_segfeat_nb,list_segfeat_azu,i,j,seg_seq,feature)
i+=1;j+=1
else: # azu segment not in nb, but nb segment in azu : insertion
if (variation.type=='substitution') | (variation.type=='deletion'): # print the current variation before treating the insertion
print_current_var(variation,feat_start,list_segfeat_azu,feat,i,j)
else: # azu segment not in nb, but nb segment in azu : insertion or continue substitution
if variation.type=='deletion': # print the current variation before treating the insertion
print_current_var(variation,feat_start,list_segfeat_azu,feat,i)
print(list_segfeat_nb[i],list_segfeat_azu[j],variation.type,"\n")
reset_var(variation)
var_count+=1
variation.last_seg_in_target=list_segfeat_azu[j][1:]
if variation.type=='insertion':
continue_var(variation,seg_seq,list_segfeat_nb,list_segfeat_azu,i,j)
continue_var(variation,seg_seq,list_segfeat_nb,list_segfeat_azu,i,j,0)
elif variation.type=="substitution":
while list_segfeat_azu[j]!=list_segfeat_nb[i]:
continue_var(variation,seg_seq,list_segfeat_nb,list_segfeat_azu,i,j,2)
j+=1
print_current_var(variation,feat_start,list_segfeat_azu,feat,i)
print(list_segfeat_nb[i],list_segfeat_azu[j],variation.type,"\n")
reset_var(variation)
var_count+=1
j-=1
else: # intiate insertion
init_new_var(variation,"insertion",list_segfeat_nb,list_segfeat_azu,i,j,seg_seq,feature)
j+=1
elif list_segfeat_nb[i] not in list_segfeat_azu: # nb segment not in azu, but azu segment in nb : deletion
if (variation.type=='substitution') | (variation.type=='insertion'): # print the current variation before treating the deletion
print_current_var(variation,feat_start,list_segfeat_azu,feat,i,j)
elif list_segfeat_nb[i] not in list_segfeat_azu: # nb segment not in azu, but azu segment in nb : deletion or continue substitution
if variation.type=='insertion': # print the current variation before treating the deletion
print_current_var(variation,feat_start,list_segfeat_azu,feat,i)
print(list_segfeat_nb[i],list_segfeat_azu[j],variation.type,"\n")
reset_var(variation)
var_count+=1
if variation.type=='deletion':
continue_var(variation,seg_seq,list_segfeat_nb,list_segfeat_azu,i,j)
continue_var(variation,seg_seq,list_segfeat_nb,list_segfeat_azu,i,j,0)
elif variation.type=="substitution":
while list_segfeat_azu[j]!=list_segfeat_nb[i]:
continue_var(variation,seg_seq,list_segfeat_nb,list_segfeat_azu,i,j,1)
i+=1
print_current_var(variation,feat_start,list_segfeat_azu,feat,i)
print(list_segfeat_nb[i],list_segfeat_azu[j],variation.type,"\n")
reset_var(variation)
var_count+=1
i-=1
else: # intiate deletion
init_new_var(variation,"deletion",list_segfeat_nb,list_segfeat_azu,i,j,seg_seq,feature)
i+=1
......@@ -199,19 +220,22 @@ def print_variations(first_seg,last_seg,feat,paths,seg_seq):
else: # segment present in both, no variation. print the running indel if there is one
if variation.type!='': # print the current variation if there is one
print_current_var(variation,feat_start,list_segfeat_azu,feat,i,j)
print_current_var(variation,feat_start,list_segfeat_azu,feat,i)
print(list_segfeat_nb[i],list_segfeat_azu[j],variation.type,"\n")
var_count+=1
reset_var(variation)
variation.last_seg_in_target=list_segfeat_azu[j][1:]
i+=1;j+=1
if (variation.type!=''): # if there was a current variation when we reached the end, print it
print_current_var(variation,feat_start,list_segfeat_azu,feat,i,j)
print_current_var(variation,feat_start,list_segfeat_azu,feat,i)
print(list_segfeat_nb[i],list_segfeat_azu[j-1],variation.type,"\n")
var_count+=1
reset_var(variation)
if i<=len(list_segfeat_nb)-1: # if we didn't reach the length of the segment list for the first genome, the end is missing for the second genome
print_last_deletion(variation,list_segfeat_nb,i,feat_start,feature,seg_seq)
print(list_segfeat_nb[i],"end deletion","\n")
var_count+=1
reset_var(variation)
......@@ -219,7 +243,7 @@ def print_variations(first_seg,last_seg,feat,paths,seg_seq):
print_novar(variation)
def print_current_var(variation,feat_start,list_segfeat_azu,feat,i,j):
def print_current_var(variation,feat_start,list_segfeat_azu,feat,i):
if variation.type=='insertion':
[pos_old,pos_new]=get_old_new_pos_insertion(variation,feat_start,list_segfeat_azu,feat)
line=f'{variation.feature_id}\t{variation.feature_type}\t{variation.chr}\t{variation.start_new}\t{variation.stop_new}\t{variation.size_new}\t{variation.inversion}\t{variation.size_diff}\tinsertion\t-\t{variation.alt}\t{len(variation.alt)}\t{pos_old}\t{pos_new}\n'
......@@ -229,7 +253,7 @@ def print_current_var(variation,feat_start,list_segfeat_azu,feat,i,j):
line=f'{variation.feature_id}\t{variation.feature_type}\t{variation.chr}\t{variation.start_new}\t{variation.stop_new}\t{variation.size_new}\t{variation.inversion}\t{variation.size_diff}\tdeletion\t{variation.ref}\t-\t{len(variation.ref)}\t{pos_old}\t{pos_new}\n'
write_line(line,output_variations,False)
elif variation.type=='substitution':
[pos_old,pos_new]=get_old_new_pos_substitution(feat_start,variation,list_segfeat_azu,feat,j)
[pos_old,pos_new]=get_old_new_pos_substitution(feat_start,variation,list_segfeat_azu,feat)
if len(variation.ref) == len(variation.alt): # if the substituion is between two segment of the same size, print it
size_subs=len(variation.ref)
line=f'{variation.feature_id}\t{variation.feature_type}\t{variation.chr}\t{variation.start_new}\t{variation.stop_new}\t{variation.size_new}\t{variation.inversion}\t{variation.size_diff}\tsubstitution\t{variation.ref}\t{variation.alt}\t{size_subs}\t{pos_old}\t{pos_new}\n'
......
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