I wanted to convert the map file from hg18 to hg19. I noticed the liftoverplink on github and the liftMap.py Script, but I run into this :
Converting MAP file to UCSC BED file...
SUCC: map->bed succ
Lifting BED file...
sh: 1: liftOver: not found
Traceback (most recent call last):
File "liftOverPlink.py", line 172, in <module>
makesure(liftBed(oldBed, newBed, unlifted, args.chainFile, liftOverPath),
File "liftOverPlink.py", line 64, in liftBed
for ln in myopen(params['UNLIFTED']):
File "liftOverPlink.py", line 34, in myopen
IOError: [Errno 2] No such file or directory: 'lifted.bed.unlifted'
[email protected]:/home/xueenci/liftOver# exit
I have noticed that someone has encountered the same problem, but I don't know how to solve it. I hope someone can help me！