import ClassSegFeat as Class
# functions to create the segments and the features
# create segment
def init_seg(line,feature):
line=line.split()
seg_id=line[3][1:]
chr=line[0]
start=line[1]
stop=line[2]
# add the current feature (stranded) to the list of features that are on the segment
feature_strand=line[10]
feature_stranded=feature_strand+feature
feat=list()
feat.append(feature_stranded)
Segments[seg_id]=Class.Segment(seg_id,feat,chr,start,stop)
# create feature
def init_feature(line):
line=line.split()
feature_id=line[12].split(';')[0].split("=")[1].replace(".","_").replace(":","_")
type=line[6]
annot=line[12]
chr=line[4]
start=line[7]
stop=line[8]
childs=list()
# add the current segment (stranded) to the list of segments that have the feature
seg=line[3][1:]
strand=line[10]
seg_stranded=strand+seg
segments_list=list()
segments_list.append(seg_stranded)
# if the current feature as a parent, add the feature un the childs list of its parent
if annot.split(";")[1].split("=")[0]=="Parent":
# for annotations like : ID=LOC_Os01g01010.1:exon_7;Parent=LOC_Os01g01010.1, where the parent is in the field 1
parent=annot.split(";")[1].split("=")[1].replace(".","_").replace(":","_")
add_child(parent,feature_id)
elif annot.split(";")[2].split("=")[0]=="Parent":
# for annotations like : ID=LOC_Os01g01010.1;Name=LOC_Os01g01010.1;Parent=LOC_Os01g01010, where the parent is in the field 2
parent=annot.split(";")[2].split("=")[1].replace(".","_").replace(":","_")
add_child(parent,feature_id)
else: parent=""
Features[feature_id]=Class.Feature(feature_id,type,chr,start,stop,annot,childs,parent,segments_list)
# add a feature (stranded) to an existing segment
def add_feature(seg,new_feature,strand):
new_feature_stranded=strand+new_feature
if new_feature_stranded not in Segments[seg].features:
Segments[seg].features.append(new_feature_stranded)
# add a child to an existing feature
def add_child(feat,new_child):
if feat in Features.keys():
if new_child not in Features[feat].childs:
Features[feat].childs.append(new_child)
# add a segment (stranded) to an existing feature
def add_seg(feat,new_seg,strand):
seg_stranded=strand+new_seg
if seg_stranded not in Features[feat].segments_list:
Features[feat].segments_list.append(seg_stranded)
# create all the Segment and Feature objects in the dictionnaries Segments and Features
def create_seg_feat(intersect_path):
global Features
global Segments
Segments={}
Features={}
# open the intersect between the segments and the gff
file = open(intersect_path, 'r')
lines=file.readlines()
for line in lines:
# get the ids for the dictionnaries' keys
feature_id=line.split()[12].split(';')[0].split("=")[1].replace(".","_").replace(":","_")
segment_id=line.split()[3][1:]
if feature_id not in Features: # if the feature doesn't exist, create it and add the current segment to its seg list
init_feature(line)
else: # add the current segment to the list of segments that have the existing feature
strand=line.split()[10]
add_seg(feature_id,segment_id,strand)
if segment_id not in Segments: # if the segment doesn't exist, create it and add the current feature to its feat list
init_seg(line, feature_id)
else: # add the current feature to the existing segment
strand=line.split()[10]
add_feature(segment_id,feature_id,strand)
file.close()
# functions to generate the graph's gff from the segments and features created with create_seg_feat
# get the feature's start position on the segment
def get_start(seg,feat):
s=Segments[seg]
f=Features[feat]
if s.start>f.start:
result=1
else:
result=f.start-s.start
return result
# get the feature's stop position on the segment
def get_stop(seg,feat):
s=Segments[seg]
f=Features[feat]
if s.stop<f.stop:
result=s.size
else:
result=f.stop-s.start
return result
# go through all the segments in Segments and prints the gff, with one line for each segment/feature intersection
def graph_gff(file_out):
print("generation of the graph's gff")
file_out = open(file_out, 'w')
for segment in Segments:
# get the list of the features on the segment
features_seg=Segments[segment].features
# go through all these features, and print the gff line for each
for feature_stranded in features_seg:
strand=feature_stranded[0:1]
feature=feature_stranded[1:]
segment_stranded=strand+segment
type=Features[feature].type
#start=max(1,get_start(segment,feature))
start=get_start(segment,feature)
stop=get_stop(segment,feature)
# get the rank and the total number of ocurrences for the feature
rank=str(Features[feature].segments_list.index(segment_stranded)+1)
total=str(len(Features[feature].segments_list))
# create the annotation with the rank information
annotation=Features[feature].annot+";Rank_occurrence="+rank+";Total_occurrences="+total
# generate the gff line
ligne=segment+"\tgraph_gff\t"+type+"\t"+str(start)+"\t"+str(stop)+"\t.\t"+strand+"\t.\t"+annotation+"\n"
#print(ligne)
file_out.write(ligne)
file_out.close()
# functions to generate a genome's gff from the graph's gff
# 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_start_2(seg_start, seg_ac, feat_id):
s_start=seg_ac[seg_start][1]
f_start=get_start(seg_start,feat_id)
start=int(s_start)+int(f_start)
return start
# get the stop 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_stop_2(seg_stop, seg_ac, feat_id):
s_start=seg_ac[seg_stop][1]
f_stop=get_stop(seg_stop,feat_id)
stop=int(s_start)+int(f_stop)
return stop
# get the position of a piece of a feature on the complete feature (on the original genome)
def get_position(seg_start,seg_stop,gene_start,feature,seg_ac):
# start position of the complete gene on the reference
start_gene_start=Segments[gene_start].start+get_start(gene_start,feature.id)-1
# start position of the piece of the feature on the reference
start_first_seg=Segments[seg_start].start+get_start(seg_start,feature.id)-1
# start and stop position of the feature on azucena, to get the length of the piece of the feature
start_azu=get_start_2(seg_start,seg_ac,feature.id)
stop_azu=get_stop_2(seg_stop,seg_ac,feature.id)
# start position of the piece of the feature on the complete feature
start_gene=int(start_first_seg)-int(start_gene_start)+1
# stop position : start+length
stop_gene=start_gene+(stop_azu-start_azu)
position=";position="+str(start_gene)+"-"+str(stop_gene)
#position=";start_position_on_feature="+str(start_gene)+":stop_position_on_feature="+str(stop_gene)
return position
# get the proportion of the piece of the feature on the total length
def get_proportion(seg_start,seg_stop,seg_ac,feature):
start_azu=get_start_2(seg_start,seg_ac,feature.id) # start position of the feature on azucena
stop_azu=get_stop_2(seg_stop,seg_ac,feature.id) # stop position of the feature on azucena
proportion=";proportion="+str(stop_azu-start_azu+1)+"/"+str(feature.size)
#proportion=";number_bases="+str(stop_azu-start_azu+1)+";total_bases="+str(feature.size)
return proportion
# returns the gff line to write in the output file
def write_line(list_seg,i,feat,seg_start,gene_start,seg_ac):
seg_stop=list_seg[i-1][1:]
feature=Features[feat]
chr=seg_ac[seg_start][0]
strand=list_seg[i-1][0:1]
# start and stop position of the feature on azucena
start_azu=get_start_2(seg_start,seg_ac,feature.id)
stop_azu=get_stop_2(seg_stop,seg_ac,feature.id)
proportion=get_proportion(seg_start,seg_stop,seg_ac,feature)
position=get_position(seg_start,seg_stop,gene_start,feature,seg_ac)
annotation=feature.annot+proportion+position
out_line=chr+"\tgraph_gff\t"+feature.type+"\t"+str(start_azu)+"\t"+str(stop_azu)+"\t.\t"+strand+"\t.\t"+annotation+"\n"
return out_line
# writes the gff of azucena using the gff of the graph
def genome_gff(pos_seg, gff, out):
print("generation of the genome's gff ")
# create a dictionnary with the positions of the segments on azucena
seg_ac={}
bed=open(pos_seg,'r')
lines=bed.readlines()
for line in lines:
line=line.split()
s_id=line[3][1:]
ch=line[0]
start=line[1]
stop=line[2]
seg_ac[s_id]=list([ch,start,stop])
bed.close()
gff=open(gff,'r')
file_out = open(out, 'w')
lines=gff.readlines()
# get the list of all the features to transfer
list_feature=list()
for line in lines:
id=(line.split()[8].split(";")[0].split("=")[1].replace(".","_").replace(":","_"))
if id not in list_feature:
list_feature.append(id)
# stats on how many segments are absent in azucena, their average length, etc
stats=False
if stats==True:
seg_first=list()
seg_middle=list()
seg_last=list()
seg_total=list()
seg_ok=list()
seg_entier=list()
feature_missing_first=list()
feature_missing_middle=list()
feature_missing_last=list()
feature_missing_all=list()
feature_missing_total=list()
# for each feature, get list of the segments where it is
for feat in list_feature:
list_seg=Features[feat].segments_list
size_list=len(list_seg)
# stats on how many segments are absent in azucena, their average length, etc
if stats==True:
for segment in list_seg:
seg_len=Segments[segment[1:]].size
if segment[1:] not in seg_ac:
seg_total.append(seg_len)
if feat not in feature_missing_total:
feature_missing_total.append(feat)
if segment==list_seg[0]:
if segment==list_seg[size_list-1]:
seg_entier.append(seg_len)
if feat not in feature_missing_all:
feature_missing_all.append(feat)
else:
seg_first.append(seg_len)
if feat not in feature_missing_first:
feature_missing_first.append(feat)
elif segment==list_seg[size_list-1]:
seg_last.append(seg_len)
if feat not in feature_missing_last:
feature_missing_last.append(feat)
else:
seg_middle.append(seg_len)
if feat not in feature_missing_middle:
feature_missing_middle.append(feat)
else:
seg_ok.append(seg_len)
gene_start="empty"
seg_start="empty"
seg_stop="empty"
# loop that goes through all the segments that have the current feature
# keeps the first segment present in azucena found, and when it finds a segment absent in azucena, prints the piece of the fragment, and resets the first segment present.
# at the end of the loop, prints the last piece of the fragment.
for i in range(0,size_list):
if list_seg[i][1:] in seg_ac:
if gene_start=="empty":
gene_start=list_seg[i][1:]
if seg_start=="empty":
seg_start=list_seg[i][1:]
#else: if we already have a start, keep going though the segments until we find a stop (segment not in azucena)
else:
if seg_start!="empty": # found a stop. so print the line, reset seg_start, and keep going through the segments to find the next seg_start
out_line=write_line(list_seg,i,feat,seg_start,gene_start,seg_ac)
file_out.write(out_line)
seg_start="empty"
seg_stop="empty"
#else: if the current segment is not in azucena but there is no start, keep looking for a start
# print the last piece of the feature in the end
if list_seg[i][1:] in seg_ac:
out_line=write_line(list_seg,i+1,feat,seg_start,gene_start,seg_ac)
file_out.write(out_line)
file_out.close()
gff.close()
# print stats
from statistics import median, mean
if stats==True:
print(len(seg_first),"segments missing at the beginning of a feature, of mean length", round(mean(seg_first),2), "and median length",median(seg_first))
print(len(seg_middle),"segments missing in the middle of a feature, of mean length", round(mean(seg_middle),2), "and median length",median(seg_middle))
multiple_3=0
for seg in seg_middle:
if seg%3==0:multiple_3+=1
print(multiple_3,"segments missing in the middle of a feature, of length=3k")
print(len(seg_last), "segments missing at the end of a feature, of mean length", round(mean(seg_last),2), "and median length",median(seg_last))
print(len(seg_entier),"segments that have an entiere feature (not in beggining/middle/end) missing, of mean length", round(mean(seg_entier),2), "and median length",median(seg_entier))
print(len(seg_total),"segments that have a feature piece missing, of mean length", round(mean(seg_total),2), "and median length",median(seg_total))
print(len(seg_ok),"segments that have a feature found, of mean length", round(mean(seg_ok),2), "and median length", median(seg_ok))
print("\nthe first segment is missing for", len(feature_missing_first) ,"features, including",round(100*(117+5)/153,2),"% hypothetical or putative.")
print("a middle segment is missing for", len(feature_missing_middle) ,"features, including",round(100*(180+3)/263,2),"% hypothetical or putative.")
print("the last segment is missing for", len(feature_missing_last) ,"features, including",round(100*(115+7)/156,2),"% hypothetical or putative.")
print(len(feature_missing_all) ,"features are entirely missing, including",round(100*(314+24)/404,2),"% hypothetical or putative.")
print("there is at least one segment missing", len(feature_missing_total) ,"features, including",round(100*(606+36)/817,2),"% hypothetical or putative.")
print("there is", len(list_feature) ,"features in total, including",round(100*(2108+171)/3510,2),"% hypothetical or putative.")
feat_miss_first=open('features_missing_first.txt','w')
feat_miss_first.write("features missing the first segment on azucena :\n")
for first in feature_missing_first :
feat_miss_first.write(Features[first].annot)
feat_miss_first.write("\n")
feat_miss_first.close()
feat_miss_middle=open('features_missing_middle.txt','w')
feat_miss_middle.write("\nfeatures missing a middle segment on azucena :\n")
for middle in feature_missing_middle :
feat_miss_middle.write(Features[middle].annot)
feat_miss_middle.write("\n")
feat_miss_middle.close()
feat_miss_last=open('features_missing_last.txt','w')
feat_miss_last.write("\nfeatures missing the last segment on azucena :\n")
for last in feature_missing_last :
feat_miss_last.write(Features[last].annot)
feat_miss_last.write("\n")
feat_miss_last.close()
feat_miss=open('features_missing.txt','w')
feat_miss.write("\nfeatures missing entirely on azucena :\n")
for entier in feature_missing_all :
feat_miss.write(Features[entier].annot)
feat_miss.write("\n")
feat_miss.close()
feat_miss_total=open('features_missing_total.txt','w')
feat_miss_total.write("\nfeatures missing a segment on azucena :\n")
for total in feature_missing_total :
feat_miss_total.write(Features[total].annot)
feat_miss_total.write("\n")
feat_miss_total.close()
feat_all=open('all_features.txt','w')
for feat in list_feature:
feat_all.write(Features[feat].annot)
feat_all.write("\n")
feat_all.close()
# writes the gff of azucena using the gff of the graph
def genome_gff_test(pos_seg, gff, out):
print("generation of the genome's gff ")
# create a dictionnary with the positions of the segments on azucena
seg_ac={}
bed=open(pos_seg,'r')
lines=bed.readlines()
for line in lines:
line=line.split()
s_id=line[3][1:]
ch=line[0]
start=line[1]
stop=line[2]
seg_ac[s_id]=list([ch,start,stop])
bed.close()
gff=open(gff,'r')
file_out = open(out, 'w')
lines=gff.readlines()
# get the list of all the features to transfer
list_feature=list()
for line in lines:
id=(line.split()[8].split(";")[0].split("=")[1].replace(".","_").replace(":","_"))
if id not in list_feature:
list_feature.append(id)
# for each feature, get list of the segments where it is
for feat in list_feature:
list_seg=Features[feat].segments_list
size_list=len(list_seg)
gene_start="empty"
seg_start="empty"
seg_stop="empty"
# prints all gene fragments.
for i in range(0,size_list):
if (list_seg[i][1:] in seg_ac) & (1==1):
feature=Features[feat]
seg_start=list_seg[i][1:]
seg_stop=list_seg[i][1:]
chr=seg_ac[seg_start][0]
start_azu=get_start_2(seg_start,seg_ac,feature.id)
stop_azu=get_stop_2(seg_stop,seg_ac,feature.id)
out_line=chr+" "+str(start_azu)+" "+str(stop_azu)+" "+seg_start+" "+seg_stop+" "+feature.id+"\n"
file_out.write(out_line)
file_out.close()
gff.close()