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index_reads_IGH_Tn5_AB_fuzzy.py
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index_reads_IGH_Tn5_AB_fuzzy.py
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from __future__ import division
import time
import sys
import os
import distance
path_root=sys.argv[1]+'//'
path1=sys.argv[2]+'//'
path2=sys.argv[3]+'//'
cutoff=int(sys.argv[4])
def find_match(Library,index, split_index1,split_index2,split_index3):
index1=index[:6]
index2=index[6:12]
index3=index[12:18]
query_set=set()
for subindex,split_index in [(index1,split_index1),(index2,split_index2),(index3,split_index3)]:
try:
for element in split_index[subindex]:
query_set.add(element)
except:
pass
min1=cutoff
index_number=''
for entry in list(query_set):
dis=distance.hamming(index,entry[0])
if dis<=min1:
index_number=entry[1]
min1=dis
if index_number!='':
out=open(path_root+'indexed_reads_Uncut_AB.txt','a')
if Library=='A':
out.write(Library+'\t'+str(index_number)+'\t\t'+index+'\t'+read1+'\t'+qual1+'\t'+str(int(x/4))+'\t'+str(position)+'\n')
if Library=='B':
out.write(Library+'\t'+str(index_number)+'\t'+index+'\t\t'+read1+'\t'+qual1+'\t'+str(int(x/4))+'\t'+str(position)+'\n')
out.close()
else:
out=open(path_root+'indexed_reads_Orphan_AB.txt','a')
if Library=='A':
out.write(Library+'\t'+str(index_number)+'\t'+index+'\t\t'+read1+'\t'+qual1+'\t'+str(int(x/4))+'\t'+str(position)+'\n')
if Library=='B':
out.write(Library+'\t'+str(index_number)+'\t\t'+index+'\t'+read1+'\t'+qual1+'\t'+str(int(x/4))+'\t'+str(position)+'\n')
out.close()
def gather_indices(path_root):
infile=path_root+'/indexed_reads_Uncut_mismatch_sorted.txt'
split_index1={}
split_index2={}
split_index3={}
split_index4={}
split_index5={}
split_index6={}
index_dict={}
molecule_dict={}
for line in open(infile):
out=open(path_root+'indexed_reads_Uncut_AB.txt','a')
out.write(line)
out.close()
a=line.strip().split('\t')
read_id=a[-1]
index_number=a[1]
relevant_index=a[2]+a[3]
index_dict[relevant_index]=index_number
index1=relevant_index[:6]
index2=relevant_index[6:12]
index3=relevant_index[12:18]
index4=relevant_index[18:24]
index5=relevant_index[24:30]
index6=relevant_index[30:36]
for subindex,split_index in [(index1,split_index1),(index2,split_index2),(index3,split_index3)]:
try:
split_index[subindex].append((relevant_index[:18],index_number))
except:
split_index[subindex]=[]
split_index[subindex].append((relevant_index[:18],index_number))
for subindex,split_index in [(index4,split_index4),(index5,split_index5),(index6,split_index6)]:
try:
split_index[subindex].append((relevant_index[18:],index_number))
except:
split_index[subindex]=[]
split_index[subindex].append((relevant_index[18:],index_number))
return split_index1,split_index2,split_index3,split_index4,split_index5,split_index6
def file_len(fileName):
i=0
for line in open(fileName):
i+=1
return i
out=open(path_root+'indexed_reads_Uncut_AB.txt','w')
out.close()
length1=file_len(path1+'/R1_trimmed.txt')
infile1_1=path1+'/R1_trimmed.txt'
infile1_2=path1+'/R2_trimmed.txt'
length2=file_len(path2+'/R1_trimmed.txt')
infile2_1=path2+'/R1_trimmed.txt'
infile2_2=path2+'/R2_trimmed.txt'
split_index1,split_index2,split_index3,split_index4,split_index5,split_index6=gather_indices(path_root)
in1=open(infile1_1,'r')
in2=open(infile1_2,'r')
start=time.time()
x=4
A_total=0
while x<=length1:
a=in1.readline()
b=in1.readline()
c=in1.readline()
d=in1.readline()
e=in2.readline()
f=in2.readline()
g=in2.readline()
h=in2.readline()
position=a.strip().split(' ')[0]
index2=f[0:18]
read1=b.strip()+'~~~~'+f[18:].strip()
qual1=d.strip()+'~~~~'+h[18:].strip()
find_match('A',index2,split_index4,split_index5,split_index6)
x+=4
in1=open(infile2_1,'r')
in2=open(infile2_2,'r')
x=4
B_total=0
while x<=length2:
a=in1.readline()
b=in1.readline()
c=in1.readline()
d=in1.readline()
e=in2.readline()
f=in2.readline()
g=in2.readline()
h=in2.readline()
position=a.strip().split(' ')[0]
index1=b[0:18]
read1=b[18:].strip()+'~~~~'+f.strip()
qual1=d[18:].strip()+'~~~~'+h.strip()
find_match('B',index1,split_index1,split_index2,split_index3)
x+=4
print A_total,B_total
os.system('sort -k2,2n -k7,7n '+path_root+'/indexed_reads_Uncut_AB.txt >'+path_root+'//indexed_reads_Uncut_AB_sorted.txt')