Writing JSON Serialised Objects

Note

These docs now use the new_type core objects via the following setting.

import os

# using new types without requiring an explicit argument
os.environ["COGENT3_NEW_TYPE"] = "1"

Using JSON, we can serialise cogent3 objects to a file for easy storage and retrieval.

Create an example object to serialise

Let’s create a LikelihoodFunction object to use in this example. It is generated from fitting the General Nucleotide (GN) model to an alignment of BRCA1 in primates.

from cogent3 import get_app

# Load the alignment
load_aligned_app = get_app("load_aligned", moltype="dna", format="fasta")
aln = load_aligned_app("data/primate_brca1.fasta")

# Fit the GN model
gn_model_app = get_app("model", "GN", tree="data/primate_brca1.tree")
model_result = gn_model_app(aln)
model_result.lf

GN

log-likelihood = -6987.9632

number of free parameters = 22

Global params

A>C	A>G	A>T	C>A	C>G	C>T	G>A	G>C	G>T	T>A
0.8699	3.6640	0.9110	1.5907	2.1246	6.0241	8.2213	1.2295	0.6296	1.2502

continuation

T>C
3.4168

Edge params

edge	parent	length
Galago	root	0.1734
HowlerMon	root	0.0450
Rhesus	edge.3	0.0215
Orangutan	edge.2	0.0078
Gorilla	edge.1	0.0025
Human	edge.0	0.0061
Chimpanzee	edge.0	0.0028
edge.0	edge.1	0.0000
edge.1	edge.2	0.0033
edge.2	edge.3	0.0121
edge.3	root	0.0077

Motif params

A	C	G	T
0.3757	0.1742	0.2095	0.2406

write_json - writing JSON-serialised object to file

Using the write_json app, we can write out the likelihood function as a JSON-serialised object, making it easy to retrieve the model parameters for future reference if required.

We need to provide the write_json app with a data store to which it will write. Optionally when we apply the app we can specify an identifier for the data, which will name the file.

from cogent3 import get_app, open_data_store

# Initialise the write_json app with a data store
out_dstore = open_data_store(path_to_dir, mode="w", suffix="json")
write_json_app = get_app("write_json", data_store=out_dstore)

write_json_app(model_result.lf, identifier="gn_params.json")

DataMember(data_store=/home/runner/work/cogent3.github.io/cogent3.github.io/c3org/doc/doc/tmpsnjlywae, unique_id=gn_params.json)

Note

Learn how to load a JSON serialised object in the loading JSON serialised objects section!

Tip

When running this code on your machine, remember to replace path_to_dir with an actual directory path.