Accessing an object's tag in a TreeSequence

[Alfredo Marin]

Hi all!

In my simulation, I set the tagL0 property of some individuals to True. Is there a way to access this information in the output TreeSequence using tskit? For example, can I  simplify my TreeSequence such that I keep only the individuals with tagL0=T?

Thanks!

[Peter Ralph]

To do this, you need to explicitly store it, best is probably in top-level metadata. So, for instance:

treeSeqOutput("out.trees", metadata=Dictionary("tags", p1.individuals.tagL0, "ids", p1.individuals.pedigreeID))

Then, after loading the tree sequence, you'd extract this like:

tags = ts.metadata['SLiM']['user_metadata']['tags']

ids = ts.metadata['SLiM']['user_metadata']['ids']

... and then you could use this to figure out which nodes to simplify to. Here I'm outputting IDs, so that you can make sure you know which tags match which individuals in the tree sequence; and then remember that simplify wants nodes, not individuals.

--peter

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Subject: Accessing an object's tag in a TreeSequence

 

Hi all! In my simulation, I set the tagL0 property of some individuals to True. Is there a way to access this information in the output TreeSequence using tskit? For example, can I  simplify my TreeSequence such that I keep only the individuals

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Hi all!

In my simulation, I set the tagL0 property of some individuals to True. Is there a way to access this information in the output TreeSequence using tskit? For example, can I  simplify my TreeSequence such that I keep only the individuals with tagL0=T?

Thanks!

--
SLiM forward genetic simulation: http://messerlab.org/slim/
Before posting, please read http://benhaller.com/slim/bugs_and_questions.html
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[Alfredo Marin]

Oh okay, so the idea is to make the information I want a metadata of the TreeSequence itself instead of the individuals in the TreeSequence. Also, just for completeness, to use p1.individuals.pedigreeID, I need to add initializeSLiMOptions(keepPedigrees=T) to my script, right?