API#

Utility Functions For#

Loading data from file#

These are all top level imports. For example,

from cogent3 import load_unaligned_seqs

Making cogent3 types from standard Python types#

These are all top level imports. For example,

from cogent3 import make_unaligned_seqs

Getting commonly used cogent3 types#

These are all top level imports. For example,

from cogent3 import get_code

Displaying cogent3 builtins#

These are all top level imports. For example,

from cogent3 import available_codes

Major cogent3 Data Types#

To enforce usage of the new type classes (e.g. sequence, alignment etc…) add the following to the top of your scripts.

import os

os.environ["COGENT3_NEW_TYPE"] = "1"

Composable Apps#

Datastore#

Deserialising#