co 0.2.0

你好，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())

使用功能注释

组件是根据Biopython的SeqRecord建模的，它们既有序列，又有特性：

>>>fromBio.SeqFeatureimport*>>>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)).seqSeq('components',Alphabet())>>>[f.seqforfinslogan.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.seqSeq('Co is for components',Alphabet())>>>new_slogan.featuresComponentFeatureSet([Feature(FeatureLocation(ExactPosition(0),ExactPosition(2)),type='name'),Feature(FeatureLocation(ExactPosition(10),ExactPosition(20)))])>>>[f.seqforfinnew_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'),))