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|
Getting a genetic code
----------------------
The standard genetic code.
.. doctest::
>>> from cogent.core.genetic_code import GeneticCodes
>>> standard_code = GeneticCodes[1]
The vertebrate mt genetic code.
.. doctest::
>>> from cogent.core.genetic_code import GeneticCodes
>>> mt_gc = GeneticCodes[2]
>>> print mt_gc.Name
Vertebrate Mitochondrial
To see the key -> genetic code mapping, use a loop.
.. doctest::
>>> for key, code in GeneticCodes.items():
... print key, code.Name
1 Standard Nuclear
2 Vertebrate Mitochondrial
3 Yeast Mitochondrial...
Translate DNA sequences
-----------------------
.. doctest::
>>> from cogent.core.genetic_code import DEFAULT as standard_code
>>> standard_code.translate('TTTGCAAAC')
'FAN'
Conversion to a ``ProteinSequence`` from a ``DnaSequence`` is shown in :ref:`translation`.
Translate all six frames
------------------------
.. doctest::
>>> from cogent import DNA
>>> from cogent.core.genetic_code import DEFAULT as standard_code
>>> seq = DNA.makeSequence('ATGCTAACATAAA')
>>> translations = standard_code.sixframes(seq)
>>> print translations
['MLT*', 'C*HK', 'ANI', 'FMLA', 'LC*H', 'YVS']
Find out how many stops in a frame
----------------------------------
.. doctest::
>>> from cogent import DNA
>>> from cogent.core.genetic_code import DEFAULT as standard_code
>>> seq = DNA.makeSequence('ATGCTAACATAAA')
>>> stops_frame1 = standard_code.getStopIndices(seq, start=0)
>>> stops_frame1
[9]
>>> stop_index = stops_frame1[0]
>>> seq[stop_index:stop_index+3]
DnaSequence(TAA)
Translate a codon
-----------------
.. doctest::
>>> from cogent.core.genetic_code import DEFAULT as standard_code
>>> standard_code['TTT']
'F'
or get the codons for a single amino acid
.. doctest::
>>> standard_code['A']
['GCT', 'GCC', 'GCA', 'GCG']
Look up the amino acid corresponding to a single codon
------------------------------------------------------
.. doctest::
>>> from cogent.core.genetic_code import DEFAULT as standard_code
>>> standard_code['TTT']
'F'
Or get all the codons for one amino acid
----------------------------------------
.. doctest::
>>> standard_code['A']
['GCT', 'GCC', 'GCA', 'GCG']
For a group of amino acids
--------------------------
.. doctest::
>>> targets = ['A','C']
>>> codons = [standard_code[aa] for aa in targets]
>>> codons
[['GCT', 'GCC', 'GCA', 'GCG'], ['TGT', 'TGC']]
>>> flat_list = sum(codons,[])
>>> flat_list
['GCT', 'GCC', 'GCA', 'GCG', 'TGT', 'TGC']
Converting the ``CodonAlphabet`` to codon series
------------------------------------------------
.. doctest::
>>> from cogent import DNA
>>> my_seq = DNA.makeSequence("AGTACACTGGTT")
>>> sorted(my_seq.CodonAlphabet())
['AAA', 'AAC', 'AAG', 'AAT'...
>>> len(my_seq.CodonAlphabet())
61
Obtaining the codons from a ``DnaSequence`` object
--------------------------------------------------
Use the method ``getInMotifSize``
.. doctest::
>>> from cogent import LoadSeqs,DNA
>>> my_seq = DNA.makeSequence('ATGCACTGGTAA','my_gene')
>>> codons = my_seq.getInMotifSize(3)
>>> print codons
['ATG', 'CAC', 'TGG', 'TAA']
You can't translate a sequence that contains a stop codon.
.. doctest::
>>> pep = my_seq.getTranslation()
Traceback (most recent call last):
AlphabetError: TAA
Remove the stop codon first
^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. doctest::
>>> from cogent import LoadSeqs,DNA
>>> my_seq = DNA.makeSequence('ATGCACTGGTAA','my_gene')
>>> seq = my_seq.withoutTerminalStopCodon()
>>> pep = seq.getTranslation()
>>> print pep.toFasta()
>my_gene
MHW
>>> print type(pep)
<class 'cogent.core.sequence.ProteinSequence'>
Or we can just grab the correct slice from the ``DnaSequence`` object
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. doctest::
>>> from cogent import LoadSeqs,DNA
>>> my_seq = DNA.makeSequence('CAAATGTATTAA','my_gene')
>>> pep = my_seq[:-3].getTranslation().toFasta()
>>> print pep
>my_gene
QMY
|
