0

I have a list of objects:

Data:

0         RS_GCF_001999625.1
1         RS_GCF_001658645.1
2         RS_GCF_900117665.1
3         RS_GCF_000652055.1
4         RS_GCF_003037025.1
5         RS_GCF_002138225.1
6         RS_GCF_001186785.1
7         RS_GCF_001671475.1
8         RS_GCF_000153745.1
9         RS_GCF_002814015.1
10        GB_GCA_900471825.1
...

And I also have a phylogenetic tree (a tree-like data structure) that is stored like this 

((((((((((((((((((((((((((((((((((((((((((((((((((((GB_GCA_900317315.1:0.04615,GB_GCA_900316815.1:0.04778)100.0:0.02419,GB_GCA_900317595.1:0.06625)33.0:0.0103,((GB_GCA_900316435.1:0.00693,GB_GCA_900318905.1:0.01341)96.0:0.00933,GB_GCA_900315195.1:0.01321)100.0:0.03115)26.0:0.01004,GB_GCA_900317875.1:0.045)100.0:0.04319,((GB_GCA_900315085.1:0.0231,GB_GCA_900318495.1:0.03029)100.0:0.01288,GB_GCA_003520555.1:0.03868)100.0:0.03609)70.0:0.01129,(((RS_GCF_900100595.1:0.03254,GB_GCA_900320415.1:0.04749)100.0:0.02208,GB_GCA_900316555.1:0.04989)100.0:0.03981,GB_GCA_900319655.1:0.10366)88.0:0.01387)100.0:0.02225,GB_GCA_900315605.1:0.07632)100.0:0.02364,RS_GCF_900101355.1:0.07185)86.0:0.01434,(((RS_GCF_002834235.1:0.00897,RS_GCF_002834225.1:0.00767)100.0:0.05389,GB_GCA_002493005.1:0.06092)100.0:0.02495,(GB_GCA_002491825.1:0.02107,GB_GCA_003521625.1:0.00495)100.0:0.03844)45.0:0.01157)46.0:0.01147,GB_GCA_002493635.1:0.0779)95.0:0.02318,GB_GCA_003526955.1:0.09126)100.0:0.0663,((GB_GCA_900315785.1:0.03418,GB_GCA_900316385.1:0.04382)100.0:0.05347,GB_GCA_002350765.1:0.07654)100.0:0.08554)100.0:0.03171,GB_GCA_900314705.1:0.18199)88.0:0.02358,(((((((GB_GCA_002394725.1:0.01259,GB_GCA_003499325.1:0.01449)45.0:0.00402,GB_GCA_900314795.1:0.01139)92.0:0.00728,GB_GCA_900320995.1:0.01735)100.0:0.02748,GB_GCA_900313865.1:0.06193)98.0:0.01767,GB_GCA_900319615.1:0.05467)100.0:0.0367,(GB_GCA_900313895.1:0.05183,GB_GCA_900315815.1:0.04148)100.0:0.0325)100.0:0.07701,GB_GCA_002353935.1:0.14242)100.0:0.08383)'100.0:g__Ruminococcus_E':0.05063,RS_GCF_002160515.1:0.16245)100.0:0.03238,(((GB_GCA_900313125.1:0.05466,GB_GCA_900317025.1:0.04564)95.0:0.01875,GB_GCA_900317815.1:0.07418)100.0:0.07807,((GB_GCA_900315255.1:0.0423,GB_GCA_900315715.1:0.04172)100.0:0.05538,GB_GCA_900320535.1:0.10753)100.0:0.03534)'100.0:g__RUG592':0.14947)94.0:0.02308,((((GB_GCA_900316615.1:0.02438,GB_GCA_900316025.1:0.01638)100.0:0.09448,GB_GCA_000435335.1:0.07944)'100.0:g__CAG-964':0.09347,GB_GCA_002391625.1:0.11943)88.0:0.04386,GB_GCA_002493755.1:0.19241)98.0:0.03042)99.0:0.03425,...

This tree is huge and what I want is to reduce the tree. I want to maintain in this tree all the leaves I have on my list data and remove the rest.

I am not familiar with working with ete3, can anyone put me in the right direction?

eyllanesc
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Manolo Dominguez Becerra
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1 Answers1

1

It seems you need to prune your target tree. Check example 25 of the below case study https://www.programcreek.com/python/example/93895/ete3.Tree

Ziqi

ziqi deng
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  • A link to a solution is welcome, but please ensure your answer is useful without it: [add context around the link](//meta.stackexchange.com/a/8259) so your fellow users will have some idea what it is and why it’s there, then quote the most relevant part of the page you're linking to in case the target page is unavailable. [Answers that are little more than a link may be deleted.](//stackoverflow.com/help/deleted-answers) – janw Feb 21 '20 at 15:22