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biocore / taxster

taxster: assigning taxonomy to organisms you've never even heard of
BSD 3-Clause "New" or "Revised" License
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adds uc processing #6

Closed gregcaporaso closed 8 years ago

gregcaporaso commented 8 years ago

@wasade, @audy I'm working on porting some code from QIIME 1 related to taxonomy assignment for use in a revision of this paper, and ultimately a QIIME 2 plugin. Are you ok with this repo being for all things taxonomy-related? We can add the sklearn classifiers in here too ultimately.

wasade commented 8 years ago

:+1: glad to help and review too! On Mar 2, 2016 08:15, "Greg Caporaso" notifications@github.com wrote:

@wasade https://github.com/wasade, @audy https://github.com/audy I'm working on porting some code from QIIME 1 related to taxonomy assignment for use in a revision of this paper, and ultimately a QIIME 2 plugin. Are you ok with this repo being for all things taxonomy-related? We can add the

sklearn classifiers in here too ultimately.

You can view, comment on, or merge this pull request online at:

https://github.com/biocore/taxster/pull/6 Commit Summary

  • set package up for testing

File Changes

Patch Links:

— Reply to this email directly or view it on GitHub https://github.com/biocore/taxster/pull/6.

gregcaporaso commented 8 years ago

Cool, thx. The initial version is going to be pretty sparse, just adding some API calls for uc to taxonomy processing (so we can adapt the uclust consensus assigner to be a vsearch consensus assigner). I'm going to push that in this morning.

wasade commented 8 years ago

Excellent, looking forward to seeing it On Mar 2, 2016 08:30, "Greg Caporaso" notifications@github.com wrote:

Cool, thx. The initial version is going to be pretty sparse, just adding some API calls for uc to taxonomy processing (so we can adapt the uclust consensus assigner to be a vsearch consensus assigner). I'm going to push that in this morning.

— Reply to this email directly or view it on GitHub https://github.com/biocore/taxster/pull/6#issuecomment-191238603.

gregcaporaso commented 8 years ago

@wasade, this is ready for review if you're interested/available. There is only one public API function for now, and README documents how to use it. We're doing some experiments with this code - we can clean it up and add niceties if the package ends up going anywhere, but am not going to invest a ton of time in it at the moment in case our experiments don't pan out.

wasade commented 8 years ago

Only minor comments given the intent/focus

audy commented 8 years ago

I'm okay with this but it might be good to start with a clean master branch.

--austin

On Mar 2, 2016, at 05:15, Greg Caporaso notifications@github.com wrote:

@wasade, @audy I'm working on porting some code from QIIME 1 related to taxonomy assignment for use in a revision of this paper, and ultimately a QIIME 2 plugin. Are you ok with this repo being for all things taxonomy-related? We can add the sklearn classifiers in here too ultimately.

You can view, comment on, or merge this pull request online at:

https://github.com/biocore/taxster/pull/6

Commit Summary

set package up for testing File Changes

A .travis.yml (17) D prototyping/Naive bayes start.ipynb (146) A setup.py (24) A taxster/init.py (9) A taxster/_uc.py (7) A taxster/tests/init.py (7) Patch Links:

https://github.com/biocore/taxster/pull/6.patch https://github.com/biocore/taxster/pull/6.diff — Reply to this email directly or view it on GitHub.

gregcaporaso commented 8 years ago

@audy, there's not much in master (3 commits) so I'm not too concerned about it. If you feel strongly, could you let me know what you'd like me to do specifically?

wasade commented 8 years ago

Just a note, I'm :+1: on merge

gregcaporaso commented 8 years ago

Thanks guys!