Hi,

I want to split an Ensembl GTF file into individual files by gene id. I tried using awk to little avail:

awk '{gsub(/"|;/, "", $10); print >> ($10".gtf")}' Homo_sapiens.GRCh38.82.gtf

This splits the file as expected but also strips the quotes and semicolon from the gene_id entry in each GTF file:

gene_id ENSG00000142733

instead of the correct

gene_id "ENSG00000142733";

This was fixed easily:

find . -type f -name "*.gtf" | xargs sed -i "" 's/\(ENSG[0-9]\{11\}\)/"\1";/'

However, the remaining problem is that awk also replaces all tabs separating the nine columns/fields with spaces rendering the resulting GTF files invalid.

If anyone can hint me at a possible solution, that would be fantastic!

Thanks, Kemal