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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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add `guppy error` #205

Closed habnabit closed 12 years ago

habnabit commented 12 years ago

takes two placefiles; measures the distance between same-named placements.

matsen commented 12 years ago

What do you think about the CLI having a flag to specify the "correct" one, or do you think that order is fine?

The only reason it might make a difference is how the expectation works-- I would think that we would take the best placement from the "correct" file.

BTW, feel free to use then wipe out errplace.ml.

On Fri, Jan 6, 2012 at 1:22 PM, Aaron Gallagher reply@reply.github.com wrote:

takes two placefiles; measures the distance between same-named placements.

Reply to this email directly or view it on GitHub: https://github.com/matsen/pplacer/issues/205

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

habnabit commented 12 years ago

Order would be easier than having a flag in this case.

matsen commented 12 years ago

Following the discussion with team EPA, we should scale read attachment proportionally when passed the --scale-experimental-bl flag.

That is, say our reference tree has an edge of length our_bl and the corresponding length on the rescaled tree is their_bl.

The read is placed with distal branch length their_distal on their tree, so the distal branch length on our tree should be our_bl * their_distal / their_bl.

matsen commented 12 years ago

The following could use comments:

Gtree.renumber
Newick_gtree.consolidate

Otherwise, looks great!