format the gtf file

Question

[bright602]

Hi there, I have a gtf file. Could some one let me know how to move the third column with "transcript" to the first line of each gene block with the same gene id?

Thanks so much!

[Pierre Lindenbaum]

1) do not use excel.

2) why would you want to do this ?

[cpad0112]

Do not post the images of the data.

Answer 1

[Juke34]

Here several tools that can help you https://agat.readthedocs.io/en/latest/topological-sorting-of-gff-features.html

Answer 2

[Carambakaracho]

You want to do this in excel? Rename all transcript to AAA_transcript in col 3, sort by coordinate and then by feature type (col 3), rename back. You can implement something similar in Python, but I'm not sure it's worth the effort.

Also not sure why you want this but it's certainly not common practice, so there's unlikely a tool for this.