Initial fetch of fungal gene models from VEuPathDB mostly a 'beautiful work in progress' ;)

I attempted to automate fetching fungal genomes' gene model and community annotation (apollo) files from VEuPathDB (fungidb.org). I obtained 279 GFF files. Of those GFF files, 8 were converted to bigbeds that be passed on to UCSC. The remain fail into three categories:
1. No mapping of the VEuPathDB abbreviations to NCBI Geneomes accessions (112) Note that some of these may actually correspond to accessions but VEuPathDB didn't include that in their metadata or they are really similar to existing accessions. Who knows 🤷‍♂️
2. No chromAlias file for the NCBI accession at UCSC
3. Failure to use the chromAlias file to generate a bigbed (probably because names of chromosomes/contigs don't match). These might be relatively simple to fix but will still probably be manual. One example I looked at had the same names for chromosomes, only UCSC had a '.versionnumber' but VEuPathDB did not.

Even with the successes, it would probably be a good idea to verify that the sequences that VEuPathDB has actually correspond to the sequences with those accessions at NCBI (with a checksum presumably).

I'll post the IDs of the various failure states in individual comments below.

Start by reviewing the 279 GFF files and the failure categories described in the issue, including missing NCBI accession mappings, absent UCSC chromAlias files, and failed bigBed conversion. Compare VEuPathDB metadata and sequences with the corresponding NCBI accessions, including checksum verification where possible. Done would require a defined, reproducible handling for the failure states and documented results.

Written by the indexing model from the issue text.