Basic usage

If this is your first time using AbPyTools you won’t have any JSON or pb2 files that are compatible with it’s parsers. The simplest is to either instantiate a Chain from a string, or load from a FASTA file with ChainCollection.

• Chain

This object represents either a light or heavy chain of an antibody.

>>> from abpytools.core import Chain
>>> my_seq = "MYFANCYLIGHTCHAIN"
>>> chain = Chain.load_from_string(sequence=my_seq)

• ChainCollection

This is a container that accesses Chain objects and used to perform analysis of a dataset. the easiest is to load sequences from a string.

>>> from abpytools.core import ChainCollection
>>> collection = ChainCollection.load_from_fasta(path="secret.fasta")

Containers such as ChainCollection can then be dumped on disk to be used later on. This can be done either using JSON format or pb2 (Protocol Buffer).

>>> from abpytools.core import ChainCollection
>>> collection = ChainCollection.load_from_fasta(path="secret.fasta")
>>> # save to JSON
>>> collection.save_to_json("loaded_secret")
>>> # save to pb2
>>> collection.save_to_pb2("loaded_secret")

And in a different session these two can be loaded just as easily.

>>> from abpytools.core import ChainCollection
>>> collection_json = ChainCollection.load_from_json("loaded_secret.json")
>>> collection_pb2 = ChainCollection.load_from_pb2("loaded_secret.pb2")