Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
After pulling your changes (begin preprocess refactor) there were some errors with filepaths and small syntax ones here and there. I was able to make it work. But there were some notable changes to the Makefile that I'd like to draw your attention to. It will necessitate you renaming the files on your end. As well as the revised TE file.
Makefile: I updated the input filenames in the makefile to keep track of everything. For the sake of clarity, I have 3 files in my input data folder Camarosa_EDTA_TEs.gff, Camarosa_Genes.gtf, and Camarosa_RepeatMasker_TEs.gff. The old TE annotation is the repeatmasker one, the new one is the EDTA one. You can identify which one is which by looking at the second column of the file if you are confused.
It is my hope that the new names will help us keep track of which one is which a little bit easier.
After pulling your changes (begin preprocess refactor) there were some errors with filepaths and small syntax ones here and there. I was able to make it work. But there were some notable changes to the Makefile that I'd like to draw your attention to. It will necessitate you renaming the files on your end. As well as the revised TE file.
Makefile: I updated the input filenames in the makefile to keep track of everything. For the sake of clarity, I have 3 files in my input data folder
Camarosa_EDTA_TEs.gff,Camarosa_Genes.gtf, andCamarosa_RepeatMasker_TEs.gff. The old TE annotation is the repeatmasker one, the new one is the EDTA one. You can identify which one is which by looking at the second column of the file if you are confused.It is my hope that the new names will help us keep track of which one is which a little bit easier.