Skip to content

Create DELLYtoVCF.py #9

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
gmykim wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Create DELLYtoVCF.py #9

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
23 changes: 23 additions & 0 deletions Scripts/modification_scripts/DELLYtoVCF.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
# This script is used to convert the output of delly (WHOLE GENOME) into the standard vcf format!!
import sys
f=open(sys.argv[1],"r")
lines=f.readlines()
software_result=[]
for x in lines:
if (x[0].isdigit() or x[0]=="Y" or x[0]=="X"):
software_result.append(x.split())
f.close()
bmark = [0] * (len(software_result))

with open(sys.argv[2],'w') as f1:
f1.write('##fileformat=VCFv4.2\n##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant detected">\n##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of structural variant">\n##INFO=<ID=END,Number=1,Type=Integer,Description="End position of structural variant">\n#CHROM POS ID REF ALT QUAL FILTER INFO\n')
for j in range(len(software_result)):
if(software_result[j][4]=="<DEL>"):
f1.write(software_result[j][0]) #CHROM
f1.write('\t') # tab
f1.write(software_result[j][1]) #POS
f1.write('\t'+'.'+'\t'+'.'+'\t'+'<DEL>'+'\t'+'.'+'\t'+'PASS'+'\t'+'SVTYPE=DEL;SVLEN=')
f1.write(str( int((software_result[j][7].split(";")[4]).split("=")[1] )- int (software_result[j][1] ) ) ) #start pos - end pos
f1.write(";END=")
f1.write( (software_result[j][7].split(";")[4]).split("=")[1] ) #END in FORMAT
f1.write('\n')