help info for use as a library

[jianshu93]

Hello Jim,

Is that possible that a detailed function of comparing 2 genomes using skani can be added to readme so that when users want to rely on skani as library in other tools et.al. (or in other words make it modular). I can see that it is somewhere in the dist.rs

Thanks,

Jianshu

[bluenote-1577]

Hi jianshu,

If there is enough interest in using skani as a library, I'm not opposed to setting a more detailed Readme to use skani as a rust library with actual docs. I'll leave this up for now to see if there is other interest.

Maybe also, see https://github.com/althonos/pyskani by @althonos for how python bindings were generated for skani. His code is cleaner than mine and gives an idea for how to use skani's rust internals.

I can probably set up a small Readme for how to compare two genomes. Would that be sufficient for you?

[jianshu93]

Hello Jim,
Thanks for pointing me to pyani and I think it will be very useful for many who love python. Yes a readme for Rust users will be very helpful, for example reading 2 genomes and then print out ANI (or even compare 2 list of genomes in parallel et.al., two main usage cases).

Thanks,

Jianshu

[bluenote-1577]

Hi Jianshu,

I've written up a quick minimal example on how to use skani here: https://github.com/bluenote-1577/skani-lib-example.

Let me know how it goes. For now, you'll have to go through skani's code to understand the function specifications (or https://docs.rs/skani/0.1.0/skani/), but maybe I'll support skani as a true library with docs one day :), depending on requests.

Jim

[jianshu93]

Oh Many thanks！

This is very helpful！ I am going to try to use it a another tool.

Jianshu.

[AroneyS]

Are you planning on updating the crate (https://docs.rs/skani/latest/skani/)? I can only find up to v0.1.1.

[bluenote-1577]

Hi @AroneyS,

I currently am not planning on updating crate for two reasons.

1. I have not changed the underlying algorithms much in 0.1; changes have mostly been bug fixes and file-io things unrelated to the core algorithm.
2. Cargo has an annoying thing where you can not publish a crate if you specify a dependency directly from github. I had to swap to a github dependency in v0.1.3 so I can't publish it on crates.io right now.

If you have any questions about usage, let me know. I'm still keeping this open to gauge interest in skani's usage as a library