matsen/pplacer — Issue #192: `rppr infer` infers conservative classifications for unclassified reference package sequences
Author: matsen
Created: 2011-12-20 18:55:32+00:00
State: open
Labels: top

Given a reference package such that some sequences are unclassified, spit out a complete CSV seq info file with
taxonomic annotations for the unclasified ones. These classifications should be conservative!

Steps include

- cutting the unclassified reference sequences out of the ref tree
- placing and classifying (for a conservative classification, take the most specific classification that contains 100% of the mass)
- spitting out the classifications

First step is writing a test first for the tree surgery. In the case of an entirely unclassified subtree, it will all want to get taken out (an MRCA approach would be useful here).