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import ClassSegFeat as Class
# create global variables to manipulate them in the functions below and to pass them to Functions.py
global Features
global Segments
Segments={}
Features={}
# functions to create the segments and the features
# create a segment with its first feature
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 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)
# create the segment
Segments[seg_id]=Class.Segment(seg_id,feat,chr,start,stop)
# create a feature with the first segment its on
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 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)
parent=get_parent(annot,feature_id)
# create the feature
Features[feature_id]=Class.Feature(feature_id,type,chr,start,stop,annot,childs,parent,segments_list)
# if there is a parent, get the id of the parent feature and add the child to the parent
def get_parent(annot,feature_id):
# if the current feature has a parent, add the current feature in the childs list of its parent
if annot.split(";")[1].split("=")[0]=="Parent":
# for annotations that look 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 that look 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=""
return parent
# add a feature 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 feature to an existing feature
def add_child(feat,new_child):
if feat in Features.keys(): # if the parent feature exists
if new_child not in Features[feat].childs:
Features[feat].childs.append(new_child)
# add a segment 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 a note for the child features that do not have annotation.
def set_note(id):
# the note contains information on the function of the feature and is used for statistics on hypothetical/putatives features.
# in the gff, the notes are only on the "gene" features. it's easier to have it for the childs than to check the parent's note (or the parent's parent).
feat=Features[id]
if feat.type=="gene": # if the feature is a gene, the note is the last field of its annotation.
feat.note=feat.annot.split(';')[-1]
else: # else, the note will be the note of the gene that contains the feature. in my gff, only the genes have an annotation.
# we go back to the parent of the feature, and its parent if necessary, etc, until we find the gene.
# this is because for example the parent of an exon is the mrna, not the gene itself, so we need to go up until we find the gene.
curent=feat.parent
annot_found=False
while annot_found==False:
if Features[curent].type=="gene": # if/once we found the gene, we get its note to transfer it to the child feature
note=Features[curent].annot.split(';')[-1]
feat.note=note
annot_found=True
else: # if we didn't find the gene, we go up to the current feature's parent until we find it
curent=Features[Features[curent].parent].id
# create all the Segment and Feature objects in the dictionnaries Segments and Features
def create_seg_feat(intersect_path):
# open the file with the intersect between the segments and the gff
file = open(intersect_path, 'r')
lines=file.readlines()
file.close()
for line in lines: # for each line in the intersect file
# 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: # if it exists, 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: # if it exists, add the current feature to the list of features on the existing segment
strand=line.split()[10]
add_feature(segment_id,feature_id,strand)
# for all the features, add the note (information on the function of the feature), and the positions on the first and last seg.
# cant always do it before because for that i need to have all the parents in the dict Features, and all the segments in the list segments_list for each feature.
for feat_id in Features:
feat=Features[feat_id]
set_note(feat.id)
feat.pos_start=get_start(feat.segments_list[0][1:],feat.id)
feat.pos_stop=get_stop(feat.segments_list[-1][1:],feat.id)
# 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_id,feat_id):
s=Segments[seg_id]
f=Features[feat_id]
if s.start>=f.start:
result=1
else:
result=f.start-s.start+1
return result
# get the feature's stop position on the segment
def get_stop(seg_id,feat_id):
s=Segments[seg_id]
f=Features[feat_id]
if s.stop<=f.stop:
result=s.size
else:
result=f.stop-s.start+1
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')
string_out=""
cpt_out=0
for segment in Segments:
# get the list of the features on the segment
features_seg=Segments[segment].features
# go through all the segment's features, and print the gff line for each
for feature_stranded in features_seg:
strand=feature_stranded[0:1]
feature=feature_stranded[1:]
# feature[feature]
#[strand,feature]=[feature_stranded[0:1],feature_stranded[1:]]
segment_stranded=strand+segment
type=Features[feature].type
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
# write the gff line in the output file
line=segment+"\tGrAnnot\t"+type+"\t"+str(start)+"\t"+str(stop)+"\t.\t"+strand+"\t.\t"+annotation+"\n"
string_out+=line
cpt_out+=1
#file_out.write(line)
if cpt_out==1000:
file_out.write(string_out)
string_out=""
cpt_out=0
# faire un fct print
file_out.write(string_out)
file_out.close()