my ultimate goal is to use the genewise option in popoolation to evaluate allele frequency variation at mitochondrial snps between two divergent populations. I need to convert the gff file to a gtf file first. So I have buried myself in different ways of annotating the GFF3 file to get popoolation to read it, and I get nowhere. So I have tried several gff converters. The original GFF3 file comes from MITOS or sometimes I import that into Geneious and export it again. I have worked for days on different annotation types, with lines for parents included or omitted. Nothing seems to work. I have been using the GenomeTools website to validate the file and I do find some errors. It looks like the command line version of GenomeTools would work a lot better, but its hard for me to figure out how to properly install it in macOS. Here's the output of that command (I used the biostars installation to get conda installed a few weeks ago and have been able to install other programs that way. But I just get errors when I try to install GenomeTools.
My ultimate goal is to get a gff that will convert to a gtf that will be readable by popoolation. So if there is another route to that goal without needing GenomeTools I would be happy to take it.
$ conda install genometools Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: \ Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: Specifications: - genometools -> python=2.7 Your python: python=3.7 If python is on the left-most side of the chain, that's the version you've asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that. (base)