Using pre-created kmer distances

[balags1]

Is there a way (a command specific to) using pre-created distance matrices with PopPUNK? Or alternatively, is there way to provide our own settings for sketch size and kmer length?
Thanks in advance for your support.

[johnlees]

Please see https://poppunk.bacpop.org/sketching.html#choosing-the-right-k-mer-lengths

[balags1]

So we can only use the software settings? We cannot use pre-created distance matrices not from POPPunk?

[johnlees]

Sorry we don't have this implemented directly (nor any plans to at this point).

You could make your own .npy distance file which should work for a lot of functions, but I wouldn't be able to guarantee there wouldn't then be steps which recompute distances from the sketches.

If you want to do this I would instead import PopPUNK as a module in your own code and use the functions called in __main__.py with the right arguments -- most of these take a numpy distance matrix as input.