How do I index GTF for pysam

[Alex Rogozhnikov]

Tried to open GTF file with pysam, index seems like a hard requirement to do anything (even plain fetch).

OSError: index `.../Homo_sapiens.GRCh38.96.gtf.tbi` not found

I've tried pysam.index (that's for bam, I know, but I should've tried!)

/Homo_sapiens.GRCh38.96.gtf" is in a format that cannot be usefully indexed\n'

I've tried tabix - also doesn't work. Super helpful error:
tbx_index_build failed: Homo_sapiens.GRCh38.96.gtf

If there is a simple way to get mapping transcript to genome in python - please let me know

Thank you!

[Alex Rogozhnikov]

Ok, here is the way that worked for me

0. install tabix with apt get

1.sort (there are some perl/python utils around which I didn’t check)

(grep -v "Parent=" Homo_sapiens.GRCh38.96.gtf|sort -k1,1 -k4,4n -k5,5n;grep "Parent=" Homo_sapiens.GRCh38.96.gtf|sort -k1,1 -k4,4n -k5,5n)| sort -k1,1 -k4,4n -s > Homo_sapiens.GRCh38.96.sorted.gtf

2. compress with bgzip (indexing works only on compressed)

bgzip -c Homo_sapiens.GRCh38.96.sorted.gtf > Homo_sapiens.GRCh38.96.sorted.gtf.gz

3. create index with tabix

tabix Homo_sapiens.GRCh38.96.sorted.gtf.gz

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[Alex Rogozhnikov]

even better solution is to use pyensembl package which handles downloading/parsing and has a nice python interface.
So you'll not meet this problem