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Add dTiter_sanofi attribute to branches

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sidneymbell committed Nov 18, 2017
1 parent 6a65bf0 commit 4adafcd3eb2a2876b4fed5bf6c64fdc3c0a524f7
Showing with 2 additions and 1 deletion.
  1. +2 −1 builds/dengue/dengue_titers.py
@@ -118,13 +118,14 @@ def titer_model(process, sanofi_strain = None, plot_symmetry=False, **kwargs):
# find the vaccine strain in the tree
sanofi_tip = [i for i in process.tree.tree.find_clades() if i.name==sanofi_strain][0]
# sum up dTiter on all the branches on the path between the vaccine strain and each other strain
for tip in process.tree.tree.get_terminals():
for tip in process.tree.tree.find_clades():
if tip == sanofi_tip:
tip.attr['dTiter_sanofi']=0.00
else:
trace = process.tree.tree.trace(tip, sanofi_tip)
trace_dTiter = sum([i.dTiter for i in trace])
tip.attr['dTiter_sanofi']= round(trace_dTiter, 2)
# export for auspice visualization
process.config["auspice"]["color_options"]["dTiter_sanofi"] = {
"menuItem": "antigenic dist. from vaccine", "type": "continuous", "legendTitle": "log2 titer distance from sanofi vaccine strain",

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