mpoelchau

Glad to provide some motivation :). No rush on my part though - I was just grateful that you posted the issue since it saved me some time!

@spficklin it would be great if additional SO types beyond mRNA or lnc_RNA could be added. I could give you a list of what we currently have on our site,...

Sure, if it's not too much manual work on your part to add all of these. A lot of the child terms are not very likely to occur in gene...

Hi @dcopetti - that's an interesting use case! I suppose you could hack a qc report file to get that done. The qc reports are line-based because not every feature...

Hi @seaward901 , Can you provide the full output of the installation command? Also, what version of python are you using?

Are you installing within a virtual environment? E.g.: ``` #make new python environment and source it python3 -m venv my-newenv source my-newenv/bin/activate #sometimes you have to upgrade pip and install...

I'm not 100% sure what's going on. My first guess is permissions. It looks like you're not using a python virtual environment. Could you try that? ``` python3 -m venv...

@yjx1217 Sorry, I'm not sure what's going on. I ran a fresh install of miniconda (Mac) and did the following: ``` (base) :~ $ ~/miniconda3/bin/pip install gff3tool Collecting gff3tool Using...

Hi Jing, Sorry you're running into issues. Looks like the program is having issues with ID attributes. Can you send me the 2 gff3 files and reference fasta file so...

Hi @lijing28101 - the problem you see is occurring because our merge program is making some (possibly unreasonable) assumptions about the way the ID attribute is formatted. We'll try to...