Loading 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"
The load_json app loads JSON serialised cogent3 objects from a file, returning whatever was stored.
In the writing JSON section, we wrote a likelihood function object to disk in JSON serialised format, now let’s load it back! All we need is the path to which it was written. Since write_json writes to a data store, this will be <path_to_dstore>/<identifier>.
Tip
To follow along with this example, first head to the writing JSON section to write out this data, or replace the path with a JSON file on your machine.
from cogent3 import get_app
load_json_app = get_app("load_json")
lf = load_json_app(f"{path_to_dstore}/gn_params.json")
lf
GN
log-likelihood = -6987.9632
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 | 2.1246 | 6.0241 | 8.2213 | 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 |