Add hp, dayhoff options to manysketch

[olgabot]

Fixes #337 to add support for dayhoff and hp moltypes to manysketch.

To create sketches using the new functionality from protein sequences only (no translation from DNA sequences, sorry), the dayhoff, hp, moltypes can be specified in the parameter string:

sourmash scripts manysketch proteins.csv -o proteins.zip -p dayhoff,k=16 -p protein,k=10 -p hp,k=42

Where proteins.csv looks like:

name,genome_filename,protein_filename
protein1,,protein1.fa
protein2,,protein2.fa

[ctb]

hi @olgabot this looks great to me!

I note that it doesn't look like the manysketch docs need any changes. We still don't do translation, but that's ok ;)

I would like to ask you to change the PR title and description -

• right now it talks about multisketch not manysketch
• the PR description should be updated to close How to do manysketch on dayhoff, hp moltypes? #337 when this is merged (i.e. Fixes #337) and also should include a brief description of the new functionality.

If you'd like to add yourself to the authorship list in the README and pyproject.toml that would also be fine! No push either way - this may be too small a PR - but if you want to, please do!

[olgabot]

I note that it doesn't look like the manysketch docs need any changes. We still don't do translation, but that's ok ;)

Added a section about protein sketching with manysketch!

the PR description should be updated to close #337 when this is merged (i.e. Fixes #337) and also should include a brief description of the new functionality.

Added! Let me know if more elaboration is needed.

If you'd like to add yourself to the authorship list in the README and pyproject.toml that would also be fine! No push either way - this may be too small a PR - but if you want to, please do

By the time I finish #354, I'll probably have forgotten to add myself, so I'm doing it now.

[ctb]

nice work! One suggestion for you to consider on documentation, but otherwise - go ahead and merge! (You should be able to merge now - if not, lmk.)

[ctb]

hi @olgabot is it ok if I update with my suggestion and then merge? I'm hoping to do a new release in the next day or two.

[olgabot]

hi @olgabot is it ok if I update with my suggestion and then merge? I'm hoping to do a new release in the next day or two.

Yes, totally fine to merge!