These are chat archives for dereneaton/ipyrad

5th
Apr 2016
Deren Eaton
@dereneaton
Apr 05 2016 17:39
svd4tet CLI is starting to look pretty sharp:
 --------------------------------------------------
  Analysis tools of ipyrad [v.0.1.83]
  svd4tet -- fast quartet and tree inference 
 --------------------------------------------------
  loading Assembly: cli
  from saved path: ~/Documents/ipyrad/tests/cli/cli.json
  ipyparallel setup: Local connection to 4 Engines

  starting new svd4tet analysis for [cli]
  loading array [12 taxa x 4679 bp]
  loading all 495 possible quartets
  populating array with 495 quartets
  inferring 495 x 3 quartet trees
  [####################] 100% 
  running 100 bootstrap replicates
  [####################] 100% 

  Finished. Intermediate tree files: 
  /home/deren/Documents/ipyrad/tests/cli/cli_analysis_svd/cli_svd4tet.tre
  /home/deren/Documents/ipyrad/tests/cli/cli_analysis_svd/cli_svd4tet.boots
  /home/deren/Documents/ipyrad/tests/cli/cli_analysis_svd/cli_svd4tet.w.tre
  /home/deren/Documents/ipyrad/tests/cli/cli_analysis_svd/cli_svd4tet.w.boots

  Final trees with bootstraps as edge labels: 
  /home/deren/Documents/ipyrad/tests/cli/cli_analysis_svd/cli_svd4tet.tre
  /home/deren/Documents/ipyrad/tests/cli/cli_analysis_svd/cli_svd4tet.w.tre

  Trees with extra quartet info in NHX format: 
  /home/deren/Documents/ipyrad/tests/cli/cli_analysis_svd/cli_svd4tet.nhx
  /home/deren/Documents/ipyrad/tests/cli/cli_analysis_svd/cli_svd4tet.w.nhx

  Quick view of unrooted topology from unweighted analysis
  For tips on plotting trees see: ipyrad.readthedocs.org/cookbook.html

            /-3I_0
         /-|
      /-|   \-3J_0
     |  |
   /-|   \-3K_0
  |  |
  |   \-3L_0
  |
  |         /-1A_0
  |      /-|
  |   /-|   \-1B_0
  |  |  |
--|--|   \-1C_0
  |  |
  |   \-1D_0
  |
  |         /-2E_0
  |      /-|
  |   /-|   \-2F_0
  |  |  |
   \-|   \-2G_0
     |
      \-2H_0

  To properly cite this software see ipyrad.readthedocs.org/svd4tet.html
Isaac Overcast
@isaacovercast
Apr 05 2016 17:41
Yes! Ascii art tree, that rulessss!
Did you code that? or is it a ascii tree library?
Deren Eaton
@dereneaton
Apr 05 2016 17:48
its from ete2
its just:
tre <- ete2.Tree(newick)
print(tre)
it has a fancy plotting library too, but I like the simple ascii tree for printing to screen.
Isaac Overcast
@isaacovercast
Apr 05 2016 17:54
Oh man that makes me really want to design an ascii art logo for ipyrad
Deren Eaton
@dereneaton
Apr 05 2016 17:58
oooh, I dig the idea of a fancy logo...
as long as it's not too big, giant splash pages get annoying.
Isaac Overcast
@isaacovercast
Apr 05 2016 18:01
Screen Shot 2016-04-05 at 2.01.17 PM.png
;p
Deren Eaton
@dereneaton
Apr 05 2016 18:02
lol, looks like you have some experience with this
Isaac Overcast
@isaacovercast
Apr 05 2016 18:02
you know it!
gtg to class, i'll work on a real one later....
Deren Eaton
@dereneaton
Apr 05 2016 18:03
later