def output(pas_dict,scan_file,out,window,max_shift,species):
extend = int(window/2)
f = open(scan_file,'r')
lines = f.readlines()
ww = open(out,'w')
for i,line in enumerate(lines):
line = line.rstrip('\n')
pas_id,rpm,base = line.split('\t')
chromosome,pos,strand = pas_id.split(':')
pos = int(pos)
if pos in pas_dict.keys():
pas_type = pas_dict[pos]
symbol = 'unknown'
if(i-extend>0 and i+extend+1<len(lines)):
for j in range(-max_shift,max_shift+1):
k = i+j
start = k-extend
end = k+extend
if(start>0 and end+1<len(lines)):
if(check(lines[start],lines[end],window)):
collpase(pas_id,pas_type,symbol,lines[start:end+1],ww,species,j)
ww.close()
f.close()
def output(pas_array,scan_file,out,window,max_shift,species,prob,number_pas,rst):
extend = int(window/2)
f = open(scan_file,'r')
lines = f.readlines()
ww = open(out,'w')
pre_pos = 0
negative_candidate = dict()
for i,line in enumerate(lines):
line = line.rstrip('\n')
pas_id,rpm,base = line.split('\t')
chromosome,pos,strand = pas_id.split(':')
pos = int(pos)
if(i-extend>0 and i+extend+1+max_shift<len(lines)):
if(random.random()<prob):
accept = 1
if (abs(pos-pre_pos)<Threshold):
continue
for true_pos in pas_array:
if(abs(pos-true_pos)<Threshold):
accept = 0
if(accept==0):
continue
pre_pos = pos
negative_candidate[pas_id] = i
count = 0
items = list(negative_candidate.items())
random.shuffle(items)
for pas_id,i in items:
start = i-extend
end = i+extend
if(not check(lines[start-max_shift],lines[end+max_shift],window+2*max_shift)):
continue
success = collpase(pas_id,'unknown','unknown',lines[start:end+1],ww,species,0,rst)
count += success
if(success==0):
continue
for j in range(-max_shift,max_shift+1):
if(j==0):
continue
k = i+j
start = k-extend
end = k+extend
if(start>0 and end+1<len(lines)):
if(check(lines[start],lines[end],window)):
collpase(pas_id,'unknown','unknown',lines[start:end+1],ww,species,j,rst)
if(count>=number_pas):
break
if(count<number_pas):
raise Warning("not engough negative candidates, please incerase the probability for selecting!")
else:
print("successfully randomly get same number of negative pas as ground truth")
f.close()