@jlhudd , I am trying to use baltic with a nexus file downloaded from auspice.
Here is the nexus file:
#nexus
begin trees;
tree one = (Argentina/C97133/2020[&clade_membership=20B,num_date=2020.886612021858,num_date_CI={2020.886612021858,2020.886612021858},pangolin_lineage=P.2,localidade=South America,division=Argentina,country=Argentina,region=South America,host=Human,age=49,sex=Male,recency=Older,division_exposure=Argentina,region_exposure=South America,subclade_membership=20B/S.484K,div=23]:0.022244654877567882,(Brazil/AM-21143316HC/2021[&clade_membership=20B,num_date=2021.009589041096,num_date_CI={2021.009589041096,2021.009589041096},pangolin_lineage=P.2,localidade=Brazil,location=Manaus,division=Amazonas BR,country=Brazil,region=South America,host=Human,age=35,sex=Male,recency=One week ago,division_exposure=Amazonas BR,region_exposure=South America,subclade_membership=20B/S.484K,div=23]:0.06563654070760094,Brazil/AM-L87-CD2680/2020[&clade_membership=20B,num_date=2020.9767759562842,num_date_CI={2020.9767759562842,2020.9767759562842},pangolin_lineage=B.1.1.28,localidade=Brazil,location=Manaus,division=Amazonas BR,country=Brazil,region=South America,host=Human,recency=One week ago,division_exposure=Amazonas BR,region_exposure=South America,subclade_membership=20B/S.484K,div=23]:0.03282345589582292)NODE_0004335[&clade_membership=20B,num_date=2020.9439525003884,num_date_CI={2020.7799157869863,2020.9690196954846},localidade=Brazil,subclade_membership=20B/S.484K,div=22]:0.0795851334080453)NODE_0002344[&clade_membership=20B,num_date=2020.8643673669803,num_date_CI={2020.784333364771,2020.886612021858},localidade=Brazil,subclade_membership=20B/S.484K,div=22]:0;
end;
When I try to load the file using baltic, the following error occurs:
myTree = bt.loadNexus(nexus_file)
AssertionError Traceback (most recent call last)
in
----> 1 myTree = bt.loadNexus(nexus_file)
~/miniconda3/envs/pandas/lib/python3.9/site-packages/baltic/baltic.py in loadNexus(tree_path, tip_regex, date_fmt, treestring_regex, variableDate, absoluteTime, verbose)
1286 tipFlag=False
1287
â 1288 assert ll,âRegular expression failed to find tree stringâ
1289 ll.traverse_tree() ## traverse tree
1290 ll.sortBranches() ## traverses tree, sorts branches, draws tree
AssertionError: Regular expression failed to find tree string
Do you know what might be the problem? Nwk tree load with any problem.
Thank you very much.