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Protein sequences
-----------------
.. authors, Gavin Huttley, Kristian Rother, Patrick Yannul
Creating a ProteinSequence with a name
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. doctest::
>>> from cogent import PROTEIN
>>> p = PROTEIN.makeSequence('THISISAPRQTEIN','myProtein')
>>> type(p)
<class 'cogent.core.sequence.ProteinSequence'>
>>> str(p)
'THISISAPRQTEIN'
Converting a DNA sequence string to protein sequence string
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. 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`.
Loading protein sequences from a Phylip file
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. doctest::
>>> from cogent import LoadSeqs, PROTEIN
>>> seq = LoadSeqs('data/abglobin_aa.phylip', moltype=PROTEIN,
... aligned=True)
Loading other formats, or collections of sequences is shown in :ref:`load-seqs`.
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