Nabil-Fareed Alikhan

Python - setuptools

3

Your setup in the python template probably wont work if the user doesnt have setuptools installed. which is actually common. Something like this in setup.py would be good: ``` try:...

I don' think it checks for duplicate taxon on runtime. It should.

Better exception handling if query directory is empty or do_run fails

1

If do_run fails or input file directory is empty (so do_run does nothing). cluster_matrix throws a big ugly exception that makes no sense to the user. Should be exception handling/checks...

Scott doesn't like (or didnt like) megablast scoring parameters, now used by default in BLAST+'s blastn. He may ask the option to override this with legacy blast's scoring parameters. i.e....

CLI

1

CLI . For BRIG?

Move the manual to Read the docs.

There really should directions that point people here to post issues.

Seems to get hidden under a fold.

https://www.researchgate.net/post/Why_does_BRIG_fail_to_create_rings_for_some_of_the_genomes