Add metadata to individuals

[andrei-barysenka]

How can I add metadata info to individuals in my tree sequence ? I do something like this:

ts1=msprime.sim_ancestry( ... )
for I in ts1.individuals():
I.metadata=b"META"
for I in ts1.individuals():
print(I)

but metadata is still empty

[jeromekelleher]

Hi @andrei-barysenka 👋

The TreeSequence object is read-only, and any modifications that you make to the Python objects you get back will either fail, or be transitory (as you have here with the Individual objects). If you want the changes to "stick" you need to work with the underlying TableCollection. For your example:

import msprime

ts = msprime.sim_ancestry(3, random_seed=2)

tables = ts.dump_tables()
tables.individuals.clear()
for individual in ts.individuals():
    individual.metadata = b"META"
    tables.individuals.append(individual)

print(tables.individuals)
ts2 = tables.tree_sequence()
for i in ts2.individuals():
    print(i)

However, you probably want to use a schema if you're adding metadata. This is the simplest way:

import tskit

tables = ts.dump_tables()
tables.individuals.clear()
tables.individuals.metadata_schema = tskit.MetadataSchema.permissive_json()
for individual in ts.individuals():
    individual.metadata = {"key": "value"}
    tables.individuals.append(individual)

print(tables.individuals)
ts2 = tables.tree_sequence()
for i in ts2.individuals():
    print(i)

You might find these tutorials useful:

• https://tskit.dev/tutorials/tables_and_editing.html
• https://tskit.dev/tutorials/metadata.html