search

KennthShang / PhaBOX

Local version of the virus identification and analysis web server (tool set)
https://phage.ee.cityu.edu.hk/
Academic Free License v3.0
37 stars 5 forks source link

CLI help typo #37

Closed bernt-matthias closed 2 weeks ago

bernt-matthias commented 2 weeks ago

This should probably be --ccov?

KennthShang commented 2 weeks ago

Yes, it is --ccov. Thanks for catching this. Will update it in the next patch.

Best, Jiayu

bernt-matthias commented 2 weeks ago

Maybe also correct here to Minimum shared percent of proteins for AAI based genus grouping?:

https://github.com/KennthShang/PhaBOX/blob/bf962b247784f75ad851ca7521a4f82ff0a173e9/src/phabox2/phabox2.py#L256

bernt-matthias commented 2 weeks ago

https://github.com/KennthShang/PhaBOX/blob/f90abd7083fdc15976294a9118cfff454416d143/src/phabox2/phabox2.py#L282

-        portal protein || 84 percent prokaryotic viruses have portal
+        portal         || 84 percent prokaryotic viruses have portal
bernt-matthias commented 2 weeks ago

Wonder if the detailed docs for --task cherry miss the description for --magonly?

bernt-matthias commented 2 weeks ago

Was also asking myself: The --aai argument is used in two tasks. Is it intended that uses can only choose the same value for both tasks?

KennthShang commented 2 weeks ago

Thanks for the corrections. I have revised the mentioned descriptions.

Wonder if the detailed docs for --task cherry miss the description for --magonly?

Yes, it seems I forgot to add this new option. I have mentioned it to the phabox2.py scripts in the GitHub, and also update the wiki.

Was also asking myself: The --aai argument is used in two tasks. Is it intended that uses can only choose the same value for both tasks?

Yes, if the user calls the end_to_end task, --aai, --share, and --pcov can only choose the same value. This is because some submodules in CHERRY will reuse the results from PhaGCN. （According to our experiments, the taxonomy classification of virus aids the host prediction).

Thanks for your reports.

Best, Jiayu

KennthShang commented 2 weeks ago

I will update a new release if we figure out why the tree task is stuck on your data.

By the way, I have updated the WIKI so that users can learn how to install the latest PhaBOX with GitHub. Sorry for the inconvenience.

Best, Jiayu

KennthShang commented 2 weeks ago

The above-mentioned issues are fixed in v2.1.5

Best, Jiayu