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Expose branch length function on CLI for EMDUnifrac #33

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dkoslicki opened this issue May 20, 2020 · 3 comments
Closed

Expose branch length function on CLI for EMDUnifrac #33

dkoslicki opened this issue May 20, 2020 · 3 comments
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@dkoslicki

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@dkoslicki
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Currently the branch length function is hard coded here. Want to expose this as an option on the command line.
@dkoslicki dkoslicki self-assigned this May 20, 2020
dkoslicki added a commit that referenced this issue Jun 24, 2020
@dkoslicki
significant refactor of ProfilingTools fixes #35 fixes #34 fixes #33
428cd05 
change log:
- exposed branch_length_function to Profile (defaults to 1/(depth in tree)
- added ability to not normalize the unifrac input vectors
- added better test data (that includes incorrectly formatted profiles)
- added test cases
@dkoslicki
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Can close after merge to master pending coordination with @fernandomeyer after Friday meeting.
Will need to see if we should make this a CLI option for opal.py itself

@fernandomeyer
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Branch length CLI option added with commit e9d555e.

@dkoslicki
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Great! Looks to be working well: closing

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@dkoslicki @fernandomeyer