GTF to GFF transformation

Question

GTF to GFF transformation

Closed this issue 4 years ago · 6 comments

I downloaded the Homo_sapiens.GRCh38.102.gtf from Ensembl, but I am getting this error for the GTF to GFF transformation.

python /opt/anaconda3/lib/R/library/DEXSeq/python_scripts/dexseq_prepare_annotation.py Homo_sapiens.GRCh38.102.gtf dexseq.gff

File "/opt/anaconda3/lib/R/library/DEXSeq/python_scripts/dexseq_prepare_annotation.py", line 129
raise ValueError, "Same name found on two chromosomes: %s, %s" % ( str(l[i]), str(l[i+1]) )

^
SyntaxError: invalid syntax

so how can I to fix it?
thank you!

Answer 1 · 2021-01-09T11:37:15.000Z

I think its related to the python version. Could you tell me your python version?

Answer 2 · 2021-01-10T07:26:48.000Z

My python version is 3.6.8

Answer 3 · 2021-01-11T15:42:59.000Z

Yes, the original script was in python2 (which is what you seem to have used and got the error). We have updated the script for python3 in this repository. Could you try it from our repo here?

Answer 4 · 2021-01-12T02:34:51.000Z

You mean I should download it from github?
I downloaded DEXSeq-1.28.0 from bioconductor before. It was in python2 , right?
But my R version is 3, is it suitable for your script?

Answer 5 · 2021-01-12T09:39:13.000Z

That's correct. the github version should be compatible to your python. And yes, the R version is not an issue.

Answer 6 · 2021-01-12T13:26:36.000Z

OK, I will try it! Thanks!!!