Writing JSON Serialised Objects#
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 = -6987.9604
number of free parameters = 22
| 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 | 2.1245 | 6.0240 | 8.2212 | 1.2295 | 0.6296 | 1.2502 |
| T>C |
|---|
| 3.4168 |
| 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 |
| 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/tmph2_tyo82, 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.