Complete genomes can be 'complete' or 'chromosome'

We have a problem with bacterial genomes that sometimes the assembly_summary.txt file says complete and sometimes it says chromosome for finished bacterial genomes.

This is partially to do with the fact that bacteria usually only have 1 chromosome, but partially because they have plasmids too. It’s confusing.

If I want both, can I do -l complete -l chromosome to get both? Or so I run 2 commands with same -o folder?

[tseemann]

I am thinking if --assembly-level or --format contain a “comma” , character then you could convert into a regexp and match using regexps in your filtering logic.

For example --format genbank,fasta,wgs would become ^(genbank|fasta|wgs)$

And --format protein-cds would just be ^(protein-cds)$ etc

I’ve used this method in my tools before and it works well. You could also use a hash/dict lookup by creating a want_format[ xxx ] = True/False system instead of regexp. This method also has the advantage that if you preset all the valid options to False then you can validate input easily.

[kblin]

I will add this to the documentation. I’m just beginning to think that the features are outgrowing the README file and I need to start doing this properly.