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###
API
###
*********************
Utility Functions For
*********************
Loading data from file
======================
These are all top level imports. For example,
.. code-block:: python
from cogent3 import load_unaligned_seqs
.. toctree::
:maxdepth: 1
__init__/cogent3.__init__.load_seq
__init__/cogent3.__init__.load_aligned_seqs
__init__/cogent3.__init__.load_unaligned_seqs
__init__/cogent3.__init__.load_delimited
__init__/cogent3.__init__.load_table
__init__/cogent3.__init__.load_tree
__init__/cogent3.__init__.load_annotations
__init__/cogent3.__init__.open_data_store
__init__/cogent3.__init__.open_
Making cogent3 types from standard Python types
===============================================
These are all top level imports. For example,
.. code-block:: python
from cogent3 import make_unaligned_seqs
.. toctree::
:maxdepth: 1
__init__/cogent3.__init__.make_seq
__init__/cogent3.__init__.make_aligned_seqs
__init__/cogent3.__init__.make_unaligned_seqs
__init__/cogent3.__init__.make_table
__init__/cogent3.__init__.make_tree
Getting commonly used cogent3 types
===================================
These are all top level imports. For example,
.. code-block:: python
from cogent3 import get_code
.. toctree::
:maxdepth: 1
__init__/cogent3.__init__.get_code
__init__/cogent3.__init__.get_moltype
__init__/cogent3.__init__.get_model
Displaying cogent3 builtins
===========================
These are all top level imports. For example,
.. code-block:: python
from cogent3 import get_code
.. toctree::
:maxdepth: 1
__init__/cogent3.__init__.available_codes
__init__/cogent3.__init__.available_moltypes
__init__/cogent3.__init__.available_models
__init__/cogent3.__init__.available_apps
****************************
The Major cogent3 Data Types
****************************
.. toctree::
:maxdepth: 1
alignment/alignment
annotation/annotation
annotation_db/annotation_db
sequence/sequence
genetic_code/genetic_code
moltype/moltype
alphabet/alphabet
table/table
tree/tree
***************
Composable Apps
***************
.. toctree::
:maxdepth: 1
app/composable/define_app
*********
Datastore
*********
.. toctree::
:maxdepth: 1
app/io/classes/cogent3.app.io.register_datastore_reader
app/data_store/classes/cogent3.app.data_store.DataMember
app/data_store/classes/cogent3.app.data_store.DataStoreDirectory
app/data_store/classes/cogent3.app.data_store.ReadOnlyDataStoreZipped
app/sqlite_data_store/classes/cogent3.app.sqlite_data_store.DataStoreSqlite
*************
Deserialising
*************
.. toctree::
:maxdepth: 1
util/deserialise/deserialise_object
util/deserialise/classes/cogent3.util.deserialise.register_deserialiser
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