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matsen / pplacer

Phylogenetic placement and downstream analysis
http://matsen.fredhutch.org/pplacer/
GNU General Public License v3.0
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Clarify descriptions of `--normalize-by-specimen` flag functionality in scripts/classif_rect.py #312

Closed metasoarous closed 10 years ago

metasoarous commented 11 years ago

The functionality in question is much easier to understand if "normalized tally" for a specimen is described as the "frequency" of some taxon for that specimen. As such, the "normalized_tally" output in by_taxon can be described as an "average_frequency".

metasoarous commented 11 years ago

I've realized this functionality was only in the the three-study branch, so will be merging this in as part of this ticket as well.

metasoarous commented 11 years ago

This task ballooned a bit into a bit of an overhaul for increased consistency and ease of understanding what the output/input options are. See branch 312-classif-rect-average-frequency for the current status.

@nhoffman - There are a few other things we chatted about that would be nice, but these might have to wait. I can open up separate ticket(s) for those though.

nhoffman commented 11 years ago

@metasoarous - thanks for this - is this ready for a pull request? I'm updating the pipeline (depends on changes already in dev) and it would be nice to start using this. If not, no problem - I can always grab the script and use it standalone.

metasoarous commented 11 years ago

@matsen - Noah and I just chatted about this. While these changes are ready to be merged, they are breaking changes. Since we've also renamed the script (as classif_table.py), we're wondering if it doesn't make sense to leave the old script in and deprecate it with a warning that the script will be removed eventually. What do you think?

matsen commented 11 years ago

Sounds great!

On Thu, Nov 21, 2013 at 1:40 PM, Christopher Small <notifications@github.com

wrote:

@matsen https://github.com/matsen - Noah and I just chatted about this. While these changes are ready to be merged, they are breaking changes. Since we've also renamed the script (as classif_table.py), we're wondering if it doesn't make sense to leave the old script in and deprecate it with a warning that the script will be removed eventually. What do you think?

— Reply to this email directly or view it on GitHubhttps://github.com/matsen/pplacer/issues/312#issuecomment-29027232 .

Frederick "Erick" Matsen, Assistant Member Fred Hutchinson Cancer Research Center http://matsen.fhcrc.org/

metasoarous commented 10 years ago

Good to merge?

matsen commented 10 years ago

@nhoffman shall I just click on the big green button?

nhoffman commented 10 years ago

Yes!

On Mon, Feb 3, 2014 at 10:14 AM, Erick Matsen notifications@github.comwrote:

@nhoffman https://github.com/nhoffman shall I just click on the big green button?

Reply to this email directly or view it on GitHubhttps://github.com/matsen/pplacer/pull/312#issuecomment-33982732 .