I'm running dexseq_prepare_annotation.py on ENSEMBL GTF (I have tried gtf files from a couple of releases) files and have the following error.
File "dexseq_prepare_annotation.p", line 129
raise ValueError, "Same name found on two chromosomes: %s, %s" % ( str(l[i]), str(l[i+1]) )
SyntaxError: invalid syntax
<font face="monospace">I'm not particularly familiar with python and will be grateful for any pointers on how to deal with this problem.</font>
Thanking You,
Vakul
Hi,
I changed the script to:
raise ValueError ("Same name found on two chromosomes: %s, %s") % ( str(l[i]), str(l[i+1]) )
and it did the trick in my case (at least for this particular syntax error). I would guess that this is a python 2/python 3 issue. I hope that I made a good choice :D
worked for me too, thx & dzięki! To adapt to python3, you need also replace xrange with range around those lines.