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filter.py
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filter.py
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#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Mon Apr 6 20:31:18 2020
@author: awad
"""
import os
def filteration(bed,vc_file,output_path=os.getcwd(),output_name='var_call_awad'):
a=list(open(bed))
b=list(open(vc_file))
z={}
x,y={},{}
for base in b:
z[base.split('\t')[0]]=[]
for base in b:
z[base.split('\t')[0]]+=[base]
aaa=[]
bbb=[]
for base in a:
aaa.append(int(base.split('\t')[1]))
bbb.append(int(base.split('\t')[2]))
cccc={}
for nnn in range(0,max(bbb)+1):
cccc[nnn]=0
ddd=[]
for nnn in range(0,len(bbb)):
ddd.append((aaa[nnn],bbb[nnn]))
for base in ddd:
for nnn in range(base[0],base[1]+1):
cccc[nnn]+=1
ccc={}
for nnn in range(0,max(bbb)+1):
ccc[nnn]=[]
del z['awad']
for key in z.keys():
q=z[key]
for base in q:
try:
ccc[int(base.split('\t')[1])]+=[base]
except:
awad=0
del q
eee={}
for nnn in range(1,max(bbb)+1):
eee[nnn]=[['.','A',0],['.','T',0],['.','C',0],['.','G',0],['.','A',0],['.','T',0],['.','C',0],['.','G',0],['.','.',0],['N','N',0]]
chr_name=list(z.keys())[0]#del it in the update
for base in ccc.keys():
q=ccc[base]
#chr_name=base#del it in the update
for ba in q:
if ba.split('\t')[3]=='.':
if ba.split('\t')[4]=='A':
eee[base][0][-1]+=1
elif ba.split('\t')[4]=='T':
eee[base][1][-1]+=1
elif ba.split('\t')[4]=='C':
eee[base][2][-1]+=1
elif ba.split('\t')[4]=='G':
eee[base][3][-1]+=1
else:
eee[base][9][-1]+=1
else:
if ba.split('\t')[4]=='A':
eee[base][4][-1]+=1
eee[base][4][0]=ba.split('\t')[3]
eee[base][5][0]=ba.split('\t')[3]
eee[base][6][0]=ba.split('\t')[3]
eee[base][7][0]=ba.split('\t')[3]
eee[base][8][0]=ba.split('\t')[3]
elif ba.split('\t')[4]=='T':
eee[base][5][-1]+=1
eee[base][4][0]=ba.split('\t')[3]
eee[base][5][0]=ba.split('\t')[3]
eee[base][6][0]=ba.split('\t')[3]
eee[base][7][0]=ba.split('\t')[3]
eee[base][8][0]=ba.split('\t')[3]
elif ba.split('\t')[4]=='C':
eee[base][6][-1]+=1
eee[base][4][0]=ba.split('\t')[3]
eee[base][5][0]=ba.split('\t')[3]
eee[base][6][0]=ba.split('\t')[3]
eee[base][7][0]=ba.split('\t')[3]
eee[base][8][0]=ba.split('\t')[3]
elif ba.split('\t')[4]=='G':
eee[base][7][-1]+=1
eee[base][4][0]=ba.split('\t')[3]
eee[base][5][0]=ba.split('\t')[3]
eee[base][6][0]=ba.split('\t')[3]
eee[base][7][0]=ba.split('\t')[3]
eee[base][8][0]=ba.split('\t')[3]
elif ba.split('\t')[4]=='.':
eee[base][8][-1]+=1
eee[base][4][0]=ba.split('\t')[3]
eee[base][5][0]=ba.split('\t')[3]
eee[base][6][0]=ba.split('\t')[3]
eee[base][7][0]=ba.split('\t')[3]
eee[base][8][0]=ba.split('\t')[3]
else:
eee[base][9][-1]+=1
ff=[]
for base in eee.keys():
qq=eee[base]
qqq=cccc[base-1]
if qqq==0:
qqq=1
qqqq=qqq-(qq[0][-1]+qq[1][-1]+qq[2][-1]+qq[3][-1]+qq[4][-1]+qq[5][-1]+qq[6][-1]+qq[7][-1]+qq[8][-1]+qq[9][-1])
if qqqq==0:
qqqq=-1
for ba in qq:
if ba[0]=='.' and ba[2]!=0:
ff.append(chr_name+'\t'+str(base)+'\t'+str(ba[0])+'\t'+str(ba[1])+'\t+1\t'+str(qqq)+'\t'+str(qqqq)+'\t'+str(ba[2])+'\t'+str(float(float(qqqq)/float(qqq)))+'\t'+str(float(float(ba[2])/float(qqq)))+'\t'+str(float(float(ba[2])/float(qqqq)))+'\n')
else:
if ba[1]=='.' and ba[2]!=0:
ff.append(chr_name+'\t'+str(base)+'\t'+str(ba[0])+'\t'+str(ba[1])+'\t-1\t'+str(qqq)+'\t'+str(qqqq)+'\t'+str(ba[2])+'\t'+str(float(float(qqqq)/float(qqq)))+'\t'+str(float(float(ba[2])/float(qqq)))+'\t'+str(float(float(ba[2])/float(qqqq)))+'\n')
elif ba[1]!='.' and ba[2]!=0:
ff.append(chr_name+'\t'+str(base)+'\t'+str(ba[0])+'\t'+str(ba[1])+'\t*1\t'+str(qqq)+'\t'+str(qqqq)+'\t'+str(ba[2])+'\t'+str(float(float(qqqq)/float(qqq)))+'\t'+str(float(float(ba[2])/float(qqq)))+'\t'+str(float(float(ba[2])/float(qqqq)))+'\n')
x[chr_name]=ff
fff=[]
for key in x.keys():
q=x[key]
for base in q:
if abs(float(base.split('\t')[-1][:-1]))>1:#7.2.2020
fff.append(base)
elif int(base.split('\t')[-5])<0 and abs(float(base.split('\t')[-2]))>=0.5:#6.4.2020
fff.append(base)
ffff={}
for bas in fff:
ffff[bas.split('\t')[1]]=[]
for bas in fff:
ffff[bas.split('\t')[1]]+=[bas]
fff=[]
for bas in ffff.keys():
if len(ffff[bas])==1:
fff.append(ffff[bas][0])
else:
fffff=sorted(ffff[bas], key=lambda i:abs(float(i.split('\t')[-1])), reverse=True)
for nec in fffff:#6.4.2020
if abs(float(nec.split('\t')[-2]))>=0.5:
fff.append(nec)
y[chr_name]=fff
h=open(output_path+'/'+output_name+'_final.vc','w')
for key in x.keys():
q=x[key]
for base in q:
h.writelines(base)
h.close()
h=open(output_path+'/'+output_name+'_filtered.vc','w')
hh=open(output_path+'/'+output_name+'_filtered.sdi','w')
for key in y.keys():
q=y[key]
q=sorted(q, key=lambda i:(int(i.split('\t')[1]),int(i.split('\t')[4].replace('*1','1').replace('+1','0').replace('-1','2'))))#7.4.2020
for base in q:
h.writelines(base)
hh.writelines(base.split('\t')[0]+'\t'+base.split('\t')[1]+'\t'+base.split('\t')[4].replace('+','').replace('*1','0')+'\t'+base.split('\t')[2]+'\t'+base.split('\t')[3]+'\t*\t*\n')
h.close()
hh.close()
return(x,y)
import argparse
parser = argparse.ArgumentParser(prog="variant_caller",usage='%(prog)s -h [options] -b <bed_file> -r <ref_genome> -g <draft>',description='Variant caller',)
parser.add_argument("-b",nargs=1,type=str,required=True,metavar='mapping bed file',dest="bed")
parser.add_argument("-v",nargs=1,type=str,required=True,metavar='vc_file',dest="vc")
parser.add_argument("-o",nargs=1, type=str, default=[os.getcwd()], metavar='output path',dest="output")
parser.add_argument("-f",nargs=1, type=str, default=['var_call_awad'], metavar='output file name',dest="name")
args = parser.parse_args()
bed=args.bed[0]
vc_file=args.vc[0]
output=args.output[0]
name=args.name[0]
filteration(bed=bed,vc_file=vc_file,output_path=output,output_name=name)