30 lines
862 B
Python
Executable File
30 lines
862 B
Python
Executable File
#!/usr/bin/env python
|
|
|
|
import os
|
|
|
|
hapmap_dir = os.getcwd()+"/" ##CHANGE ME
|
|
|
|
def convert(line):
|
|
line = line.replace("chr","",1)
|
|
if ( line.startswith("M") ):
|
|
line = line.replace("M","MT",1)
|
|
return line
|
|
|
|
for file in os.listdir(hapmap_dir):
|
|
if ( file.endswith('vcf') ):
|
|
chrM_lines = list()
|
|
print("converting: "+file)
|
|
in_vcf = open(hapmap_dir+file)
|
|
out_vcf_filename = file.replace("hg18","b36")
|
|
out_vcf = open(out_vcf_filename,'w')
|
|
for line in in_vcf.readlines():
|
|
if ( line.startswith("#") ):
|
|
out_vcf.write(line)
|
|
else:
|
|
if ( line.startswith("chrM") ):
|
|
chrM_lines.append(line)
|
|
else:
|
|
out_vcf.write(convert(line))
|
|
for line in chrM_lines:
|
|
out_vcf.write(convert(line))
|