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vcf_af_search.py
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#! /bin/python3.8
from mymodule import *
import sys
#check that script use is correct
if len(sys.argv)<3:
print ('Usage: vcf_as_search.py VCF_file outfile')
sys.exit()
#assign arguments to file names
else:
vcffile=sys.argv[1]
outfile=sys.argv[2]
#generate cygwin path files
vcffile=open(cygwinpath(vcffile), 'r')
outfile=open(cygwinpath(outfile), 'w')
#user choice input
choice=int(input("Enter 1: To generate list of SNPs\nEnter 2: To generate list of insertions\nEnter 3: To generate list of deletions\nEnter 4: To generate list of positions with more that one variation\nEnter 5: to generate list with all of the above\n"))
#Choice 1: Make SNP list
if choice==1:
snpnum=0
linenum=0
outfile.write('#CHROM\tPOS\tPOS\tREF\tALT\tID\tInfo\n')
for Line in vcffile:
Line=Line.strip('\n') #strip end of line
if Line[0]=='#':
continue #ignore meta and header
Columns=Line.split('\t')
Chr=Columns[0]
Pos=Columns[1]
ID=Columns[2]
Ref=Columns[3]
Alt=Columns[4]
Info=Columns[7]
Info=Info.split(';')
SAS=Info[9]
EUR=Info[8]
EAS=Info[5]
AMR=Info[6]
AFR=Info[7]
if ',' in Alt: #if >1 alt base
nuc=Alt.split(',')
for i in nuc:
Alti=i #help make one variant per line
if len(i)==1 and len(Ref)==1: #snp
outsnpv='\t'.join([Chr,Pos,Pos,Ref,Alt,ID,EAS,AMR,AFR,EUR,SAS])+'\n'
outfile.write(outsnpv)
snpnum+=1
continue
if len(Ref)==1 and len(Alt)==1: #check for snps
outsnp='\t'.join([Chr,Pos,Pos,Ref,Alt,ID,AFR,AMR,EAS,EUR,SAS])+'\n'
outfile.write(outsnp)
snpnum+=1
linenum+=1
if linenum%1000==0: #check status
status=str(linenum)+' finished'
sys.stderr.write(status+'\r')
vcffile.close()
outfile.close()
print('Number of SNPs: ',snpnum)
#Choice 2: Make insertion list
if choice==2:
insnum=0
linenum=0
outfile.write('#CHROM\tPOS\tPOS\tREF\tALT\tID\n')
for Line in vcffile:
Line=Line.strip('\n') #strip end of line
if Line[0]=='#':
continue #ignore meta and header
Columns=Line.split('\t')
Chr=Columns[0]
Pos=Columns[1]
ID=Columns[2]
Ref=Columns[3]
Alt=Columns[4]
Info=Columns[7]
Info=Info.split(';')
SAS=Info[9]
EUR=Info[8]
EAS=Info[5]
AMR=Info[6]
AFR=Info[7]
if ',' in Alt: #if >1 alt base
nuc=Alt.split(',')
for i in nuc:
Alti=i
if len(i)>len(Ref): #insertion
outinsv='\t'.join([Chr,Pos,Pos,Ref,Alti,ID,EAS,AMR,AFR,EUR,SAS])+'\n'
outfile.write(outinsv)
insnum+=1
continue
if len(Ref)<len(Alt): #check for insertion
outins='\t'.join([Chr,Pos,Pos,Ref,Alt,ID,EAS,AMR,AFR,EUR,SAS])+'\n'
outfile.write(outins)
insnum+=1
linenum+=1
if linenum%1000==0: #check status
status=str(linenum)+' finished'
sys.stderr.write(status+'\r')
vcffile.close()
outfile.close()
print('Number of Insertions: ',insnum)
#Choice 3: Make deletion list
if choice==3:
delnum=0
linenum=0
outfile.write('#CHROM\tPOS\tPOS\tREF\tALT\tID\n')
for Line in vcffile:
Line=Line.strip('\n') #strip end of line
if Line[0]=='#':
continue #ignore meta and header
Columns=Line.split('\t')
Chr=Columns[0]
Pos=Columns[1]
ID=Columns[2]
Ref=Columns[3]
Alt=Columns[4]
Info=Columns[7]
Info=Info.split(';')
SAS=Info[9]
EUR=Info[8]
EAS=Info[5]
AMR=Info[6]
AFR=Info[7]
if ',' in Alt: #if >1 alt base
nuc=Alt.split(',')
for i in nuc:
Alti=i
if len(i)<len(Ref): #deletion
outdelv='\t'.join([Chr,Pos,Pos,Ref,Alti,ID,EAS,AMR,AFR,EUR,SAS])+'\n'
outfile.write(outdelv)
delnum+=1
continue
if len(Ref)<len(Alt): #check for insertion
outdel='\t'.join([Chr,Pos,Pos,Ref,Alt,ID,EAS,AMR,AFR,EUR,SAS])+'\n'
outfile.write(outdel)
delnum+=1
linenum+=1
if linenum%1000==0: #check status
status=str(linenum)+' finished'
sys.stderr.write(status+'\r')
vcffile.close()
outfile.close()
print('Number of Deletions: ',delnum)
#Choice 4: Make >1 variation list
if choice==4:
varnum=0
linenum=0
outfile.write('#CHROM\tPOS\tPOS\tREF\tALT\tID\n')
for Line in vcffile:
Line=Line.strip('\n') #strip end of line
if Line[0]=='#':
continue #ignore meta and header
Columns=Line.split('\t')
Chr=Columns[0]
Pos=Columns[1]
ID=Columns[2]
Ref=Columns[3]
Alt=Columns[4]
Info=Columns[7]
Info=Info.split(';')
SAS=Info[9]
EUR=Info[8]
EAS=Info[5]
AMR=Info[6]
AFR=Info[7]
if ',' in Alt: #if >1 alt base
outvar='\t'.join([Chr,Pos,Pos,Ref,Alt,ID,EAS,AMR,AFR,EUR,SAS])+'\n'
outfile.write(outvar)
varnum+=1
linenum+=1
if linenum%1000==0: #check status
status=str(linenum)+' finished'
sys.stderr.write(status+'\r')
vcffile.close()
outfile.close()
print('Number of positions with more than one variation: ',varnum)
#Choice 5: Make all of the above list
if choice==5:
allnum=0
linenum=0
outfile.write('#CHROM\tPOS\tPOS\tREF\tALT\tID\n')
for Line in vcffile:
Line=Line.strip('\n') #strip end of line
if Line[0]=='#':
continue #ignore meta and header
Columns=Line.split('\t')
Chr=Columns[0]
Pos=Columns[1]
ID=Columns[2]
Ref=Columns[3]
Alt=Columns[4]
Info=Columns[7]
Info=Info.split(';')
SAS=Info[9]
EUR=Info[8]
EAS=Info[5]
AMR=Info[6]
AFR=Info[7]
if ',' in Alt: #if >1 alt base
nuc=Alt.split(',')
for i in nuc:
Alti=i
outall='\t'.join([Chr,Pos,Pos,Ref,Alti,ID,EAS,AMR,AFR,EUR,SAS])+'\n'
outfile.write(outall)
allnum+=1
continue
outall='\t'.join([Chr,Pos,Pos,Ref,Alt,ID,EAS,AMR,AFR,EUR,SAS])+'\n'
outfile.write(outall)
allnum+=1
linenum+=1
if linenum%1000==0: #check status
status=str(linenum)+' finished'
sys.stderr.write(status+'\r')
vcffile.close()
outfile.close()
print('Number of variations: ',allnum)
if choice!=1 and choice!=2 and choice!=3 and choice!=4 and choice!=5:
print("Invalid choice\nPlease try again choosing a number 1-5")
sys.exit()