.. |travis| image:: https://travis-ci.org/biosustain/co.svg
.. _travis: https://travis-ci.org/biosustain/co
Co
==
|travis|_
**Co** is a Python library for altering annotated DNA sequences. It keeps track of components and lifts
over feature annotations when a component is "mutated" by applying a series of mutations. With ``co`` you can
build new consensus sequences for cloned organisms and trace changes to features within a lineage.
For more information, check out the `Documentation <http://co.readthedocs.org/en/latest/>`_.
Hello Co!
---------
::
>>> from co import Component
>>> from co.mutation import *
>>> hello = Component('Hello X!')
>>> hello.seq
Seq('Hello X!', Alphabet())
>>> hello_world = hello.mutate([Mutation(6, 1, 'world')])
>>> hello_world.seq
Seq('Hello world!', Alphabet())
Working with Feature Annotations
--------------------------------
Components are modeled after BioPython's ``SeqRecord`` -- they have both a sequence, and features:
.. code-block:: python
>>> from Bio.SeqFeature import *
>>> slogan = Component('CoPy is for DNA components', features=[
... SeqFeature(FeatureLocation(0, 4), type='name'),
... SeqFeature(FeatureLocation(12, 15), id='DNA')])
>>>
>>> # features are bound to components -- and you can always access their DNA sequence
...
>>> slogan.features.add(FeatureLocation(16, 26)).seq
Seq('components', Alphabet())
>>> [f.seq for f in slogan.features]
[Seq('CoPy', Alphabet()), Seq('DNA', Alphabet()), Seq('components', Alphabet())]
>>>
>>> # New Components are made through series of mutations
... # You not only get the new sequence but a mutated component: Features are translated to the
... # new sequence as well.
...
>>> new_slogan = slogan.mutate([DEL(2, 2), DEL(12, 4)])
>>> new_slogan.seq
Seq('Co is for components', Alphabet())
>>> new_slogan.features
ComponentFeatureSet([Feature(FeatureLocation(ExactPosition(0), ExactPosition(2)), type='name'),
Feature(FeatureLocation(ExactPosition(10), ExactPosition(20)))])
>>> [f.seq for f in new_slogan.features]
[Seq('Co', Alphabet()), Seq('components', Alphabet())]
>>> list(new_slogan.features.find(type='name')) # features can be filtered by type, id, strand, position, and qualifiers
[Feature(FeatureLocation(ExactPosition(0), ExactPosition(2)), type='name')]
>>>
>>> # Using Component.fdiff you can get a summary of what features where affected by mutation. (Unchanged features
... # that have a new coordinate -- e.g. the 'components' feature in this example -- are not included).
...
>>> slogan.fdiff(new_slogan)
Diff(added=(Feature(FeatureLocation(ExactPosition(12), ExactPosition(15)), id='DNA'),
Feature(FeatureLocation(ExactPosition(0), ExactPosition(4)), type='name')),
removed=(Feature(FeatureLocation(ExactPosition(0), ExactPosition(2)), type='name'),))
Authors
=======
`Lars Schöning <https://github.com/lyschoening>`_ has created Co. Contributions are very welcome.
Contact the main author for bigger changes.
