I have a custom annotation file (gtf) that has custom annotations that were made using an older version of a genome, and I want to update those annotations so I can use them on the newest genome version. These annotations are simple single genomic ranges (no gaps) and range from ~150bp to ~250,000bp in length. I am working in the Tetrahymena thermophila model organism whose genome changes every few years as new sequencing experiments are complete.
I have started writing a custom python script to extract the sequences from the old genome, BLAT them to the new genome, and extract the new coordinates but the script is taking a long time to write and I was wondering if there was already a program/tool out there that I could use for this (what I assume is a) common task. Any suggestions?