biosustain/co

Make mutated copies of DNA components in BioPython

Co

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.

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:

>>> 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 has created Co. Contributions are very welcome. Contact the main author for bigger changes.